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view sort_bam.xml @ 2:0d8315be76b7

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author biomonika
date Tue, 17 Feb 2015 21:59:51 -0500
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<tool id="sort_bam" name="sort_bam" version="1.1">
      <description>Sort bam file based on chromosomal coordinates.</description>
      <requirements>
        <requirement type="set_environment">LINKYX_PATH</requirement>
        <requirement type="set_environment">SAMTOOLS</requirement>
        <requirement type="package" version="0.1.19">samtools-fpic</requirement>
        <requirement type="package" version="1.6.922">bioperl</requirement>
      </requirements>
      <command interpreter="bash">sort_bam.sh $output $input1</command>
      <inputs>
        <param format="bam" name="input1" type="data" label="Alignment file"/>
      </inputs>
      <outputs>
        <data format="bam" name="output" />
      </outputs>
  
     <tests>
       <test>
       </test>
     </tests>
   
     <help>
   Sort bam file based on chromosomal coordinates.
     </help>
   
   </tool>