<tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="0.4.0">
  <description>extract transcript to gene map from trinity</description>
  <requirements>
    <requirement type="package" version="1.3.0">rsem</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
  </stdio>
  <command>
    extract-transcript-to-gene-map-from-trinity $trinity_fasta_file $map_file
  </command>
  <inputs>
    <param name="trinity_fasta_file" type="data" format="fasta" label="Trinity fasta file" />
  </inputs>
  <outputs>
    <data format="tabular" name="map_file" label="${tool.name} on ${on_string}: gene map file"/>
  </outputs>
  <tests>
    <test>
      <param name="trinity_fasta_file" value="trinity_assembled_transcripts.fasta" ftype="fasta"/>
      <output name="map_file" file="trinity_gene_map.tabular"/>
    </test>
  </tests>
  <help>
  

RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/

NAME
    extract-transcript-to-gene-map-from-trinity

SYNOPSIS
    extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file

DESCRIPTION
    generates a gene_mp_file from a trinity fasta file
 

  </help> 
    <citations>
      <citation type="doi">10.1038/nbt.1883</citation>
    </citations>
</tool>