view defuse_trinity_analysis.xml @ 36:4353f776dfa3

Add defuse_trinity_analysis

<?xml version="1.0"?>
<tool id="defuse_trinity_analysis" name="Defuse Trinity" version="0.6.1">
  <description>verify fusions with trinity</description>
  <command interpreter="python">defuse_trinity_analysis.py --input $defuse_results --transcripts $trinity_transcripts --peptides $trinity_orfs 
  --nbases $nbases --min_pep_len $min_pep_len --ticdist $ticdist
  --output $output 
  </command>
  <inputs>
    <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/> 
    <param name="trinity_transcripts" type="data" format="fasta" label="TrinityRNAseq: Assembled Transcripts"/> 
    <param name="trinity_orfs" type="data" format="fasta" label="transcriptsToOrfs: Candidate Peptide Sequences"/> 
    <param name="nbases" type="integer" value="12" min="1" label="Number of bases on either side of the fusion to compare"/> 
    <param name="min_pep_len" type="integer" value="100" min="0" label="Minimum length of peptide to report"/> 
    <param name="ticdist" type="integer" value="1000000" min="0" label="Maximum intrachromosomal distance to be classified a Transcription-induced chimera (TIC)"/> 
  </inputs>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <outputs>
    <data name="output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusion Report"/>
  </outputs>
  <tests>
    <test>
      <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
      <output name="vcf" file="mm10_results.filtered.vcf"/>
    </test>
  </tests>
  <help>
**Defuse Results **

Verifies DeFuse_ results.tsv with TrinityRNAseq_ assembled transcripts and ORFs.   

This program relies on the header line of the results.tsv to determine which columns to use for analysis.   
.. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
.. _TrinityRNAseq: http://trinityrnaseq.github.io/
  </help>
</tool>