<tool id="purgegtffrommultichromgenes" name="Purge GTF" version="@WRAPPER_VERSION@">
  <description>from multi-chromosomes genes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
  <requirements>
  </requirements>
    <stdio>
        <exit_code range="1:" level="warning" description="Tool exception" />
    </stdio>
  <command detect_errors="exit_code"><![CDATA[
      python '$__tool_directory__'/purge_gtf_from_multichrom_genes.py
          --input '$input'
          --output '$output'
          --log '$log'

  ]]></command>
  <inputs>
    <param name="input" type="data" format="gtf" label="GTF input file to be purged of multichromosome genes" />
  </inputs>

  <outputs>
    <data format="tabular" name="log" label="gtf purge LOG" />
    <data format="gtf" name="output" label="purged_${input.name}" />
  </outputs>

  <tests>
   <test>
      <param name="input" value="GTF_to_purge.gtf"/>
      <output name="output" value="purged.gtf" ftype="gtf" /> 
      <output name="log" value="purged.gtf.log" ftype="tabular" /> 
    </test>
  </tests>

  <help>
.. class:: infomark

This script removes genes with multichromosome locations from gtf file. This avoid rsem error
due to ambiguous feature coordinates on multiple chromosomes.


  </help> 
  <citations>
    <citation type="doi">10.1186/1471-2105-12-323</citation>
  </citations>

</tool>