view LINKYX_identify_X_linked_SNPs.xml @ 1:4c5de3a2c54e

toolshed2

<tool id="LINKYX_X" name="LINKYX_X">
      <description>Identify X 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</requirement>
        <requirement type="package" version="1.0.4">fastq_groomer</requirement>
        <requirement type="package" version="0.0.1">trinityrnaseq</requirement>
        <requirement type="package" version="1.2.3">bwa_wrappers</requirement>
        <requirement type="package" version="1.1.4">sam_to_bam</requirement>
        <requirement type="package" version="1.0.2">samtools_sort</requirement>
        <requirement type="package" version="1.56.0">picard</requirement>
      </requirements>
      <command interpreter="bash">LINKYX_identify_X_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $input6 $input7 $input8 $input9 $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="vcf" name="input3" type="data" label="Mother - Variant call format"/>
        <param format="bam" name="input4" type="data" label="Father - Binary alignment format"/>
        <param format="vcf" name="input5" type="data" label="Father - Variant call format"/>
        <param format="bam" name="input6" type="data" label="Daughter - Binary alignment format"/>
        <param format="vcf" name="input7" type="data" label="Daughter - Variant call format"/>
        <param format="bam" name="input8" type="data" label="Son - Binary alignment format"/>
        <param format="vcf" name="input9" type="data" label="Son - Variant call format"/>
      </inputs>
      <outputs>
        <data format="txt" name="output" />
        <data format="fasta" name="output1" label="X_sequences.fasta " />
        <data format="bam" name="output2" label="Mother bam file - X linked " />
        <data format="bam" name="output3" label="Father bam file - X linked " />
        <data format="bam" name="output4" label="Daughter bam file - X linked " />
        <data format="bam" name="output5" label="Son bam file - X linked " />
      </outputs>
  
     <tests>
       <test>
        <output name="out_file1" file="X_results.txt"/>
       </test>
     </tests>
   
     <help>
   This tool identifies X linked contigs from cross (represented as 4 VCF files).
     </help>
   
   </tool>