view LINKYX_mpileup_wrapper.xml @ 1:4c5de3a2c54e

toolshed2

<tool id="LINKYX_mpileup" name="LINKYX_mpileup">
      <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</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>
   This tool tests if primers are present in gorilla female or on human Y or chimp Y chromosome.
     </help>
   
   </tool>