comparison msconvert_macros.xml @ 7:e638f7fad66a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292

6:6b6bba73eadb

<macros>
  <xml name="generic_requirements">
    <requirements>
      <requirement type="package" version="3.0.9992">proteowizard</requirement>
    </requirements>
  </xml>
  <token name="@VERSION@">3.0.9992</token>
  
  <xml name="msconvertCommand">
    <command interpreter="python">
<![CDATA[
    #import re
    #set $ext = $input.ext

    ## sanitize display name for use as temp filename
    #set basename = 'pwiz_in'
    
    #if hasattr($input, 'display_name')
      ## explicit inclusion or exclusion ??
      #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.display_name)
      ##set basename = $re.sub(r'[\/\\\;\|\&\>\<]','_',$input.display_name)
    #end if

    msconvert_wrapper.py

    #if $ext == 'wiff':
      --input='${input.extra_files_path}/wiff'
      --input_name='${basename}.wiff'
      --implicit='${input.extra_files_path}/wiff_scan'
      --input='${input.extra_files_path}/wiff_scan'
      --input_name='${basename}.wiff.scan'
    #else
      --input='${input}'
      --input_name='$basename'
    #end if
    --output='${output}'
    ## BEGIN_VERSION_DEFAULT
    --fromextension=$ext
    ## END_VERSION_DEFAULT
    --toextension=${output_type}

    ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
      #if $data_processing.precursor_refinement.use_mzrefinement
        #set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext))
      --ident='$data_processing.precursor_refinement.input_ident'
      --ident_name='$input_ident_name'
      --refinement='$output_refinement'
      --filter "mzRefiner $input_ident_name
        msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
        thresholdScore=$data_processing.precursor_refinement.thresholdScore
        thresholdValue=$data_processing.precursor_refinement.thresholdValue
        thresholdStep=$data_processing.precursor_refinement.thresholdStep
        maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
      #end if

      #if $data_processing.peak_picking.pick_peaks
        --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
      #end if

      #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
      --filter "chargeStatePredictor
        overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge

      #if $data_processing.etd_filtering.do_etd_filtering
        --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
          $data_processing.etd_filtering.remove_charge_reduced
          $data_processing.etd_filtering.remove_neutral_loss
          $data_processing.etd_filtering.blanket_removal
          $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
      #end if

      #if $data_processing.ms2denoise.denoise
        --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
      #end if

      #if str($filtering.analyzer) != "false"
        --filter "analyzer $filtering.analyzer"
      #end if
      
    ## OUTPUT ENCODING
      -- 
      #set $mz_encoding = str($settings.mz_encoding)
      #set $intensity_encoding = str($settings.intensity_encoding)
      #if $mz_encoding == $intensity_encoding
        #if $mz_encoding == "64"
          --64

      #if $settings.gzip_compression
        --gzip
      #end if

]]>
    </command>
  </xml>

  <xml name="msconvertInputParameters">
    <param name="output_type" type="select" label="Output Type">
      <option value="mz5" selected="true">mz5</option>
      <option value="mzML">mzML</option>
      <option value="mzXML">mzXML</option>
      <option value="mgf">mgf</option>
      <option value="ms2">ms2</option>
    </param>

    <section name="data_processing" title="Data Processing Filters">
      
      <conditional name="peak_picking">
        <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
        <when value="false" />
        <when value="true">
          <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
            <option value="1">MS1 Only (1)</option>
            <option value="2">MS2 Only (2)</option>
            <option value="2-">MS2 and on (2-)</option>
            <option value="1-" selected="true">All Levels (1-)</option>
          </param>
          <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
            <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
            <option value="cwt">CantWaiT - continuous wavelet transform</option>
          </param>
        </when>
      </conditional>

      <conditional name="precursor_refinement">
        <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
        <when value="false"></when>

        <option value="IT">Ion trap</option>
        <option value="TOF">Time of flight</option>
      </param>
    </section>


    <section name="settings" title="Output Encoding Settings">
      <param type="select" name="mz_encoding" label="m/z Encoding Precision">
        <option value="64" selected="true">64</option>
        <option value="32">32</option>

    </section>
  </xml>
  
  <xml name="msconvertOutput">
    <outputs>
      <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
        <change_format>
          <when input="output_type" value="mz5" format="mz5" />
          <when input="output_type" value="mzXML" format="mzxml" />
          <when input="output_type" value="ms2" format="ms2" />
          <when input="output_type" value="mgf" format="mgf" />
        </change_format>
      </data>
      <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
        <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
      </data>
    </outputs>
  </xml>


  <xml name="msconvert_tests">
    <test>
      <param name="input" value="small.mzML" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="cwt" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
    </test>

    <!-- this data file only has profile MS1, so the result is the same -->
    <test>
      <param name="input" value="small.mzML" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="cwt" />
      <param name="pick_peaks_ms_levels" value="1" />
      <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> 
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mz5" />
      <param name="mz_encoding" value="64" />
      <param name="intensity_encoding" value="64" />
      <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzXML" />
      <param name="mz_encoding" value="32" />
      <param name="intensity_encoding" value="32" />
      <output name="output" file="small-zlib-32.mzXML" />
    </test>
    <!-- TODO: how to test gzipped output?
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzXML" />

      <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
    </test>-->

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-numpressLP.mzML" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearSlof" />
      <output name="output" file="small-numpressLS.mzML" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinear" />
      <output name="output" file="small-numpressL.mzML" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressPic" />
      <output name="output" file="small-numpressP.mzML" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressSlof" />
      <output name="output" file="small-numpressS.mzML" />
    </test>

    <test>
      <param name="input" value="Rpal_01.mz5" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="use_mzrefinement" value="true" />
      <param name="input_ident" value="Rpal_01.pepXML" />
      <param name="thresholdScore" value="mvh" />

      <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
    </test>
    
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="charge_state_calculation_method" value="predictor" />
      <param name="predictor_overrideExistingCharge" value="true" />
      <param name="minMultipleCharge" value="2" />
      <param name="maxMultipleCharge" value="5" />
      <param name="singleChargeFractionTIC" value="0.95" />
      <param name="maxKnownCharge" value="8" />
      <output name="output" file="small-chargeStatePredictor.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="charge_state_calculation_method" value="turbocharger" />
      <param name="minCharge" value="1" />
      <param name="maxCharge" value="5" />
      <param name="precursorsBefore" value="1" />
      <param name="precursorsAfter" value="1" />
      <param name="halfIsoWidth" value="1.5" />
      <param name="defaultMinCharge" value="1" />
      <param name="defaultMaxCharge" value="5" />
      <output name="output" file="small-turbocharger.mzML" />
    </test>
    <test>
      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
      <param name="output_type" value="mzML" />
      <param name="do_etd_filtering" value="true" />
      <param name="remove_precursor" value="true" />
      <param name="remove_charge_reduced" value="true" />
      <param name="remove_neutral_loss" value="false" />

      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="thresholds_0|threshold_type" value="count" />
      <param name="thresholds_0|value" value="100" />
      <param name="thresholds_0|orientation" value="most-intense" />
      <param name="thresholds_1|threshold_type" value="absolute" />
      <param name="thresholds_1|value" value="1" />
      <param name="thresholds_1|orientation" value="most-intense" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-threshold.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="do_mzwindow_filter" value="true" />
      <param name="mz_window_from" value="420" />
      <param name="mz_window_to" value="840" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-mzWindow.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="denoise" value="true" />
      <param name="num_peaks" value="10" />
      <param name="window_width" value="40" />
      <param name="relax" value="false" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-denoise.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="ms2deisotope" value="true" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-deisotope.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="activation" value="CID" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-activation.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="indices_0|from" value="2" />
      <param name="indices_0|to" value="4" />
      <param name="indices_1|from" value="10" />
      <param name="indices_1|to" value="10" />
      <param name="indices_2|from" value="13" />
      <param name="indices_2|to" value="15" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-index-filter.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="strip_it" value="true" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-strip-it.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="do_ms_level_filter" value="true" />
      <param name="ms_level_from" value="2" />
      <param name="ms_level_to" value="2" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-ms-level-filter.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="polarity" value="positive" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-polarity-filter.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="analyzer" value="IT" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-analyzer-filter.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzML" />
      <param name="scan_numbers_0|from" value="3" />
      <param name="scan_numbers_0|to" value="5" />
      <param name="scan_numbers_1|from" value="11" />
      <param name="scan_numbers_1|to" value="11" />
      <param name="scan_numbers_2|from" value="14" />
      <param name="scan_numbers_2|to" value="16" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
    </test>
    <!--<test>
      <param name="input" value="small.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />

    </test>-->
  </xml>
  <xml name="msconvert_help">
**What it does**

Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.

You can view the original documentation here_.

.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
  </xml>

7:e638f7fad66a

<macros>
  <token name="@VERSION@">3.0.19052</token>
  <token name="@FULL_VERSION@">@VERSION@-089e81090</token>
  
  <xml name="msconvertCommand">
    <command detect_errors="exit_code">
<![CDATA[
    #import re
    #set $ext = $input.ext

    ## sanitize display name for use as temp filename
    #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier)

    #if $ext == 'wiff':
      ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
      ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
    #elif $ext.endswith('tar'):
      ln -s '$input' '${basename}' &&
      tar xf '${basename}' &&
      #set basename = $os.path.splitext($basename)[0]
    #else
      ln -s '$input' '${basename}' &&
    #end if
    
    #if $data_processing.precursor_refinement.use_mzrefinement
      #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
      #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
      ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
    #end if

    uid=`id -u` &&
    gid=`id -g` &&

    wine64_anyuser msconvert '${basename}'
    --outdir outputs
    --${output_type}

    #if $general_options.combineIonMobilitySpectra:
    --combineIonMobilitySpectra
    #end if

    #if $general_options.simAsSpectra:
    --simAsSpectra
    #end if

    #if $general_options.srmAsSpectra:
    --srmAsSpectra
    #end if

    #if $general_options.acceptZeroLengthSpectra:
    --acceptZeroLengthSpectra
    #end if

    #if $general_options.ignoreUnknownInstrumentError:
    --ignoreUnknownInstrumentError
    #end if

    #if $general_options.scan_summing.do_scan_summing:
      --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
    #end if

    #if $general_options.multi_run_output.do_multi_run_output:
      #if len($general_options.multi_run_output.run_index_set) > 0
        --runIndexSet "
        #for $index in $general_options.multi_run_output.run_index_set
          [${index.from},${index.to}]
        #end for
        "
      #end if
    #else
      --runIndexSet $general_options.multi_run_output.runIndexSet
    #end if

    ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests
    --stripLocationFromSourceFiles

    ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
      #if $data_processing.peak_picking.pick_peaks
        --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
      #end if

      #if $data_processing.precursor_refinement.use_mzrefinement
      --filter "mzRefiner $input_ident_name
        msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
        thresholdScore=$data_processing.precursor_refinement.thresholdScore
        thresholdValue=$data_processing.precursor_refinement.thresholdValue
        thresholdStep=$data_processing.precursor_refinement.thresholdStep
        maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"
      #end if

      #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
      --filter "chargeStatePredictor
        overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge

      #if $data_processing.etd_filtering.do_etd_filtering
        --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
          $data_processing.etd_filtering.remove_charge_reduced
          $data_processing.etd_filtering.remove_neutral_loss
          $data_processing.etd_filtering.blanket_removal
          $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"
      #end if

      #if $data_processing.ms2denoise.denoise
        --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
      #end if

      #if str($filtering.analyzer) != "false"
        --filter "analyzer $filtering.analyzer"
      #end if
      
    ## OUTPUT ENCODING
      #set $mz_encoding = str($settings.mz_encoding)
      #set $intensity_encoding = str($settings.intensity_encoding)
      #if $mz_encoding == $intensity_encoding
        #if $mz_encoding == "64"
          --64

      #if $settings.gzip_compression
        --gzip
      #end if

      #if $general_options.multi_run_output.do_multi_run_output == 'false':
        --outfile '${os.path.splitext($basename)[0]}'
        && sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}'
      #else
        && sudo chown \$uid:\$gid 'outputs' -R
        && ls -la outputs/
      #end if

      #if $data_processing.precursor_refinement.use_mzrefinement
        && sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement'
      #end if
]]>
    </command>
  </xml>

  <xml name="msconvertInputParameters">
    <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses proprietary vendor libraries; to run it you must agree to the vendor licenses. Read them at http://www.proteowizard.org/licenses.html">
        <validator type="expression" message="You must agree to the vendor licenses to run msconvert.">True == value</validator>
    </param>

    <param name="output_type" type="select" label="Output Type">
      <option value="mz5" selected="true">mz5</option>
      <option value="mzML">mzML</option>
      <option value="mzXML">mzXML</option>
      <option value="mgf">mgf</option>
      <option value="ms2">ms2</option>
    </param>

    <section name="data_processing" title="Data Processing Filters">  
        <conditional name="peak_picking">
            <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
            <when value="false" />
            <when value="true">
                <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
                    <option value="1">MS1 Only (1)</option>
                    <option value="2">MS2 Only (2)</option>
                    <option value="2-">MS2 and on (2-)</option>
                    <option value="1-" selected="true">All Levels (1-)</option>
                </param>
                <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
                    <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
                    <option value="cwt">CantWaiT - continuous wavelet transform</option>
                </param>
            </when>
      </conditional>

      <conditional name="precursor_refinement">
        <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
        <when value="false"></when>

        <option value="IT">Ion trap</option>
        <option value="TOF">Time of flight</option>
      </param>
    </section>

    <section name="general_options" title="General Options">
      <param argument="--combineIonMobilitySpectra" type="boolean" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />

      <conditional name="scan_summing">
        <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" />
        <when value="false" />
        <when value="true">
          <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." />
          <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." />
          <param name="ionMobilityTol" type="float" label="Ion mobility tolerance" value="0.01" min="0" optional="true" help="Spectra with ion mobility values with a difference less than this tolerance are summed together. Only relevant for ion mobility spectra." />
        </when>
      </conditional>

      <param argument="--simAsSpectra" type="boolean" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
      <param argument="--srmAsSpectra" type="boolean" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
      <param argument="--acceptZeroLengthSpectra" type="boolean" label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" />
      <param argument="--ignoreUnknownInstrumentError" type="boolean" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />

      <conditional name="multi_run_output">
        <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" />
        <when value="false">
          <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
        </when>
        <when value="true">
          <repeat name="run_index_set" title="Select runs for multi-run sources" help="For multi-run sources (e.g. WIFF), select only the specified run indices">
            <param name="from" type="integer" label="Run Index From" value="0" min="0" optional="false" />
            <param name="to" type="integer" label="Run Index To" value="0" min="0" optional="true" />
          </repeat>
        </when>
      </conditional>
    </section>

    <section name="settings" title="Output Encoding Settings">
      <param type="select" name="mz_encoding" label="m/z Encoding Precision">
        <option value="64" selected="true">64</option>
        <option value="32">32</option>

    </section>
  </xml>
  
  <xml name="msconvertOutput">
    <outputs>
      <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" >
        <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter>
        <change_format>
          <when input="output_type" value="mz5" format="mz5" />
          <when input="output_type" value="mzXML" format="mzxml" />
          <when input="output_type" value="ms2" format="ms2" />
          <when input="output_type" value="mgf" format="mgf" />
        </change_format>
      </data>
      <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
        <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
      </data>
      <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}">
        <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter>
        <discover_datasets pattern="__name_and_ext__" directory="outputs" />
      </collection>
    </outputs>
  </xml>


  <xml name="msconvert_tests">
    <test>
      <param name="input" value="small.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="cwt" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />
    </test>
    <test>
      <param name="input" value="small.RAW" ftype="thermo.raw" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="vendor" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="small-peakpicking-vendor-allMS.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="ThyroglobMRM000003.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="combineIonMobilitySpectra" value="true" />
      <param name="do_scan_summing" value="true" />
      <output name="output" file="ThyroglobMRM000003.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="MassLynxTest.raw.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <output name="output" file="MassLynxTest.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="AgilentMassHunterTest.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="BrukerBafTest.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="vendor" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="BrukerBafTest.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="0" />
      <output name="output" file="SciexTest-HPINalone.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="0" />
      <param name="indices_0|from" value="0" />
      <param name="indices_0|to" value="499" />
      <param name="srmAsSpectra" value="true" />
      <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="1" />
      <param name="indices_0|from" value="0" />
      <param name="indices_0|to" value="499" />
      <param name="srmAsSpectra" value="true" />
      <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="true" />
      <param name="run_index_set_0|from" value="0" />
      <param name="run_index_set_0|to" value="1" />
      <output_collection name="multi_run_output_list" type="list">
        <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" />
        <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" />
      </output_collection>
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="true" />
      <output_collection name="multi_run_output_list" type="list">
        <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" />
        <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" />
      </output_collection>
    </test>

    <!-- this data file only has profile MS1, so the result is the same -->
    <test>
      <param name="input" value="small.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="cwt" />
      <param name="pick_peaks_ms_levels" value="1" />
      <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> 
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mz5" />
      <param name="mz_encoding" value="64" />
      <param name="intensity_encoding" value="64" />
      <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="mz_encoding" value="32" />
      <param name="intensity_encoding" value="32" />
      <output name="output" file="small-zlib-32.mzXML" lines_diff="6" />
    </test>
    <!-- TODO: how to test gzipped output?
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzXML" />

      <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
    </test>-->

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-numpressLP.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearSlof" />
      <output name="output" file="small-numpressLS.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinear" />
      <output name="output" file="small-numpressL.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressPic" />
      <output name="output" file="small-numpressP.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressSlof" />
      <output name="output" file="small-numpressS.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="Rpal_01.mz5" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="use_mzrefinement" value="true" />
      <param name="input_ident" value="Rpal_01.pepXML" />
      <param name="thresholdScore" value="mvh" />

      <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
    </test>
    
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="charge_state_calculation_method" value="predictor" />
      <param name="predictor_overrideExistingCharge" value="true" />
      <param name="minMultipleCharge" value="2" />
      <param name="maxMultipleCharge" value="5" />
      <param name="singleChargeFractionTIC" value="0.95" />
      <param name="maxKnownCharge" value="8" />
      <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="charge_state_calculation_method" value="turbocharger" />
      <param name="minCharge" value="1" />
      <param name="maxCharge" value="5" />
      <param name="precursorsBefore" value="1" />
      <param name="precursorsAfter" value="1" />
      <param name="halfIsoWidth" value="1.5" />
      <param name="defaultMinCharge" value="1" />
      <param name="defaultMaxCharge" value="5" />
      <output name="output" file="small-turbocharger.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_etd_filtering" value="true" />
      <param name="remove_precursor" value="true" />
      <param name="remove_charge_reduced" value="true" />
      <param name="remove_neutral_loss" value="false" />

      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="thresholds_0|threshold_type" value="count" />
      <param name="thresholds_0|value" value="100" />
      <param name="thresholds_0|orientation" value="most-intense" />
      <param name="thresholds_1|threshold_type" value="absolute" />
      <param name="thresholds_1|value" value="1" />
      <param name="thresholds_1|orientation" value="most-intense" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-threshold.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_mzwindow_filter" value="true" />
      <param name="mz_window_from" value="420" />
      <param name="mz_window_to" value="840" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-mzWindow.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="denoise" value="true" />
      <param name="num_peaks" value="10" />
      <param name="window_width" value="40" />
      <param name="relax" value="false" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-denoise.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="ms2deisotope" value="true" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-deisotope.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="activation" value="CID" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-activation.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="indices_0|from" value="2" />
      <param name="indices_0|to" value="4" />
      <param name="indices_1|from" value="10" />
      <param name="indices_1|to" value="10" />
      <param name="indices_2|from" value="13" />
      <param name="indices_2|to" value="15" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-index-filter.mzML" lines_diff="32" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="strip_it" value="true" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-strip-it.mzML" lines_diff="100" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_ms_level_filter" value="true" />
      <param name="ms_level_from" value="2" />
      <param name="ms_level_to" value="2" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="polarity" value="positive" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="analyzer" value="IT" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="scan_numbers_0|from" value="3" />
      <param name="scan_numbers_0|to" value="5" />
      <param name="scan_numbers_1|from" value="11" />
      <param name="scan_numbers_1|to" value="11" />
      <param name="scan_numbers_2|from" value="14" />
      <param name="scan_numbers_2|to" value="16" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->
    </test>
    <!--<test>
      <param name="input" value="small.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />

    </test>-->
  </xml>
  <xml name="msconvert_help">
**What it does**

Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.

You can view the original documentation here_.

.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
  </xml>