comparison msconvert_macros.xml @ 14:3cf310697624 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"

13:9b61227976d6

<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

      #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 ${inputmask}
    --outdir outputs
    --${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

      #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

        --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>

      <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">

    </section>


    <section name="filtering" title="Scan Inclusion/Exclusion Filters">
      
      <param name="activation" type="select" label="Filter by Activation">
        <option value="false" selected="true">no</option>
        <option value="ETD">ETD</option>
        <option value="CID">CID</option>
        <option value="SA">SA</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="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)" />

        <option value="numpressSlof">numpressSlof only</option>
      </param>
      <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
    </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>

      <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="thresholdScore" value="mvh" />
      <param name="thresholdValue" value="40-" />
      <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
      <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" />

14:3cf310697624

<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

      #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


    CAN_SUDO=\$(sudo -n -l 2> /dev/null; echo \$?) &&
    if [ "\$CAN_SUDO" -eq "0" ]; then
        uid=`id -u` &&
        gid=`id -g` &&    
        WINE="wine64_anyuser";
    else
        WINE="wine64" &&
        ## create a writable copy of wine prefix (since copying fails for some html
        ## stderr and exit code is swallowed)
        export WINEPREFIX=\$(mktemp -d) &&
        (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true);
    fi
    &&
    \$WINE msconvert ${inputmask}

    --outdir outputs
    --${output_type}
    $general_options.combineIonMobilitySpectra
    $general_options.simAsSpectra
    $general_options.srmAsSpectra
    $general_options.acceptZeroLengthSpectra
    $general_options.ignoreUnknownInstrumentError

    #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

      #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

        --gzip
      #end if

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

      #if $data_processing.precursor_refinement.use_mzrefinement
      && if [ "\$CAN_SUDO" -ne "0" ]; then
        mv '$output_refinement_name' '$output_refinement';
      fi
      #end if
]]>
    </command>
  </xml>

      <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">

    </section>


    <section name="filtering" title="Scan Inclusion/Exclusion Filters">

      <param name="activation" type="select" label="Filter by Activation">
        <option value="false" selected="true">no</option>
        <option value="ETD">ETD</option>
        <option value="CID">CID</option>
        <option value="SA">SA</option>

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

    <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="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" truevalue="--simAsSpectra" falsevalue="" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
      <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)" />

        <option value="numpressSlof">numpressSlof only</option>
      </param>
      <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
    </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>

      <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="thresholdScore" value="mvh" />
      <param name="thresholdValue" value="40-" />
      <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
      <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" />