comparison chipsequtil/map_to_known_genes.xml @ 10:a92644537c7d draft

Uploaded

9:1c6c8591f760

    <requirement type="package" version="1.0">chipsequtil</requirement>
  </requirements>
  <command interpreter="python">
    map_to_known_genes.py
      $tss
      --upstream-window=$upst_win
      --downstream-window=$dnst_win
      --map-output=$peaksOutput
      --peaks-format=$peaks_fmt
      $detail
      $intergenic
      $knownGeneFile $knownGeneRef $macsPeaksFile

  </command>

    <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 format="txt" hidden="false" name="peaksOutput"/>
  </outputs>
  <help></help>
</tool>

10:a92644537c7d

    <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>

    <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>