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    W1_LC-MSMS_DIMS_DIMSn_FRAC_DMA

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    <div class="page-body p-3">
        <div>
            
    <h3>
    W1_LC-MSMS_DIMS_DIMSn_FRAC_DMA</h3>
        <div class="annotation">Annotation: </div>
    <hr/>

        </div>
        
    
    <table class="annotated-item">
        <tr><th>Step</th><th class="annotation">Annotation</th></tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 1: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Polarity (short)</label>
        <div>
                Nothing selected.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 2: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Adducts (string)</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 3: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Polarity (long)</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 4: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>DIMS mz range remove (min)</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 5: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>DIMS mz range remove (max)</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 6: Input dataset</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Sample list blank DIMS (.tsv, .tabular)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 7: Input dataset</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Sample list for DIMS (.tsv, .tabular)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 8: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Sim stitch?</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 9: Input dataset collection</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>DIMS data files blank (.raw)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 10: Input dataset collection</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>DIMS data files sample (.raw)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 11: Input dataset</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Sample list sample DIMS (.tsv, .tabular)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 12: Input dataset collection</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>LC-MS and LC-MS/MS data files (.mzML)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 13: Input dataset collection</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>DIMS data files sample (.mzML)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 14: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>XCMS mzdiff (findChromPeaks)</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 15: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>XCMS ppm</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 16: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>DIMS and DIMSn (ppm)</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 17: Input dataset</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Sample list (.tsv, .tabular)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 18: Input dataset</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Adduct list - MSnPy (.tsv, .tabular)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 19: Input dataset collection</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>DIMSn data files (.raw)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 20: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>XCMS bw (grouping)</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 21: Input dataset</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Adduct list (.tsv, .tabular)</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
            
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 22: Input parameter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>XCMS mzwid (grouping)</label>
        <div>
                Not available.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 23: Process Scans (and SIM-Stitch)</div>
                  <div class="card-body">
                    
      
      
      
      
    
    <div class="form-row">
        <label>Select the MS data file type?</label>
        <div>
                *.raw files
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Do you agree to the RawFileReader license terms?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>*.raw files</label>
        <div>
                    
                    Output dataset 'output' from step 9
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Filelist / Samplelist</label>
        <div>
                    
                    Output dataset 'output' from step 6
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Function to calculate the noise from each scan</label>
        <div>
                As shown in Xcalibur Qual Browser (Available for *.RAW files only)
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Signal-to-noise ratio threshold</label>
        <div>
                3.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Filter specific windows or scan events?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Include / Exclude scan event(s)</label>
        <div>
                Exclude
        </div>
    </div>

      <div>
          <div class="form-row"><b>Descriptions</b></div>
          
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Description 1</b></div>
                
      
    
    <div class="form-row">
        <label>Start m/z for scan event</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>End m/z for scan event</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Scan type</label>
        <div>
                Full scan
        </div>
    </div>


            </div> 
      </div>

      
      
      <div class="form-row"><b>Show options for multiple scans:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Minimum number of scans required for each m/z window or event</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ppm error tolerance</label>
        <div>
                2.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum fraction (i.e. percentage) of scans a peak has to be present in.</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Relative standard deviation threshold</label>
        <div>
                0.0
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>Show advanced options:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Skip SIM-Stitching?</label>
        <div>
                False
        </div>
    </div>

      <div>
          <div class="form-row"><b>Remove m/z range(s)?s</b></div>
          
      </div>
      
    
    <div class="form-row">
        <label>Relative intensity threshold used to remove ringing artifacts</label>
        <div>
                0.0
        </div>
    </div>


        </div>
      </div>
      
    
    <div class="form-row">
        <label>None</label>
        <div>
                tab
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 24: msPurity.purityA</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>*.mzML file</label>
        <div>
                    
                    Output dataset 'output' from step 12
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Use most intense peak within isolation window for precursor?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Use nearest full scan to determine precursor?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Interpolation PPM</label>
        <div>
                7.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>offsets</label>
        <div>
                Uses offsets determined in the mzML file
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Threshold to remove peaks below x % of the relative intensity of                precursor of interest</label>
        <div>
                0.05
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Normalisation for isolation efficiency</label>
        <div>
                No normalisation
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Handling of isotopic peaks</label>
        <div>
                Exclude C12/C13 isotopes in precursor ion purity calculation
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 25: MSnbase readMSData</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>File(s) from your history containing your chromatograms</label>
        <div>
                    
                    Output dataset 'output' from step 12
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 26: Process Scans (and SIM-Stitch)</div>
                  <div class="card-body">
                    
      
      
      
      
    
    <div class="form-row">
        <label>Select the MS data file type?</label>
        <div>
                *.raw files
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Do you agree to the RawFileReader license terms?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>*.raw files</label>
        <div>
                    
                    Output dataset 'output' from step 10
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Filelist / Samplelist</label>
        <div>
                    
                    Output dataset 'output' from step 11
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Function to calculate the noise from each scan</label>
        <div>
                As shown in Xcalibur Qual Browser (Available for *.RAW files only)
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Signal-to-noise ratio threshold</label>
        <div>
                3.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Filter specific windows or scan events?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Include / Exclude scan event(s)</label>
        <div>
                Exclude
        </div>
    </div>

      <div>
          <div class="form-row"><b>Descriptions</b></div>
          
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Description 1</b></div>
                
      
    
    <div class="form-row">
        <label>Start m/z for scan event</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>End m/z for scan event</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Scan type</label>
        <div>
                Full scan
        </div>
    </div>


            </div> 
      </div>

      
      
      <div class="form-row"><b>Show options for multiple scans:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Minimum number of scans required for each m/z window or event</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ppm error tolerance</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum fraction (i.e. percentage) of scans a peak has to be present in.</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Relative standard deviation threshold</label>
        <div>
                0.0
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>Show advanced options:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Skip SIM-Stitching?</label>
        <div>
                False
        </div>
    </div>

      <div>
          <div class="form-row"><b>Remove m/z range(s)?s</b></div>
          
      </div>
      
    
    <div class="form-row">
        <label>Relative intensity threshold used to remove ringing artifacts</label>
        <div>
                0.0
        </div>
    </div>


        </div>
      </div>
      
    
    <div class="form-row">
        <label>None</label>
        <div>
                tab
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 27: MSnPy Group Scans</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Single *.mzml or *.raw</label>
        <div>
                    
                    Output dataset 'output' from step 19
        </div>
    </div>

      
    
    <div class="form-row">
        <label>number_of_headers</label>
        <div>
                2
        </div>
    </div>

      
    
    <div class="form-row">
        <label>min_replicates</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>max_injection_time</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>split</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>merge_ms1</label>
        <div>
                True
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 28: xcms findChromPeaks (xcmsSet)</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>RData file</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 25
        </div>
    </div>

      
      
      <div class="form-row"><b>Spectra Filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Filter on Acquisition Numbers</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Filter on Retention Time</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Filter on Mz</label>
        <div>
                Empty.
        </div>
    </div>


        </div>
      </div>
      
      
      
      
    
    <div class="form-row">
        <label>Extraction method for peaks detection</label>
        <div>
                CentWave - chromatographic peak detection using the centWave method
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Max tolerated ppm m/z deviation in consecutive scans in ppm</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Min,Max peak width in seconds</label>
        <div>
                3,30
        </div>
    </div>

      
      
      <div class="form-row"><b>Advanced Options:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Signal to Noise ratio cutoff</label>
        <div>
                10
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Prefilter step for for the first analysis step (ROI detection)</label>
        <div>
                3,100
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Name of the function to calculate the m/z center of the chromatographic peak</label>
        <div>
                intensity weighted mean of the peak&#39;s m/z values
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Integration method</label>
        <div>
                peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum difference in m/z for peaks with overlapping retention times</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>fitgauss</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Noise filter</label>
        <div>
                0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>verbose Columns</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Get a list of found chromatographic peaks</label>
        <div>
                False
        </div>
    </div>

      
      
      <div class="form-row"><b>List of regions-of-interest (ROI):</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>List of regions-of-interest (ROI) representing detected mass traces</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Is continuous data within regions of interest is checked to be above the first baseline.</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Numeric vector defining the scale for each region of interest in ‘roiList’</label>
        <div>
                Empty.
        </div>
    </div>


        </div>
      </div>

        </div>
      </div>

      
      
      <div class="form-row"><b>Resubmit your raw dataset or your zip file:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Resubmit your dataset or your zip file</label>
        <div>
                no need
        </div>
    </div>

      


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 29: Merge peaklists</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Peaklist to merge</label>
        <div>
                    
                    Output dataset 'hdf5_file_out' from step 23,Output dataset 'hdf5_file_out' from step 26
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Create multiple merged peaklists?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Filelist</label>
        <div>
                    
                    Output dataset 'output' from step 7
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 30: MSnPy Process Scans</div>
                  <div class="card-body">
                    
      
      
      
      
    
    <div class="form-row">
        <label>Select the MS data file type?</label>
        <div>
                *.raw files
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Do you agree to the RawFileReader license terms?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>*.raw file</label>
        <div>
                    
                    Output dataset 'output' from step 19
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Groups</label>
        <div>
                    
                    Output dataset 'grouped_scans' from step 27
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Noise function</label>
        <div>
                As shown in Xcalibur Qual Browser (Available for *.RAW files only)
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Signal-to-noise threshold</label>
        <div>
                3.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>PPM tolerance</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Min fraction</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>RSD threshold</label>
        <div>
                0.0
        </div>
    </div>

      
      
      <div class="form-row"><b>Show advanced options:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Normalise</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Relative intensity threshold used to remove ringing artifacts</label>
        <div>
                0.05
        </div>
    </div>

      <div>
          <div class="form-row"><b>Exclusion values</b></div>
          
      </div>

        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 31: xcms findChromPeaks Merger</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>RData file</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 28
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Sample metadata file </label>
        <div>
                    
                    Output dataset 'output' from step 17
        </div>
    </div>

      
      
      <div class="form-row"><b>Resubmit your raw dataset or your zip file:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Resubmit your dataset or your zip file</label>
        <div>
                no need
        </div>
    </div>

      


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 32: Align Samples</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Peaklists (HDF5 file)</label>
        <div>
                    
                    Output dataset 'multiple_merged' from step 29
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Filelist / Samplelist</label>
        <div>
                    
                    Output dataset 'output' from step 7
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ppm error tolerance</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>None</label>
        <div>
                tab
        </div>
    </div>

      
      
      <div class="form-row"><b>Show options for addtional output (*.tsv files):</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Standard output?</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Comprehensive output?</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Should the rows or columns represent the samples?</label>
        <div>
                Rows
        </div>
    </div>

      
    
    <div class="form-row">
        <label>The Peak Matrix should contain ... values</label>
        <div>
                Intensity
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>Advanced options:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Block size</label>
        <div>
                5000
        </div>
    </div>


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 33: MSnPy Create Spectral Trees</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>HDF5 file (Peaklist objects) from step &#39;process-scans&#39;.</label>
        <div>
                    
                    Output dataset 'processed_peaklists' from step 30
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Groups</label>
        <div>
                    
                    Output dataset 'grouped_scans' from step 27
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 34: xcms groupChromPeaks (group)</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>RData file</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 31
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Method to use for grouping</label>
        <div>
                PeakDensity - peak grouping based on time dimension peak densities
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Bandwidth</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum fraction of samples</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum number of samples</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Width of overlapping m/z slices</label>
        <div>
                Not available.
        </div>
    </div>

      
      
      <div class="form-row"><b>Advanced Options:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Maximum number of groups to identify in a single m/z slice</label>
        <div>
                50
        </div>
    </div>


        </div>
      </div>

      
      
      
      
    
    <div class="form-row">
        <label>Get the Peak List</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Convert retention time (seconds) into minutes</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Number of decimal places for mass values reported in ions&#39; identifiers.</label>
        <div>
                4
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Number of decimal places for retention time values reported in ions&#39; identifiers.</label>
        <div>
                0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Reported intensity values</label>
        <div>
                into
        </div>
    </div>

      
    
    <div class="form-row">
        <label>If NA values remain, replace them by 0 in the dataMatrix</label>
        <div>
                True
        </div>
    </div>


      
      
      <div class="form-row"><b>Resubmit your raw dataset or your zip file:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Resubmit your dataset or your zip file</label>
        <div>
                no need
        </div>
    </div>

      


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 35: Blank Filter</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Peak Intensity Matrix (HDF5 file)</label>
        <div>
                    
                    Output dataset 'hdf5_file_out' from step 32
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Label for the blank samples</label>
        <div>
                BLANK
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum fraction (percentage)</label>
        <div>
                1.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Function</label>
        <div>
                mean
        </div>
    </div>

      
    
    <div class="form-row">
        <label>min_fold_change</label>
        <div>
                10.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Remove blank samples (rows)</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>None</label>
        <div>
                tab
        </div>
    </div>

      
      
      <div class="form-row"><b>Show options for addtional output (*.tsv files):</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Standard output?</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Comprehensive output?</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Should the rows or columns represent the samples?</label>
        <div>
                Rows
        </div>
    </div>

      
    
    <div class="form-row">
        <label>The Peak Matrix should contain ... values</label>
        <div>
                Intensity
        </div>
    </div>


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 36: Filter failed</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Input Collection</label>
        <div>
                    
                    Output dataset 'spectral_trees' from step 33
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 37: msPurity.frag4feature</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>xcmsSet object</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 34
        </div>
    </div>

      
    
    <div class="form-row">
        <label>purityA object</label>
        <div>
                    
                    Output dataset 'purityA_output_rdata' from step 24
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ppm error tolerance between precursor mz and XCMS feature mz</label>
        <div>
                10.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Precursor ion purity threshold</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Should the most intense precursor be used within the isolation window?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Was retention time correction used?</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>For matching fragmentation to a feature, use the grouped feature range</label>
        <div>
                False
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Resubmit your dataset</label>
        <div>
                no need
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 38: CAMERA.annotate</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>RData file</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 34
        </div>
    </div>

      
      
      <div class="form-row"><b>Group co-eluted peaks based on RT [groupFWHM]:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Multiplier of the standard deviation</label>
        <div>
                6
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Percentage of FWHM width</label>
        <div>
                0.6
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotation general options:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>General ppm error</label>
        <div>
                5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>General absolut error in m/z</label>
        <div>
                0.015
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotate Isotopes [findIsotopes]:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Max. ion charge</label>
        <div>
                3
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Max. number of expected isotopes</label>
        <div>
                4
        </div>
    </div>

      
    
    <div class="form-row">
        <label>The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation</label>
        <div>
                0.5
        </div>
    </div>


        </div>
      </div>
      
      
      
      
    
    <div class="form-row">
        <label>Mode</label>
        <div>
                All functions
        </div>
    </div>

      
      
      
      <div class="form-row"><b>Verifying grouping co-eluted peaks [groupCorr]:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>groupCorr: correlation threshold (0..1)</label>
        <div>
                0.75
        </div>
    </div>

      
    
    <div class="form-row">
        <label>groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra</label>
        <div>
                hcs
        </div>
    </div>

      
    
    <div class="form-row">
        <label>groupCorr: significant correlation threshold</label>
        <div>
                0.05
        </div>
    </div>

      
    
    <div class="form-row">
        <label>groupCorr: Use correlation inside samples for peak grouping</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>groupCorr: Use isotopic relationship for peak grouping</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>groupCorr: Use correlation across samples for peak grouping</label>
        <div>
                False
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotate Adducts [findAdducts]:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Which polarity mode was used for measuring of the ms sample</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>How much peaks will be calculated in every thread using the parallel mode</label>
        <div>
                100
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Use a personal ruleset file</label>
        <div>
                FALSE
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions</label>
        <div>
                3
        </div>
    </div>



        </div>
      </div>

      
      
      <div class="form-row"><b>Statistics and results export: [diffreport]:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Number of condition</label>
        <div>
                One condition
        </div>
    </div>

      


        </div>
      </div>
      
      
      <div class="form-row"><b>Export options:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Convert retention time (seconds) into minutes</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Number of decimal places for mass values reported in ions&#39; identifiers.</label>
        <div>
                4
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Number of decimal places for retention time values reported in ions&#39; identifiers.</label>
        <div>
                0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>General used intensity value</label>
        <div>
                into
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>Resubmit your raw dataset or your zip file:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Resubmit your dataset or your zip file</label>
        <div>
                yes
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>File(s) from your history containing your chromatograms</label>
        <div>
                    
                    Output dataset 'output' from step 12
        </div>
    </div>



        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 39: Add column</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Add this value</label>
        <div>
                intensity
        </div>
    </div>

      
    
    <div class="form-row">
        <label>to Dataset</label>
        <div>
                    
                    Output dataset 'variableMetadata' from step 34
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Iterate?</label>
        <div>
                NO
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 40: msPurity.flagRemove</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>xset_path</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 34
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Change biological sample flag parameters?</label>
        <div>
                Update biological sample flag parameters
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>rsd_i_sample</label>
        <div>
                NA
        </div>
    </div>

      
    
    <div class="form-row">
        <label>minfrac_sample</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>rsd_rt_sample</label>
        <div>
                NA
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ithres_sample</label>
        <div>
                NA
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>Change blank flag parameters?</label>
        <div>
                Update blank flag parameters
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>blank_class</label>
        <div>
                blank
        </div>
    </div>

      
    
    <div class="form-row">
        <label>rsd_i_blank</label>
        <div>
                NA
        </div>
    </div>

      
    
    <div class="form-row">
        <label>minfrac_blank</label>
        <div>
                0.1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>rsd_rt_blank</label>
        <div>
                NA
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ithres_blank</label>
        <div>
                NA
        </div>
    </div>

      
    
    <div class="form-row">
        <label>s2b</label>
        <div>
                10.0
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>Remove peaks from xcmsSet object?</label>
        <div>
                Only flag peaks (do not remove and re-group)
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Advanced parameters</label>
        <div>
                Use default advanced parameters
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Samplelist</label>
        <div>
                Use samplelist
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>samplelist</label>
        <div>
                    
                    Output dataset 'output' from step 17
        </div>
    </div>



                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 41: Get peaklists</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Peak Intensity Matrix (HDF5 file)</label>
        <div>
                    
                    Output dataset 'hdf5_file_out' from step 35
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Get...</label>
        <div>
                Average Peaklist
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Name average Peaklist</label>
        <div>
                dims
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Write Peaklists to tsv files (data collection)?</label>
        <div>
                True
        </div>
    </div>


      
    
    <div class="form-row">
        <label>None</label>
        <div>
                tab
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 42: MSnPy Annotate Spectral Trees</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Spectra trees</label>
        <div>
                    
                    Output dataset 'output' from step 36
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Molecular formulae database</label>
        <div>
                https://mfdb.bham.ac.uk
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ion mode</label>
        <div>
                Not available.
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Input type adducts</label>
        <div>
                Provide a tab-separated text file with a list of adducts
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>List of adducts</label>
        <div>
                    
                    Output dataset 'output' from step 18
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Mass tolerance in Parts per million.</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Apply heuristic rules?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Filter the spectral tree annotations?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Keep un-annotated fragments?</label>
        <div>
                False
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Use time limit?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Time limit to annotate and filter each tree (seconds)</label>
        <div>
                7200
        </div>
    </div>



                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 43: MSnPy Convert Spectral Trees</div>
                  <div class="card-body">
                    
      
      
      
      
    
    <div class="form-row">
        <label>Input type</label>
        <div>
                MSnPy JSON spectral trees
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>MSnPy Spectral Trees</label>
        <div>
                    
                    Output dataset 'output' from step 36
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>merge</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Mass tolerance in parts per million.</label>
        <div>
                Not available.
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>msp</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>MSP file type?</label>
        <div>
                European MassBank format
        </div>
    </div>


      
    
    <div class="form-row">
        <label>adjust_mz</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ms1</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Polarity</label>
        <div>
                Not applicable
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 44: msPurity.filterFragSpectra</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>purityA object with fragmentation linked to XCMS features</label>
        <div>
                    
                    Output dataset 'frag4feature_output_rdata' from step 37
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Miniumum precursor ion purity of the associated precursor for                      fragmentation spectra scan</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Peak instensity threshold</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Relative abundance threshold</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Signal-to-noise threshold</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Function to calculate noise.</label>
        <div>
                median
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Remove peaks that do not meet the filtering criteria.                       Otherwise peaks will be flagged instead.</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Perform filtering on all fragmentation spectra (not just those aligned to XCMS features)</label>
        <div>
                True
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 45: Cut</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Cut columns</label>
        <div>
                c1,c13,c14,c15
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Delimited by</label>
        <div>
                Tab
        </div>
    </div>

      
    
    <div class="form-row">
        <label>From</label>
        <div>
                    
                    Output dataset 'variableMetadata' from step 38
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 46: Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>File to process</label>
        <div>
                    
                    Output dataset 'out_file1' from step 39
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find pattern</label>
        <div>
                intensity
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace with</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find-Pattern is a regular expression</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace all occurences of the pattern</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Case-Insensitive search</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find whole-words</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ignore first line</label>
        <div>
                True
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Find and Replace text in</label>
        <div>
                entire line
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 47: Column arrange</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>file to rearrange</label>
        <div>
                    
                    Output dataset 'peaklist_filtered' from step 40
        </div>
    </div>

      <div>
          <div class="form-row"><b>Specify the first few columns by names</b></div>
          
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 1</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                &#34;grpid&#34;
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 2</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                &#34;grp_names&#34;
        </div>
    </div>


            </div> 
      </div>
      
    
    <div class="form-row">
        <label>Discard unspecified columns?</label>
        <div>
                False
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 48: Filter failed</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Input Collection</label>
        <div>
                    
                    Output dataset 'tsv_file_out' from step 41
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 49: MSnPy Rank Spectral Trees</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Spectral trees</label>
        <div>
                    
                    Output dataset 'output_trees' from step 42
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Rank threshold</label>
        <div>
                0
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 50: SIRIUS-CSI:FingerID</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>MSP file (output from Create MSP tool)</label>
        <div>
                    
                    Output dataset 'non_merged_msp' from step 43
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Select SIRIUS-CSI:FingerID Database</label>
        <div>
                Bio (all biological)
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Mass deviation of the fragment peaks in ppm</label>
        <div>
                5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Maximum number of candidates in the output</label>
        <div>
                5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ion mode</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Analysis used</label>
        <div>
                Orbitrap
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Schema</label>
        <div>
                Auto
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Choose how additional metadata columns are extracted</label>
        <div>
                
                Extra metadata columns from the Name or RECORD_TITLE
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum number of MS/MS peaks</label>
        <div>
                0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>How to handle adducts</label>
        <div>
                Use pre-selected adducts for either pos or neg ionisation mode
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 51: msp2db</div>
                  <div class="card-body">
                    
      
      
      
      
    
    <div class="form-row">
        <label>Choose source for the dataset</label>
        <div>
                Single msp file
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>MSP file</label>
        <div>
                    
                    Output dataset 'non_merged_msp' from step 43
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Polarity</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Name of spectral library (e.g. Lipids, LocalLibrary)</label>
        <div>
                dimsn
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Msp schema / format</label>
        <div>
                European MassBank
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ignore compound lookup to PubChem</label>
        <div>
                True
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 52: MetFrag</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>MSP file (Output from Create MSP tool)</label>
        <div>
                    
                    Output dataset 'merged_msp' from step 43
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Choose Compound Database</label>
        <div>
                MetChem
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>MetChem URL</label>
        <div>
                bberdb.bb2.cluster
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Relative Mass Deviation for database search (ppm)</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Fragment Peak Match Relative Mass Deviation (ppm)</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Fragment Peak Match Absolute Mass Deviation (Da)</label>
        <div>
                0.001
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Polarity</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Schema</label>
        <div>
                Auto
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Choose how additional metadata columns are extracted</label>
        <div>
                Extra metadata columns from MSP parameters
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Suspect list</label>
        <div>
                Include suspect list
        </div>
    </div>

      
      
      
      
      
    
    <div class="form-row">
        <label>Use default list of suspect compounds?</label>
        <div>
                True
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>MetFrag Score Types</label>
        <div>
                FragmenterScore
OfflineMetFusionScore
SuspectListScore
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MetFrag Score Weights</label>
        <div>
                0.2,0.3,0.5
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>How to handle adducts</label>
        <div>
                Use all available adducts for either pos or neg ionisation mode
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Skip invalid or undefined adduct types?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum number of MS/MS peaks</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Output the MetFrag command line call</label>
        <div>
                False
        </div>
    </div>

      
      
      <div class="form-row"><b>PreProcessing filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>filter non-connected compounds (e.g. salts)</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>filter compounds containing non-standard isotopes</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum Elements Filter</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Maximum Elements Filter</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Include substructures</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Exclude substructures</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Include elements</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Include elements (exclusive)</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Exclude elements</label>
        <div>
                Empty.
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>PostProcessing filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Threshold for score after MetFrag search</label>
        <div>
                0.6
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum percentage of explain peaks</label>
        <div>
                15.0
        </div>
    </div>


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 53: msPurity.averageFragSpectra</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>purityA object</label>
        <div>
                    
                    Output dataset 'filterFragSpectra_output_rdata' from step 44
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Average and filter fragmentation spectra for each XCMS feature</label>
        <div>
                within a MS data file
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Signal-to-noise threshold after averaging or summing</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Relative abundance threshold after averaging or summing</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in.</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor).</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ppm error tolerance</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Sum intensities across (averaged) scans?</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering.</label>
        <div>
                median
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead.</label>
        <div>
                True
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 54: Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>File to process</label>
        <div>
                    
                    Output dataset 'out_file1' from step 45
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find pattern</label>
        <div>
                name
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace with</label>
        <div>
                grp_names
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find-Pattern is a regular expression</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace all occurences of the pattern</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Case-Insensitive search</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find whole-words</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ignore first line</label>
        <div>
                False
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Find and Replace text in</label>
        <div>
                entire line
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 55: BEAMSpy</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Peaklist</label>
        <div>
                    
                    Output dataset 'outfile' from step 46
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Intensity matrix</label>
        <div>
                    
                    Output dataset 'dataMatrix' from step 34
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ion mode</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Library adducts</label>
        <div>
                    
                    Output dataset 'output' from step 21
        </div>
    </div>

      
      
      <div class="form-row"><b>Group Features:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label> </label>
        <div>
                False
        </div>
    </div>

      


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotate Peak Patterns:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label> </label>
        <div>
                False
        </div>
    </div>

      


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotate Molecular Formulae:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label> </label>
        <div>
                False
        </div>
    </div>

      


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotate Compounds / Metabolites:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label> </label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Ppm error tolerance</label>
        <div>
                5.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Source</label>
        <div>
                Compound databases
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Select databases</label>
        <div>
                hmdb_full_v4_0_v1
        </div>
    </div>




        </div>
      </div>
      
      
      <div class="form-row"><b>Create summary table(s):</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Multiple rows for each feature and separate columns</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Single row for each feature and separate columns</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Single row for each feature and merged columns</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Convert RT</label>
        <div>
                skip
        </div>
    </div>


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 56: Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>File to process</label>
        <div>
                    
                    Output dataset 'output' from step 47
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find pattern</label>
        <div>
                &#34;
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace with</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find-Pattern is a regular expression</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace all occurences of the pattern</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Case-Insensitive search</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find whole-words</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ignore first line</label>
        <div>
                True
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Find and Replace text in</label>
        <div>
                entire line
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 57: msPurity.dimsPredictPuritySingle</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>peaks_file</label>
        <div>
                    
                    Output dataset 'output' from step 48
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Choose the source for the dataset</label>
        <div>
                A single .mzML files to check purity from
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Single *.mzML</label>
        <div>
                    
                    Output dataset 'output' from step 13
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Threshold to remove peaks below x % of the relative intensity of                precursor of interest</label>
        <div>
                0.05
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Normalisation for isolation efficiency</label>
        <div>
                 Calculated from Q-Exactive for +/- 0.5 Da windows 
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Handling of isotopic peaks</label>
        <div>
                Exclude C12/C13 isotopes in precursor ion purity calculation
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>minoffset</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>maxoffset</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ppm</label>
        <div>
                10.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Remove rows where mz value is NA or NaN?</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>SIM-Stitch experiment?</label>
        <div>
                Not available.
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>dimspy peak matrix text file usage?</label>
        <div>
                dimspy not used to prepare the mz text file
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 58: Filter failed</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Input Collection</label>
        <div>
                    
                    Output dataset 'output_ranks' from step 49
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 59: Regex Find And Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Select lines from</label>
        <div>
                    
                    Output dataset 'structure_results' from step 50
        </div>
    </div>

      <div>
          <div class="form-row"><b>Checks</b></div>
          
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Check 1</b></div>
                
      
    
    <div class="form-row">
        <label>Find Regex</label>
        <div>
                CSI:FingerIDScore
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replacement</label>
        <div>
                Score
        </div>
    </div>


            </div> 
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 60: msPurity.spectralMatching</div>
                  <div class="card-body">
                    
      
      
      <div class="form-row"><b>Query spectra input and filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Input</label>
        <div>
                SQLite database of (LC)-MS/MS data
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Query SQLite database</label>
        <div>
                    
                    Output dataset 'out_pth' from step 51
        </div>
    </div>


      
      
      <div class="form-row"><b>Filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>ppm error of the precursor for spectra</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ppm error of the product for spectra</label>
        <div>
                5.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Filter on relative abundance threshold?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on polarity?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on precursor ion purity?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on XCMS groups ids?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on pids?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on retention time range?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on accessions?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on sources?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on instrument type?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on instrument name?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on spectral type?</label>
        <div>
                False
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Ignore any peaks flagged in the spectra in previous stages?</label>
        <div>
                True
        </div>
    </div>


        </div>
      </div>

        </div>
      </div>
      
      
      <div class="form-row"><b>Library spectra input and filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Input</label>
        <div>
                Locally configured SQLite, MySQL or PostgreSQL database
        </div>
    </div>

      

      
      
      <div class="form-row"><b>Filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>ppm error of the precursor for spectra</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ppm error of the product for spectra</label>
        <div>
                5.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Filter on relative abundance threshold?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on polarity?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Polarity</label>
        <div>
                Not available.
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>Filter on precursor ion purity?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on XCMS groups ids?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on pids?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on retention time range?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on accessions?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on sources?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on instrument type?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>l_instrumentTypes</label>
        <div>
                APCI-ITFT
APCI-ITTOF
CE-ESI-TOF
ESI-ITFT
ESI-ITTOF
ESI-QFT
ESI-QTOF
ESI-TOF
in source CID
In-silico QTOF
Ion trap
LC-APCI-ITFT
LC-APCI-QTOF
LC-APCI-Q
LC-ESI-IT
LC-ESI-ITFT
LC-ESI-ITTOF
LC-ESI-Q
LC-ESI-QFT
LC-ESI-QIT
LC-ESI-QQ
LC-ESI-QTOF
LC-ESI-TOF
LC-Q-TOF/MS
LC-QTOF
Linear Ion Trap
LIT
MALDI-QIT
MALDI-TOF
MALDI-TOFTOF
orbitrap
QIT
QIT-FT
QIT-TOF
QqQ
Q-TOF
Quattro_QQQ
        </div>
    </div>

      
    
    <div class="form-row">
        <label>l_instrumentTypesUser</label>
        <div>
                Empty.
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>Filter on instrument name?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on spectral type?</label>
        <div>
                False
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Ignore any peaks flagged in the spectra in previous stages?</label>
        <div>
                True
        </div>
    </div>


        </div>
      </div>

        </div>
      </div>
      
      
      <div class="form-row"><b>General arguments:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Filter on retention time match?</label>
        <div>
                False
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Filter on matching precursors?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Weighting for relative abundance</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Weighting for mz</label>
        <div>
                2.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Update database with results?</label>
        <div>
                False
        </div>
    </div>

      


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 61: msPurity.averageFragSpectra</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>purityA object</label>
        <div>
                    
                    Output dataset 'averageFragSpectra_output_rdata' from step 53
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Average and filter fragmentation spectra for each XCMS feature</label>
        <div>
                across MS data files
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Signal-to-noise threshold after averaging or summing</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Relative abundance threshold after averaging or summing</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in.</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor).</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ppm error tolerance</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Sum intensities across (averaged) scans?</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering.</label>
        <div>
                median
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead.</label>
        <div>
                True
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 62: Select</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Select lines from</label>
        <div>
                    
                    Output dataset 'output_summary_mr_mc' from step 55
        </div>
    </div>

      
    
    <div class="form-row">
        <label>that</label>
        <div>
                Matching
        </div>
    </div>

      
    
    <div class="form-row">
        <label>the pattern</label>
        <div>
                .*HMDB|compound_id.*
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 63: Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>File to process</label>
        <div>
                    
                    Output dataset 'outfile' from step 56
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find pattern</label>
        <div>
                rtmed
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace with</label>
        <div>
                rt
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find-Pattern is a regular expression</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace all occurences of the pattern</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Case-Insensitive search</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find whole-words</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ignore first line</label>
        <div>
                False
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Find and Replace text in</label>
        <div>
                entire line
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 64: Cut</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Cut columns</label>
        <div>
                c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c16
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Delimited by</label>
        <div>
                Tab
        </div>
    </div>

      
    
    <div class="form-row">
        <label>From</label>
        <div>
                    
                    Output dataset 'dimsPredictPuritySingle_output' from step 57
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 65: Regex Find And Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Select lines from</label>
        <div>
                    
                    Output dataset 'output' from step 58
        </div>
    </div>

      <div>
          <div class="form-row"><b>Checks</b></div>
          
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Check 1</b></div>
                
      
    
    <div class="form-row">
        <label>Find Regex</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replacement</label>
        <div>
                Empty.
        </div>
    </div>


            </div> 
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
                    Filter failed does not rename file correct. Hence this tool is required to force file rename. No regex actually performed
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 66: Filter failed</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Input Collection</label>
        <div>
                    
                    Output dataset 'matches' from step 60
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 67: msPurity.createMSP</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>msPurity purityA dataset</label>
        <div>
                    
                    Output dataset 'averageFragSpectra_output_rdata' from step 61
        </div>
    </div>

      
    
    <div class="form-row">
        <label>How to choose fragmentation spectra (if precursor was fragmented in &gt;1 scans per XCMS group feature)</label>
        <div>
                Average (inter)
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Use additional metadata?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Select XCMS groups?</label>
        <div>
                False
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Include intensity, relative abundanace or both in the MSP file</label>
        <div>
                Both intensity and relative abundance
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MSP schema to use for files</label>
        <div>
                MassBank (Europe)
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Filter peaks that have been flagged in prior processing steps</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Always include the following adduct descriptions in the MSP file</label>
        <div>
                Nothing selected.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Always include the following custom adducts</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Create MSP spectra for each adduct?</label>
        <div>
                True
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 68: Cut</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Cut columns</label>
        <div>
                c1-c14,c16
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Delimited by</label>
        <div>
                Tab
        </div>
    </div>

      
    
    <div class="form-row">
        <label>From</label>
        <div>
                    
                    Output dataset 'out_file1' from step 62
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 69: Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>File to process</label>
        <div>
                    
                    Output dataset 'outfile' from step 63
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find pattern</label>
        <div>
                mzmed
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace with</label>
        <div>
                mz
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find-Pattern is a regular expression</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace all occurences of the pattern</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Case-Insensitive search</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find whole-words</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ignore first line</label>
        <div>
                False
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Find and Replace text in</label>
        <div>
                entire line
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 70: CAMERA_DIMS</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>peaks_file</label>
        <div>
                    
                    Output dataset 'out_file1' from step 64
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ppm (adduct)</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ppm (iso)</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>mzabs (adduct)</label>
        <div>
                0.015
        </div>
    </div>

      
    
    <div class="form-row">
        <label>mzabs (iso)</label>
        <div>
                0.015
        </div>
    </div>

      
    
    <div class="form-row">
        <label>maxmol</label>
        <div>
                3
        </div>
    </div>

      
    
    <div class="form-row">
        <label>maxiso</label>
        <div>
                4
        </div>
    </div>

      
    
    <div class="form-row">
        <label>maxcharge</label>
        <div>
                3
        </div>
    </div>

      
    
    <div class="form-row">
        <label>polarity</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Intensity filter</label>
        <div>
                1000.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Rules for adducts</label>
        <div>
                Extended adducts
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Export the adduct ruleset used?</label>
        <div>
                False
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 71: msp_split</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Input MSP file</label>
        <div>
                    
                    Output dataset 'createMSP_output' from step 67
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Number of new files</label>
        <div>
                20
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Starting parameter for each spectra</label>
        <div>
                RECORD_TITLE:
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 72: Join</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>1st file</label>
        <div>
                    
                    Output dataset 'outfile' from step 69
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Column to use from 1st file</label>
        <div>
                2
        </div>
    </div>

      
    
    <div class="form-row">
        <label>2nd File</label>
        <div>
                    
                    Output dataset 'outfile' from step 54
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Column to use from 2nd file</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Output lines appearing in</label>
        <div>
                Both 1st &amp; 2nd file.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>First line is a header line</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ignore case</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Value to put in unpaired (empty) fields</label>
        <div>
                Empty.
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 73: Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>File to process</label>
        <div>
                    
                    Output dataset 'camera_annotated_peaklist' from step 70
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find pattern</label>
        <div>
                i
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace with</label>
        <div>
                intensity
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find-Pattern is a regular expression</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replace all occurences of the pattern</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Case-Insensitive search</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Find whole-words</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ignore first line</label>
        <div>
                False
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Find and Replace text in</label>
        <div>
                entire line
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 74: MetFrag</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>MSP file (Output from Create MSP tool)</label>
        <div>
                    
                    Output dataset 'multiple' from step 71
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Choose Compound Database</label>
        <div>
                MetChem
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>MetChem URL</label>
        <div>
                bberdb.bb2.cluster
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Relative Mass Deviation for database search (ppm)</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Fragment Peak Match Relative Mass Deviation (ppm)</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Fragment Peak Match Absolute Mass Deviation (Da)</label>
        <div>
                0.001
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Polarity</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Schema</label>
        <div>
                Auto
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Choose how additional metadata columns are extracted</label>
        <div>
                Extra metadata columns from the Name or RECORD_TITLE (each column is split on &#34;|&#34; and &#34;:&#34; ) 
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Suspect list</label>
        <div>
                Include suspect list
        </div>
    </div>

      
      
      
      
      
    
    <div class="form-row">
        <label>Use default list of suspect compounds?</label>
        <div>
                True
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>MetFrag Score Types</label>
        <div>
                FragmenterScore
OfflineMetFusionScore
SuspectListScore
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MetFrag Score Weights</label>
        <div>
                0.2,0.3,0.5
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>How to handle adducts</label>
        <div>
                Use adducts defined in MSP file
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Skip invalid or undefined adduct types?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum number of MS/MS peaks</label>
        <div>
                1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Output the MetFrag command line call</label>
        <div>
                False
        </div>
    </div>

      
      
      <div class="form-row"><b>PreProcessing filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>filter non-connected compounds (e.g. salts)</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>filter compounds containing non-standard isotopes</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum Elements Filter</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Maximum Elements Filter</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Include substructures</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Exclude substructures</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Include elements</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Include elements (exclusive)</label>
        <div>
                Empty.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Exclude elements</label>
        <div>
                Empty.
        </div>
    </div>


        </div>
      </div>
      
      
      <div class="form-row"><b>PostProcessing filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Threshold for score after MetFrag search</label>
        <div>
                0.6
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum percentage of explain peaks</label>
        <div>
                10.0
        </div>
    </div>


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 75: SIRIUS-CSI:FingerID</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>MSP file (output from Create MSP tool)</label>
        <div>
                    
                    Output dataset 'multiple' from step 71
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Select SIRIUS-CSI:FingerID Database</label>
        <div>
                Bio (all biological)
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Mass deviation of the fragment peaks in ppm</label>
        <div>
                5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Maximum number of candidates in the output</label>
        <div>
                5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ion mode</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Analysis used</label>
        <div>
                Orbitrap
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Schema</label>
        <div>
                Auto
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Choose how additional metadata columns are extracted</label>
        <div>
                
                Extra metadata columns from the Name or
                RECORD_TITLE (each column is split on &#34;|&#34; and &#34;:&#34; ) 
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Minimum number of MS/MS peaks</label>
        <div>
                0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>How to handle adducts</label>
        <div>
                Use adducts defined in MSP file
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 76: msPurity.createDatabase</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>xcmsSet or CAMERA object</label>
        <div>
                    
                    Output dataset 'rdata_quick_false' from step 38
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Use CAMERA object or XCMS object from RData?</label>
        <div>
                CAMERA (xa)
        </div>
    </div>

      
    
    <div class="form-row">
        <label>purityA object (frag4feature output)</label>
        <div>
                    
                    Output dataset 'averageFragSpectra_output_rdata' from step 61
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Include EIC data?</label>
        <div>
                True
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Add a different grouped peaklist to database?</label>
        <div>
                Provide group peaklist 
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>grouped peaklist</label>
        <div>
                    
                    Output dataset 'output' from step 72
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>Resubmit your dataset</label>
        <div>
                no need
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 77: BEAMSpy</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Peaklist</label>
        <div>
                    
                    Output dataset 'outfile' from step 73
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Intensity matrix</label>
        <div>
                    <i>select at runtime</i>
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Ion mode</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Library adducts</label>
        <div>
                    
                    Output dataset 'output' from step 21
        </div>
    </div>

      
      
      <div class="form-row"><b>Group Features:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label> </label>
        <div>
                False
        </div>
    </div>

      


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotate Peak Patterns:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label> </label>
        <div>
                False
        </div>
    </div>

      


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotate Molecular Formulae:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label> </label>
        <div>
                False
        </div>
    </div>

      


        </div>
      </div>
      
      
      <div class="form-row"><b>Annotate Compounds / Metabolites:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label> </label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Ppm error tolerance</label>
        <div>
                5.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Source</label>
        <div>
                Compound databases
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Select databases</label>
        <div>
                hmdb_full_v4_0_v1
        </div>
    </div>




        </div>
      </div>
      
      
      <div class="form-row"><b>Create summary table(s):</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>Multiple rows for each feature and separate columns</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Single row for each feature and separate columns</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Single row for each feature and merged columns</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Convert RT</label>
        <div>
                skip
        </div>
    </div>


        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 78: Column arrange</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>file to rearrange</label>
        <div>
                    
                    Output dataset 'results' from step 74
        </div>
    </div>

      <div>
          <div class="form-row"><b>Specify the first few columns by names</b></div>
          
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 1</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                sample_name
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 2</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                MZ
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 3</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                grpid
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 4</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                RT
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 5</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                adduct
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 6</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                CompoundName
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 7</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                ExplPeaks
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 8</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                FormulasOfExplPeaks
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 9</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                FragmenterScore
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 10</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                FragmenterScore_Values
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 11</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                Identifier
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 12</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                InChI
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 13</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                InChIKey
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 14</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                InChIKey1
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 15</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                InChIKey2
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 16</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                InChIKey3
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 17</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                MaximumTreeDepth
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 18</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                MolecularFormula
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 19</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                MonoisotopicMass
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 20</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                NoExplPeaks
        </div>
    </div>


            </div> 
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Specify the first few columns by name 21</b></div>
                
      
    
    <div class="form-row">
        <label>column</label>
        <div>
                NumberPeaksUsed
        </div>
    </div>


            </div> 
      </div>
      
    
    <div class="form-row">
        <label>Discard unspecified columns?</label>
        <div>
                False
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 79: Collapse Collection</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Collection of files to collapse into single dataset</label>
        <div>
                    
                    Output dataset 'structure_results' from step 75
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Keep one header line</label>
        <div>
                False
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Append File name</label>
        <div>
                False
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 80: msPurity.spectralMatching</div>
                  <div class="card-body">
                    
      
      
      <div class="form-row"><b>Query spectra input and filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Input</label>
        <div>
                SQLite database of (LC)-MS/MS data
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Query SQLite database</label>
        <div>
                    
                    Output dataset 'createDatabase_output_sqlite' from step 76
        </div>
    </div>


      
      
      <div class="form-row"><b>Filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>ppm error of the precursor for spectra</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ppm error of the product for spectra</label>
        <div>
                5.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Filter on relative abundance threshold?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on polarity?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on precursor ion purity?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on XCMS groups ids?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on pids?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on retention time range?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on accessions?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on sources?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on instrument type?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on instrument name?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on spectral type?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Spectra type</label>
        <div>
                Averaged inter spectra
        </div>
    </div>


      
    
    <div class="form-row">
        <label>Ignore any peaks flagged in the spectra in previous stages?</label>
        <div>
                True
        </div>
    </div>


        </div>
      </div>

        </div>
      </div>
      
      
      <div class="form-row"><b>Library spectra input and filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Input</label>
        <div>
                Locally configured SQLite, MySQL or PostgreSQL database
        </div>
    </div>

      

      
      
      <div class="form-row"><b>Filters:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
    
    <div class="form-row">
        <label>ppm error of the precursor for spectra</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>ppm error of the product for spectra</label>
        <div>
                5.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Filter on relative abundance threshold?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on polarity?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Polarity</label>
        <div>
                Not available.
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>Filter on precursor ion purity?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on XCMS groups ids?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on pids?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on retention time range?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on accessions?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on sources?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on instrument type?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>l_instrumentTypes</label>
        <div>
                APCI-ITFT
APCI-ITTOF
CE-ESI-TOF
ESI-ITFT
ESI-ITTOF
ESI-QFT
ESI-QTOF
ESI-TOF
in source CID
In-silico QTOF
Ion trap
LC-APCI-ITFT
LC-APCI-QTOF
LC-APCI-Q
LC-ESI-IT
LC-ESI-ITFT
LC-ESI-ITTOF
LC-ESI-Q
LC-ESI-QFT
LC-ESI-QIT
LC-ESI-QQ
LC-ESI-QTOF
LC-ESI-TOF
LC-Q-TOF/MS
LC-QTOF
Linear Ion Trap
LIT
MALDI-QIT
MALDI-TOF
MALDI-TOFTOF
orbitrap
QIT
QIT-FT
QIT-TOF
QqQ
Q-TOF
Quattro_QQQ
        </div>
    </div>

      
    
    <div class="form-row">
        <label>l_instrumentTypesUser</label>
        <div>
                Empty.
        </div>
    </div>


      
      
      
      
    
    <div class="form-row">
        <label>Filter on instrument name?</label>
        <div>
                False
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Filter on spectral type?</label>
        <div>
                False
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Ignore any peaks flagged in the spectra in previous stages?</label>
        <div>
                True
        </div>
    </div>


        </div>
      </div>

        </div>
      </div>
      
      
      <div class="form-row"><b>General arguments:</b></div>
      <div>
        <div class="ui-portlet-section ml-2">
          
      
      
      
      
    
    <div class="form-row">
        <label>Filter on retention time match?</label>
        <div>
                False
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>Filter on matching precursors?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Weighting for relative abundance</label>
        <div>
                0.5
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Weighting for mz</label>
        <div>
                2.0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Update database with results?</label>
        <div>
                True
        </div>
    </div>

      
      
    
    <div class="form-row">
        <label>Make a copy of the database?</label>
        <div>
                True
        </div>
    </div>



        </div>
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 81: Select</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Select lines from</label>
        <div>
                    
                    Output dataset 'output_summary_mr_mc' from step 77
        </div>
    </div>

      
    
    <div class="form-row">
        <label>that</label>
        <div>
                Matching
        </div>
    </div>

      
    
    <div class="form-row">
        <label>the pattern</label>
        <div>
                .*HMDB|compound_id.*
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 82: Collapse Collection</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Collection of files to collapse into single dataset</label>
        <div>
                    
                    Output dataset 'output' from step 78
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Keep one header line</label>
        <div>
                True
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Append File name</label>
        <div>
                False
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 83: Regex Find And Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Select lines from</label>
        <div>
                    
                    Output dataset 'output' from step 79
        </div>
    </div>

      <div>
          <div class="form-row"><b>Checks</b></div>
          
            <div class="ui-portlet-section ml-2">
                
                <div class="form-row"><b>Check 1</b></div>
                
      
    
    <div class="form-row">
        <label>Find Regex</label>
        <div>
                CSI:FingerIDScore
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Replacement</label>
        <div>
                Score
        </div>
    </div>


            </div> 
      </div>

                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 84: Cut</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Cut columns</label>
        <div>
                c1-c14,c16
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Delimited by</label>
        <div>
                Tab
        </div>
    </div>

      
    
    <div class="form-row">
        <label>From</label>
        <div>
                    
                    Output dataset 'out_file1' from step 81
        </div>
    </div>


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 85: msPurity.combineAnnotations</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Spectral matching result</label>
        <div>
                    
                    Output dataset 'sqlite_results' from step 80
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Metfrag result</label>
        <div>
                    
                    Output dataset 'output' from step 82
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Sirius CSI:FingerID result</label>
        <div>
                    
                    Output dataset 'out_file1' from step 83
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Use probmetab data</label>
        <div>
                Do not include probmetab results
        </div>
    </div>

      

      
    
    <div class="form-row">
        <label>MS1 Lookup result</label>
        <div>
                    
                    Output dataset 'out_file1' from step 68
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MS1 lookup adducts to keep</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MS1 lookup check adducts to CAMERA</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MS1 lookup database source</label>
        <div>
                hmdb
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Spectral matching weight</label>
        <div>
                0.45
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Metfrag weight</label>
        <div>
                0.15
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Sirius CSI:FingerID weight</label>
        <div>
                0.25
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Probmetab weight</label>
        <div>
                0.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MS1 Lookup weight</label>
        <div>
                0.1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Biological similarity weight</label>
        <div>
                0.05
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Create summary output</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Create a new database for the results?</label>
        <div>
                True
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>compoundDbType</label>
        <div>
                Locally configured MySQL, Postgres or SQLite database
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
            <tr><td>
              
              <div class="card mt-3 mr-3">
                  <div class="card-header">Step 86: LC-MS/MS fractionation processor - </div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>LC-MS(/MS) SQlite results</label>
        <div>
                    
                    Output dataset 'combined_annotations_sqlite' from step 85
        </div>
    </div>

      
    
    <div class="form-row">
        <label>DIMS peaklist for fractions</label>
        <div>
                    
                    Output dataset 'hdf5_file_out' from step 41
        </div>
    </div>

      
    
    <div class="form-row">
        <label>DIMSn merged</label>
        <div>
                    
                    Output dataset 'merged_hdf5' from step 43
        </div>
    </div>

      
    
    <div class="form-row">
        <label>DIMSn non merged</label>
        <div>
                    
                    Output dataset 'non_merged_hdf5' from step 43
        </div>
    </div>

      
    
    <div class="form-row">
        <label>DIMSn MS1 precursors</label>
        <div>
                    
                    Output dataset 'precursors_hdf5' from step 43
        </div>
    </div>

      
    
    <div class="form-row">
        <label>BEAMS MS1 annotation results for DIMS</label>
        <div>
                    
                    Output dataset 'out_file1' from step 84
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Metfrag results for DIMSn</label>
        <div>
                    
                    Output dataset 'results' from step 52
        </div>
    </div>

      
    
    <div class="form-row">
        <label>SIRIUS CSI:FingerID results for DIMSn</label>
        <div>
                    
                    Output dataset 'out_file1' from step 59
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Spectral matching results for DIMSn</label>
        <div>
                    
                    Output dataset 'output' from step 66
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Molecular formula annotation based on MSn (MSnPy)</label>
        <div>
                    
                    Output dataset 'out_file1' from step 65
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Additional details</label>
        <div>
                    
                    Output dataset 'camera_annotated_peaklist' from step 70
        </div>
    </div>

      
    
    <div class="form-row">
        <label>PPM error for LC-MS measurements</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>PPM error for DI-MS measurements</label>
        <div>
                5.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Tolerance in seconds to map DIMS to LC-MS</label>
        <div>
                10.0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Spectral matching weight</label>
        <div>
                0.45
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Metfrag weight</label>
        <div>
                0.15
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Sirius CSI:FingerID weight</label>
        <div>
                0.25
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MS1 Lookup weight</label>
        <div>
                0.1
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Biological similarity weight</label>
        <div>
                0.05
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Create a new database for the results?</label>
        <div>
                True
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MS1 lookup database source</label>
        <div>
                hmdb
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MS1 lookup adducts to keep</label>
        <div>
                Not available.
        </div>
    </div>

      
    
    <div class="form-row">
        <label>MS1 lookup check adducts to CAMERA</label>
        <div>
                False
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Limit for sirius annotations by rank</label>
        <div>
                0
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Limit for annotations by rank</label>
        <div>
                0
        </div>
    </div>

      
      
      
      
    
    <div class="form-row">
        <label>Compound database</label>
        <div>
                Locally configured SQLite database
        </div>
    </div>

      

      
      
      
      
    
    <div class="form-row">
        <label>Spectral library database</label>
        <div>
                Locally configured SQLite database
        </div>
    </div>

      


                  </div>
              </div>
            </td>
            <td class="annotation">
            </td>
            </tr>
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