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view LINKYX_mpileup_wrapper.xml @ 7:90098d9cb691 default tip

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workflows updated
author biomonika <biomonika@psu.edu>
date Fri, 20 Feb 2015 18:34:34 -0500
parents 0d8315be76b7
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<tool id="LINKYX_mpileup" name="LINKYX_mpileup" version="1.1">
      <description>Run mpileup with LINKYX-specific parameters</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">LINKYX_mpileup_wrapper.sh $output $input1 $input2</command>
      <inputs>
        <param format="bam" name="input1" type="data" label="Alignment file"/>
        <param format="fasta" name="input2" type="data" label="Reference file"/>
      </inputs>
      <outputs>
        <data format="vcf" name="output" />
      </outputs>
  
     <tests>
       <test>
        <output name="out_file1" file="alignent_mpileup.txt"/>
       </test>
     </tests>
   
     <help>
   Run mpileup with LINKYX-specific parameters
     </help>
   
   </tool>