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    W3_LC-MSMS_MSM_DMA

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    <div class="page-body p-3">
        <div>
            
    <h3>
    W3_LC-MSMS_MSM_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>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 2: 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 3: 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 4: 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 5: 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 6: 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 7: 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 8: 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 9: 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 10: 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 11: msPurity.purityA</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>*.mzML file</label>
        <div>
                    
                    Output dataset 'output' from step 4
        </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 12: 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 4
        </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: xcms findChromPeaks (xcmsSet)</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>RData file</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 12
        </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 14: xcms findChromPeaks Merger</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>RData file</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 13
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Sample metadata file </label>
        <div>
                    
                    Output dataset 'output' from step 5
        </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 15: xcms groupChromPeaks (group)</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>RData file</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 14
        </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 16: msPurity.frag4feature</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>xcmsSet object</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 15
        </div>
    </div>

      
    
    <div class="form-row">
        <label>purityA object</label>
        <div>
                    
                    Output dataset 'purityA_output_rdata' from step 11
        </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 17: 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 15
        </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 18: 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 16
        </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 19: Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>File to process</label>
        <div>
                    
                    Output dataset 'out_file1' from step 17
        </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 20: msPurity.averageFragSpectra</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>purityA object</label>
        <div>
                    
                    Output dataset 'filterFragSpectra_output_rdata' from step 18
        </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 21: BEAMSpy</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Peaklist</label>
        <div>
                    
                    Output dataset 'outfile' from step 19
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Intensity matrix</label>
        <div>
                    
                    Output dataset 'dataMatrix' from step 15
        </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 10
        </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 22: msPurity.averageFragSpectra</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>purityA object</label>
        <div>
                    
                    Output dataset 'averageFragSpectra_output_rdata' from step 20
        </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 23: Select</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Select lines from</label>
        <div>
                    
                    Output dataset 'output_summary_mr_mc' from step 21
        </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 24: msPurity.createMSP</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>msPurity purityA dataset</label>
        <div>
                    
                    Output dataset 'averageFragSpectra_output_rdata' from step 22
        </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 25: msPurity.createDatabase</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>xcmsSet or CAMERA object</label>
        <div>
                    
                    Output dataset 'xsetRData' from step 15
        </div>
    </div>

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

      
    
    <div class="form-row">
        <label>purityA object (frag4feature output)</label>
        <div>
                    
                    Output dataset 'averageFragSpectra_output_rdata' from step 22
        </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>
                Use default grouped peaklist
        </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 26: 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 23
        </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: msp_split</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Input MSP file</label>
        <div>
                    
                    Output dataset 'createMSP_output' from step 24
        </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 28: 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 25
        </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 29: 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 27
        </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 30: 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 27
        </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 31: 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 29
        </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 32: Column arrange</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>file to rearrange</label>
        <div>
                    
                    Output dataset 'results' from step 30
        </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 33: Regex Find And Replace</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Select lines from</label>
        <div>
                    
                    Output dataset 'output' from step 31
        </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 34: 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 32
        </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 35: msPurity.combineAnnotations</div>
                  <div class="card-body">
                    
      
    
    <div class="form-row">
        <label>Spectral matching result</label>
        <div>
                    
                    Output dataset 'sqlite_results' from step 28
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Metfrag result</label>
        <div>
                    
                    Output dataset 'output' from step 34
        </div>
    </div>

      
    
    <div class="form-row">
        <label>Sirius CSI:FingerID result</label>
        <div>
                    
                    Output dataset 'out_file1' from step 33
        </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 26
        </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>

      


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