view correctReads.xml @ 0:75c4a4c32bae draft default tip

planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

<tool id="correct_read_counter" name="correctReadCounter" version="1.8.0">
  <description>
    Correct Read Counter for GC content and mappability biases
  </description>
  <requirements>
    <requirement type="binary">Rscript</requirement>    
    <requirement type="R-module">TitanCNA</requirement>
    <requirement type="package" version="3.2.1">R</requirement>
    <requirement type="package" version="1.8.0">titancna</requirement>
  </requirements>
  <command>

    Rscript $__tool_directory__/correctReads.R $tumour $normal $gc $map 
    #if $target:
      $target 
    #else:
      NULL
    #end if
    $output 2>&amp;1

  </command>
  <inputs>
    <param type="data" format="wig" name="normal" label="Normal Read Counts"/>
    <param type="data" format="wig" name="tumour" label="Tumour Read Counts"/>
    <param type="data" format="wig" name="gc" label="GC Wig"/>
    <param type="data" format="wig" name="map" label="MAP Wig"/>
    <param type="data" format="txt,bed" name="target" label="Target File" help="Specify Targets if using Exome Data" optional="True"/>
  </inputs>
  <outputs>
    <data format="wig" name="output"/>
  </outputs>
</tool>