comparison msconvert_macros.xml @ 16:545054b15d7c draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd

15:6153e8ada1ee

      fi
      #if $general_options.multi_run_output.do_multi_run_output == 'false':
        && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
      #else
        ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
        ## TODO this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
        #if $output_type == 'mzML' or $output_type == 'mzXML'
          && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
          ## a newline is needed after `#echo ...` therefore the `;'` on the next line
;'
        #end if

      <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>

                </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>
        <when value="true">
          <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
          <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+">
            <sanitizer>

          <option value="least-intense">Least intense peaks</option>
        </param>
      </repeat>

      <conditional name="filter_mz_windows">
        <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
        <when value="false" />
        <when value="true">
          <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
          <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
        </when>
      </conditional>

      <conditional name="etd_filtering">
        <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
        <when value="false" />
        <when value="true">
          <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
            <option value="true" selected="true">yes</option>
            <option value="false">no</option>

          </param>
        </when>
      </conditional>

      <conditional name="ms2denoise">
        <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
        <when value="true">
          <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
          <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
          <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
        </when>

      </conditional>

      <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />

      <conditional name="demultiplex">
        <param name="demultiplex_on" type="boolean" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)" />
        <when value="true">
          <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
          <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
            <option value="MZ">mz</option>
            <option value="PPM" selected="true">ppm</option>
          </param>
          <param name="nnlsMaxIter" type="integer" label="Maximum iterations for NNLS solve" value="50"/>
          <param name="nnlsEps" type="float" label="Epsilon value for convergence criterion of NNLS solver" value="1e-10"/>
          <param name="demuxBlockExtra" type="float" label="DemuxBlockExtra" help="Multiplier to expand or reduce the # of spectra considered when demultiplexing. If 0, a fully determined system of equations is built. If > 1.0, the number of rows included in the system is extended DemuxBlockExtra * (# scans in 1 duty cycle)" value="0"/>
          <param name="variableFill" type="boolean" truevalue="true" falsevalue="false" label="Allow fill times to vary for each scan window"/>
          <param name="noSumNormalize" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Normalize sums" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
          <param name="optimization" type="select" label="Optimization" help="Optimizations can be applied when experimental design is known">
            <option value="none" selected="true">None</option>
            <option value="overlap_only">Overlap only</option>
          </param>
          <param name="interpolateRT" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Interpolate scan time"/>
          <param name="noWeighting" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
          <param name="minWindowSize" type="float" label="Minimum window size" value="0.2"/>
        </when>
        <when value="false" />
      </conditional>

      </repeat>

      <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />

      <conditional name="filter_ms_levels">
        <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
        <when value="false" />
        <when value="true">
          <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
          <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
        </when>

    <section name="general_options" title="General Options">
      <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" 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." />

      <param argument="--srmAsSpectra" type="boolean" truevalue="--srmAsSpectra" falsevalue=""  label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
      <param argument="--acceptZeroLengthSpectra" type="boolean" truevalue="--acceptZeroLengthSpectra" falsevalue=""  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" truevalue="--ignoreUnknownInstrumentError" falsevalue=""  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">

        </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" ftype="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" ftype="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" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.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" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.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" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="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" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="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" ftype="mzxml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="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" ftype="mzxml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="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" />

      <output_collection name="multi_run_output_list" type="list">
        <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
        <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
      </output_collection>
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="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+NE" file="SciexTest-HPINalone-NE.mzML" ftype="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" ftype="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" ftype="mzml" lines_diff="8" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mz5" delta="150000" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" />

      <param name="binary_compression" value="false" />
      <param name="gzip_compression" value="true" />
      <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" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="Rpal_01.mz5" ftype="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="thresholdValue" value="40-" />
      <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" />
      <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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="maxMultipleCharge" value="5" />
      <param name="singleChargeFractionTIC" value="0.95" />
      <param name="maxKnownCharge" value="8" />
      <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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="halfIsoWidth" value="1.5" />
      <param name="defaultMinCharge" value="1" />
      <param name="defaultMaxCharge" value="5" />
      <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="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="matching_tolerance" value="50" />
      <param name="matching_tolerance_units" value="ppm" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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_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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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_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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-deisotope-poisson.mzML" />
    </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>

  <xml name="citations">
    <citations>
        <citation type="doi">10.1093/bioinformatics/btn323</citation>
        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
                                      year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->

16:545054b15d7c

      fi
      #if $general_options.multi_run_output.do_multi_run_output == 'false':
        && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
      #else
        ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
        ## this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
        #if $output_type == 'mzML' or $output_type == 'mzXML'
          && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
          ## a newline is needed after `#echo ...` therefore the `;'` on the next line
;'
        #end if

      <option value="ms2">ms2</option>
    </param>

    <section name="data_processing" title="Data Processing Filters">
        <conditional name="peak_picking">
            <param type="select" name="pick_peaks" label="Apply peak picking?">
                <option value="true">Yes</option>
                <option value="false">No</option>
            </param>
            <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>

                </param>
            </when>
      </conditional>

      <conditional name="precursor_refinement">
        <param type="select" name="use_mzrefinement" label="Apply m/z refinement with identification data?">
            <option value="true">Yes</option>
            <option value="false" selected="true">No</option>
        </param>
        <when value="false"></when>
        <when value="true">
          <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
          <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+">
            <sanitizer>

          <option value="least-intense">Least intense peaks</option>
        </param>
      </repeat>

      <conditional name="filter_mz_windows">
        <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help="">
            <option value="true">Yes</option>
            <option value="false">No</option>
        </param>
        <when value="false" />
        <when value="true">
          <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
          <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
        </when>
      </conditional>

      <conditional name="etd_filtering">
        <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?">
            <option value="true">Yes</option>
            <option value="false">No</option>
        </param>
        <when value="false" />
        <when value="true">
          <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
            <option value="true" selected="true">yes</option>
            <option value="false">no</option>

          </param>
        </when>
      </conditional>

      <conditional name="ms2denoise">
        <param name="denoise" type="select" label="De-noise MS2 with moving window filter">
            <option value="true">Yes</option>
            <option value="false">No</option>
        </param>
        <when value="true">
          <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
          <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
          <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
        </when>

      </conditional>

      <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />

      <conditional name="demultiplex">
        <param name="demultiplex_on" type="select" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)">
            <option value="true">Yes</option>
            <option value="false">No</option>
        </param>
        <when value="true">
          <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
          <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
            <option value="MZ">mz</option>
            <option value="PPM" selected="true">ppm</option>
          </param>
          <param name="nnlsMaxIter" type="integer" label="Maximum iterations for NNLS solve" value="50"/>
          <param name="nnlsEps" type="float" label="Epsilon value for convergence criterion of NNLS solver" value="1e-10"/>
          <param name="demuxBlockExtra" type="float" label="DemuxBlockExtra" help="Multiplier to expand or reduce the # of spectra considered when demultiplexing. If 0, a fully determined system of equations is built. If > 1.0, the number of rows included in the system is extended DemuxBlockExtra * (# scans in 1 duty cycle)" value="0"/>
          <param name="variableFill" type="boolean" truevalue="true" falsevalue="false" label="Allow fill times to vary for each scan window"/>
          <param name="noSumNormalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No sum normalization?" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
          <param name="optimization" type="select" label="Optimization" help="Optimizations can be applied when experimental design is known">
            <option value="none" selected="true">None</option>
            <option value="overlap_only">Overlap only</option>
          </param>
          <param name="interpolateRT" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Interpolate scan time"/>
          <param name="noWeighting" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
          <param name="minWindowSize" type="float" label="Minimum window size" value="0.2"/>
        </when>
        <when value="false" />
      </conditional>

      </repeat>

      <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />

      <conditional name="filter_ms_levels">
        <param name="do_ms_level_filter" type="select" label="Filter MS Levels">
            <option value="true">Yes</option>
            <option value="false">No</option>
        </param>
        <when value="false" />
        <when value="true">
          <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
          <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
        </when>

    <section name="general_options" title="General Options">
      <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" 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="select" 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">
            <option value="true">Yes</option>
            <option value="false">No</option>
        </param>
        <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." />

      <param argument="--srmAsSpectra" type="boolean" truevalue="--srmAsSpectra" falsevalue=""  label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
      <param argument="--acceptZeroLengthSpectra" type="boolean" truevalue="--acceptZeroLengthSpectra" falsevalue=""  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" truevalue="--ignoreUnknownInstrumentError" falsevalue=""  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="select" 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)">
            <option value="true">Yes</option>
            <option value="false">No</option>
        </param>
        <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">

        </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} collection">
        <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 expect_num_outputs="1">
      <param name="input" value="small.mzML" ftype="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" ftype="mzml" lines_diff="8" />
    </test>
    <test expect_num_outputs="1">
      <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" ftype="mzml" lines_diff="4" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.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" ftype="mzml" lines_diff="4" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.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" ftype="mzml" lines_diff="4" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="SciexTest.wiff.tar" ftype="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" ftype="mzml" lines_diff="4" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="SciexTest.wiff.tar" ftype="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" ftype="mzxml" lines_diff="4" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="SciexTest.wiff.tar" ftype="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" ftype="mzxml" lines_diff="4" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="SciexTest.wiff.tar" ftype="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" />

      <output_collection name="multi_run_output_list" type="list">
        <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
        <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
      </output_collection>
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="SciexTest.wiff.tar" ftype="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+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
      </output_collection>
    </test>

    <!-- this data file only has profile MS1, so the result is the same -->
    <test expect_num_outputs="1">
      <param name="input" value="small.mzML" ftype="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" ftype="mzml" lines_diff="8" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mz5" delta="150000" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" />

      <param name="binary_compression" value="false" />
      <param name="gzip_compression" value="true" />
      <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
    </test>-->

    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" lines_diff="114" />
    </test>

    <test expect_num_outputs="1">
      <param name="input" value="Rpal_01.mz5" ftype="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="thresholdValue" value="40-" />
      <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" />
      <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
    </test>

    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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="maxMultipleCharge" value="5" />
      <param name="singleChargeFractionTIC" value="0.95" />
      <param name="maxKnownCharge" value="8" />
      <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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="halfIsoWidth" value="1.5" />
      <param name="defaultMinCharge" value="1" />
      <param name="defaultMaxCharge" value="5" />
      <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="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="matching_tolerance" value="50" />
      <param name="matching_tolerance_units" value="ppm" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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_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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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_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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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" ftype="mzml" />
    </test>
    <test expect_num_outputs="1">
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="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="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-deisotope-poisson.mzML" />
    </test>-->
  </xml>
  <xml name="citations">
    <citations>
        <citation type="doi">10.1093/bioinformatics/btn323</citation>
        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
                                      year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->