view msconvert_macros.xml @ 5:637e309295cf draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea

<macros>
  <xml name="msconvertCommand">
    <command>
<![CDATA[
    #set $output_type_str = str($output_type)
    #set $input_name = $input.display_name
    #set $output_name = $input_name.split(".")[0] + "." + $output_type_str
    ln -s '$input' '${input_name}' &&

    #if $data_processing.precursor_refinement.use_mzrefinement
      #set $input_ident_name = $data_processing.precursor_refinement.input_ident.display_name
      ln -s '${data_processing.precursor_refinement.input_ident}' '${input_ident_name}' &&
    #end if

    mkdir outdir &&
    msconvert ${input_name} --$output_type_str -o outdir --outfile '$output_name'

    ## 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"
      #end if

      #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
      --filter "chargeStatePredictor
        overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
        minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
        maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
        singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
        maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
      #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
      --filter "turbocharger
        minCharge=$data_processing.charge_state_calculation.minCharge
        maxCharge=$data_processing.charge_state_calculation.maxCharge
        precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
        precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
        halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
        defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
        defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
      #end if

      #for threshold_entry in $data_processing.thresholds
      --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
      #end for

      #if $data_processing.filter_mz_windows.do_mzwindow_filter
      --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
      #end if

      #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($data_processing.ms2deisotope) == "true"
      --filter "MS2Deisotope"
      #end if


    ## SCAN INCLUSION/EXCLUSION FILTERS
      #if str($filtering.activation) != "false"
      --filter "activation $filtering.activation"
      #end if

      #if len($filtering.indices) > 0
      --filter "index
      #for $index in $filtering.indices
      [${index.from},${index.to}]
      #end for
      "
      #end if

      #if len($filtering.scan_numbers) > 0
      --filter "scanNumber
      #for $scan_number in $filtering.scan_numbers
      [${scan_number.from},${scan_number.to}]
      #end for
      "
      #end if

      #if $filtering.strip_it.value
      --filter "stripIT"
      #end if

      #if $filtering.filter_ms_levels.do_ms_level_filter
      --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
      #end if

      #if str($filtering.polarity) != "false"
      --filter "polarity $filtering.polarity"
      #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 $mz_encoding == "64"
          --64
        #else
          --32
        #end if
      #else
        --mz${mz_encoding}
        --inten${intensity_encoding}
      #end if

      #set binary_compression = str($settings.binary_compression)
      #if $binary_compression == "zlib"
      --zlib
      #else if $binary_compression == "numpressLinearPic"
      --numpressLinear --numpressPic
      #else if $binary_compression == "numpressLinearSlof"
      --numpressLinear --numpressSlof
      #else if $binary_compression == "numpressLinear"
      --numpressLinear
      #else if $binary_compression == "numpressPic"
      --numpressPic
      #else if $binary_compression == "numpressSlof"
      --numpressSlof
      #end if

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

      &&

    #if $data_processing.precursor_refinement.use_mzrefinement
      mv '${input.name.rsplit('.',1)[0]}.mzRefinement.tsv' output.refinement &&
    #end if

    mv 'outdir/$output_name' output &&
    rmdir outdir
]]>
    </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>
        <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+" />
          <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10." />
          <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />
          <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
          <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - 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>
        </when>
      </conditional>

      <conditional name="charge_state_calculation">
        <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
          <option value="false">no</option>
          <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
          <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
        </param>
        <when value="false" />
        <when value="predictor">
          <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
          <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
          <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
          <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
          <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for &quot;known&quot; charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" />
        </when>
        <when value="turbocharger">
          <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
          <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
          <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
          <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
          <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
          <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
          <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
        </when>
      </conditional>

      <repeat name="thresholds" title="Filter by Threshold">
        <param type="select" label="Specify threshold on" name="threshold_type" help="">
          <option value="count">Peak count</option>
          <option value="count-after-ties">Peak count (after ties)</option>
          <option value="absolute">Peak absolute intensity</option>
          <option value="bpi-relative">Fraction of base peak intensity</option>
          <option value="tic-relative">Fraction of total ion current</option>
          <option value="tic-fraction">Aggregate fraction of total ion current</option>
        </param>
        <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the &quot;Aggregated fraction&quot; method, peaks are accepted until this fraction of the TIC is accounted for." />
        <param type="select" label="Keep" name="orientation">
          <option value="most-intense">Most intense peaks</option>
          <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>
          <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
            <option value="true" selected="true">yes</option>
            <option value="false">no</option>
          </param>
          <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
            <option value="true" selected="true">yes</option>
            <option value="false">no</option>
          </param>
          <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
            <option value="true" selected="true">yes</option>
            <option value="false">no</option>
          </param>
          <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
          <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
            <option value="MZ" selected="true">mz</option>
            <option value="PPM">ppm</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>
        <when value="false" />
      </conditional>

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

    </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="HCD">HCD</option>
        <option>BIRD</option>
        <option>ECD</option>
        <option>IRMPD</option>
        <option>PD</option>
        <option>PSD</option>
        <option>PQD</option>
        <option>SID</option>
        <option>SORI</option>
      </param>

      <repeat name="indices" title="Filter Scan Indices">
        <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
        <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
      </repeat>

      <repeat name="scan_numbers" title="Filter Scan Numbers">
        <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
        <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
      </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>
      </conditional>

      <param name="polarity" type="select" label="Filter by Polarity">
        <option value="false" selected="true">no</option>
        <option value="positive">positive</option>
        <option value="negative">negative</option>
      </param>

      <param name="analyzer" type="select" label="Filter by Analyzer">
        <option value="false" selected="true">no</option>
        <option value="quad">Quadrupole</option>
        <option value="orbi">Orbitrap</option>
        <option value="FT">Fourier-transform</option>
        <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>
      </param>
      <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
        <option value="64">64</option>
        <option value="32" selected="true">32</option>
      </param>
      <param type="select" name="binary_compression" label="Binary data compression">
        <option value="false">None</option>
        <option value="zlib" selected="true">zlib</option>
        <option value="numpressLinearPic">numpressLinear/numpressPic</option>
        <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
        <option value="numpressLinear">numpressLinear only</option>
        <option value="numpressPic">numpressPic only</option>
        <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" from_work_dir="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" from_work_dir="output.refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
        <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
      </data>
    </outputs>
  </xml>
</macros>