annotate chipsequtil/map_to_known_genes/map_to_known_genes.xml @ 22:63dace20719b draft

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<tool id="chipsequtil_maptoknowngenes" name="Map Peaks to Known Genes" version="0.1">
  <description>
    Map the peaks in &lt;peaks file&gt; to genes in &lt;knownGene file&gt;.  &lt;knownGene file&gt; isformat is as specified in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.sql.&lt;peaks file&gt; format is as produced by MACS.  If *auto* is chosen (default) file extension is examined for *.xls* for default MACS format or *.bed* for BED format.  If the --detail option is provided, the following extra fields are appended to each row:
    peak loc, dist from feature, map type, map subtype
  </description>
  <parallelism method="basic"></parallelism>
  <requirements>
    <requirement type="package" version="1.0">chipsequtil</requirement>
  </requirements>
  <command interpreter="python">
    map_to_known_genes.py
      $tss
      --peaks-format=$peaks_fmt
      --upstream-window=$upst_win
      --downstream-window=$dnst_win
      --map-output="$peaksOutput"
      $detail
      $intergenic
      $knownGeneFile $knownGeneRef $macsPeaksFile

  </command>
  <inputs>
    <param name="knownGeneFile" type="data" label="knownGene file" help="" optional="false" />
    <param name="knownGeneRef" type="data" label="knownGene xRef file" help="" optional="false" />
    <param name="macsPeaksFile" type="data" label="Peaks File" help="" optional="false" />

    <param name="upst_win" type="integer" label="Upstream Window" help="Window width in base pairs to consider promoter region [default: %default]" optional="false" value="5500" />
    <param name="dnst_win" type="integer" label="Downstream Window" help="Window width in base pairs to consider downstream region [default: %default]" optional="false" value="2500" />

    <param name="tss" checked="true" label="Calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" />

    <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false">
        <option value="MACS">MACS</option>
        <option selected="true" value="BED">BED</option>
    </param>

    <param name="detail" checked="true" label="Append the following fields to each row: peak loc, dist from feature, map type, map subtype" type="boolean" truevalue="--detail" falsevalue="" help="" />
    <param name="intergenic" checked="false" label="Write intergenic peaks to the gene file as well with None as gene ID" type="boolean" truevalue="--intergenic" falsevalue="" help="" />
  </inputs>
  <outputs>
    <data name="peaksOutput" format="txt" hidden="false" />
  </outputs>
  <help></help>
</tool>