view defuse_bamfastq.xml @ 15:337dc0fe0da1

add defuse_bamfastq

<?xml version="1.0"?>
<tool id="defuse_bamfastq" name="Defuse BamFastq" version="0.6.1">
  <description>converts a bam file to fastq files.</description>
  
  <requirements>
    <requirement type="package" version="0.6.1">defuse</requirement>
  </requirements>
  
  <version_command>bamfastq --version</version_command>

  <command>bamfastq
    #if $pair == True :
      $pair
    #end if

    #if $multiple == True :
      $multiple
    #end if

    #if $rename == True :
      $rename
    #end if
    
    -2 $fastq2
    -1 $fastq1
    -b $bamname


  </command>

  <inputs>
    <param name="bamname" type="data" format="bam" label="Bam filename."/> 
    <param name="pair" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Name contains pair info as /1 /2."/>
    <param name="multiple" type="boolean" truevalue="-m" falsevalue="" checked="true" label="Bam contains multiple mappings per read."/>
    <param name="rename" type="boolean" truevalue="-r" falsevalue="" checked="true" label="Rename with integer IDs."/>
    
    

    <stdio>
      <exit_code range="1:" level="fatal" description="Error" />
    </stdio>

  </inputs>

  <outputs>
    <data format="fastqsanger,fastqillumina" name="fastq1" label="fastq1"  />
    <data format="fastqsanger,fastqillumina" name="fastq2" label="fastq2"  />
  </outputs>

  <tests>
    <test>
      <param name="bamname" ftype="bam" value="tophat_out2h.bam" />
      <param name="pair" value="True" />
      <param name="multiple" value="True" />
      <param name="rename" value="True" />
      <output name="fastq1" file="testout_defuse1.fq" />
      <output name="fastq2" file="testout_defuse2.fq" />
      
    </test>
  </tests>

  <help>
    Turn your dry, flavorless BAM file into delicious fastq files!
  </help>
</tool>