view revertR2orientationInBam.xml @ 0:05aa21d39189 draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty

<tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.1" profile="16.04">
  <description> Revert the mapped orientation of R2 mates in a bam.</description>
  <requirements>
    <requirement type="package" version="1.9">samtools</requirement>
  </requirements>
  <stdio>
    <!-- Anything other than zero is an error -->
    <exit_code range="1:" />
    <exit_code range=":-1" />
    <!-- In case the return code has not been set propery check stderr too -->
    <regex match="Error:" />
    <regex match="Exception:" />
  </stdio>
  <command>
<![CDATA[
        bash $__tool_directory__/revertR2orientationInBam.sh $input $output
]]>
  </command>
  <inputs>
    <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
    <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/>
  </inputs>
  <outputs>
    <data format="bam" name="output" label="$input.name with R2 orientation reversed"/>
  </outputs>

  <tests>
    <test>
      <param name="input" value="input.sam"/>
      <output name="output" file="output.bam" ftype="bam"/>
    </test>
  </tests>  
  <help>
<![CDATA[
    This tool is very useful when you have paired-end stranded RNA-seq.
    Using this tool prior to a bedtools genome coverage allow to have strand specific coverage using both mates.
    It uses samtools to convert input to sam format and then awk to modify the flag "reverse strand" for the second mate of pairs.
]]>
  </help>
</tool>