biobambam_split.xml

<tool id="biobambam_split" name="BioBamBam Split" version="1.0.0">
  <description>Bam File Splitter</description>
  <requirements>
    <container type="docker">pcap_tools</container>
  </requirements>
  <command interpreter="python">
biobambam_split.py --bam_path ${input_bam} --output_dir outputs --header header.sam
  </command>
  <inputs>
    <param name="input_bam" type="data" format="bam" label="BAM to split"/>

  </inputs>
  <outputs>
    <collection name="outputs_1" type="list" label="ReadGroup BAM set (forward)">
      <discover_datasets pattern="(?P&lt;name&gt;.*)\_1\.fq?" format="fastq" directory="outputs"/>
    </collection>
    <collection name="outputs_2" type="list" label="ReadGroup BAM set (reverse)">
      <discover_datasets pattern="(?P&lt;name&gt;.*)\_2\.fq?" format="fastq" directory="outputs"/>
    </collection>
    <!-- collection name="split_output" type="list" label="ReadGroup BAM set">
      <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
    </collection -->
    <data format="text" name="bamheader" label="BamHeader" from_work_dir="header.sam"/>
  </outputs>
  <stdio>
    <exit_code range="1:" />
  </stdio>

<help>

</help>
</tool>