LINKYX_identify_Y_linked_SNPs.xml

<tool id="LINKYX_Y" name="LINKYX_Y" version="1.1">
      <description>Identify Y linked contigs from cross</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_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command>
      <inputs>
        <param format="fasta" name="input1" type="data" label="Reference"/>
        <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/>
        <param format="bam" name="input3" type="data" label="Father - Binary alignment format"/>
        <param format="bam" name="input4" type="data" label="Daughter - Binary alignment format"/>
        <param format="bam" name="input5" type="data" label="Son - Binary alignment format"/>
      </inputs>
      <outputs>
        <data format="txt" name="output" />
        <data format="fasta" name="output1" label="Y_results_sequences.fasta" />
        <data format="bam" name="output2" label="Mother male bam file - Y linked " />
        <data format="bam" name="output3" label="Father male bam file - Y linked " />
        <data format="bam" name="output4" label="Daughter male bam file - Y linked " />
        <data format="bam" name="output5" label="Son bam male file - Y linked " />
      </outputs>
  
     <tests>
       <test>
       </test>
     </tests>
   
     <help>
   This tool identifies Y linked contigs from cross (represented as 4 bam files mapped on male reference).
     </help>
   
   </tool>