view samtools_v1_1.xml @ 9:bf0eace4dd6d default tip

Fixed elements

<tool id="samtools_v1_1" name="samtools_v1_1" version="1.1">
  <requirements>
    <requirement type="package" version="1.1">samtools</requirement>
  </requirements>
  <description>samtools version 1.1.</description>
  <command interpreter="samtools flagstat">$inputfile &gt; $outfile</command>
  <inputs>
    <conditional name="command_type">
      <param name="command_type" type="select" label="Execute samtools command">
        <option value="view">view</option>
        <option value="sort">sort</option>
    	<option value="mpileup">mpileup</option>
	    <option value="depth">depth</option>
    	<option value="faidx">faidx</option>
        <option value="tview">tview</option>
	    <option value="index">index</option>
        <option value="idxstats">idxstats</option>
        <option value="fixmate">fixmate</option>
        <option value="flagstat">flagstat</option>
        <option value="calmd">calmd</option>
        <option value="merge">merge</option>
        <option value="rmdup">rmdup</option>
        <option value="reheader">reheader</option>
        <option value="cat">cat</option>
        <option value="bedcov">bedcov</option>
        <option value="targetcut">targetcut</option>
        <option value="phase">phase</option>
        <option value="bamshuf">bamshuf</option>
      </param>
      <when value="sort">
        <param name="species" type="select" label="Select a reference genome">
          <option value="mm9">mm9</option>
          <option value="mm10">mm10</option>
          <option value="hg19">hg19</option>
        </param>
      </when>
      <when value="index">
        <param format="bam" name="inputfile" type="data" label="index bam file"/>
      </when>
      <when value="flagstat">
        <param format="bam" name="inputfile" type="data" label="BAM file"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="txt" name="outfile" metadata_source="inputfile"/>
  </outputs>
</tool>