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view chipsequtil/pieplot_macs/pieplots_macs.xml @ 33:d921339de7c6 draft

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author alenail
date Thu, 14 Apr 2016 09:50:22 -0400
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<tool id="pieplots_macs" name="Pieplots MACS" version="0.1">
  <description>
    Peaks are assigned to the closest gene and then categorized according to their location at different genomic regions (promoter, intron, exon, or after the gene). Sites >10kb away from any gene are considered intergenic.
  </description>
  <parallelism method="basic"></parallelism>
  <requirements>
    <requirement type="package" version="0.14.1">pandas</requirement>
    <requirement type="package" version="1.4">matplotlib</requirement>
  </requirements>
  <command interpreter="python">
    pieplots_macs.py --genefile $genefile --peakfile $peakfile $MACS --outfile $out
  </command>
  <inputs>
    <param name="genefile" type="data" label="Gene file (map_peaks_to_genes)" help="" optional="false" />
    <param name="peakfile" type="data" label="Peaks file (narrowpeaks)" help="" optional="false" />
    <param name="MACS" checked="false" label="Set this value if you have MACS peaks" type="boolean" truevalue="--MACS" falsevalue="" help="" />
  </inputs>
  <outputs>
    <data name="out" format="pdf" hidden="false" />
  </outputs>
  <help></help>
</tool>