<?xml version="1.0"?>
<tool id="defuse_bamfastq" name="Defuse BamFastq" version="@DEFUSE_VERSION@.1">
  <description>converts a bam file to fastq files.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <expand macro="defuse_requirement" />
    </requirements>
  <command>bamfastq
    #if $pair == True :
      $pair
    #end if
    #if $multiple == True :
      $multiple
    #end if
    #if $rename == True :
      $rename
    #end if
    -b $bamfile
    -1 $fastq1
    -2 $fastq2
  </command>
  <inputs>
    <param name="bamfile" type="data" format="bam" label="Bam file"/> 
    <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."/>
  </inputs>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <outputs>
    <data format="fastqsanger" name="fastq1" label="fastq1"  />
    <data format="fastqsanger" name="fastq2" label="fastq2"  />
  </outputs>
  <tests>
    <test>
      <param name="bamfile" ftype="bam" value="tophat_out2h.bam" />
      <param name="pair" value="True" />
      <param name="multiple" value="True" />
      <param name="rename" value="True" />
      <output name="fastq1">
        <assert_contents>
          <has_text text="@test_mRNA_36_146_27/1" />
          <not_has_text text="@test_mRNA_36_146_27/2" />
          <not_has_text text="test_mRNA_150_290_0" />
        </assert_contents>
      </output>
      <output name="fastq2">
        <assert_contents>
          <has_text text="@test_mRNA_36_146_27/2" />
          <not_has_text text="@test_mRNA_36_146_27/1" />
          <not_has_text text="test_mRNA_150_290_0" />
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>
    bamfastq converts a bam file input into a pair of fastq files that can be used as input to deFuse.
  </help>
    <expand macro="citations"/>
</tool>