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<?xml version="1.0"?>
<tool id="defuse_trinity_analysis" name="Defuse Trinity" version="@DEFUSE_VERSION@.2">
  <description>verify fusions with trinity</description>
    <macros>
        <import>macros.xml</import>
    </macros>
  <command detect_errors="default"><![CDATA[
  python $__tool_directory__/defuse_trinity_analysis.py --input $defuse_results --transcripts $trinity_transcripts --peptides $trinity_orfs 
  --nbases $nbases --min_pep_len $min_pep_len --ticdist $ticdist --readthrough=$readthrough
  #if 'matched' in str($outputs).split(','):
    --matched="$matched_output"
  #end if  
  #if 'aligned' in str($outputs).split(','):
    --transcript_alignment="$aligned_output"
  #end if  
  --output $output 
  ]]></command>
  <inputs>
    <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/> 
    <param name="trinity_transcripts" type="data" format="fasta" label="TrinityRNAseq: Assembled Transcripts"/> 
    <param name="trinity_orfs" type="data" format="fasta" label="transcriptsToOrfs: Candidate Peptide Sequences"/> 
    <param name="nbases" type="integer" value="12" min="1" label="Number of bases on either side of the fusion to compare"/> 
    <param name="min_pep_len" type="integer" value="100" min="0" label="Minimum length of peptide to report"/> 
    <param name="ticdist" type="integer" value="1000000" min="0" label="Maximum intrachromosomal distance to be classified a Transcription-induced chimera (TIC)"/> 
    <param name="readthrough" type="integer" value="4" min="0" label="Number of stop_codons to read through"/> 
    <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
      <option value="matched">Matched Fusions Trinity Tanscripts and ORFs Tabular</option>
      <option value="aligned">Aligned Fusion and Trinity Transcipts Fasta</option>
    </param>
  </inputs>
  <outputs>
    <data name="matched_output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusions Trinity Matched ">
      <filter>(outputs and 'matched' in outputs)</filter>
    </data>
    <data name="aligned_output" metadata_source="defuse_results" format="fasta" label="${tool.name} on ${on_string}: Fusion Trinity Sequences">
      <filter>(outputs and 'aligned' in outputs)</filter>
    </data>
    <data name="output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusion Report"/>
  </outputs>
  <tests>
  </tests>
  <help>
**Defuse Results**

Verifies DeFuse_ fusion predictions in results.tsv with TrinityRNAseq_ assembled transcripts and ORFs.   

DeFuse provides a total fusion sequence of 200-500 nucleotides (nts) around the fusion breakpoint.  This may be insufficient to predict the effect of the fusion on protein production.  To get a view of the full transcript containing the fusion, Trinity de novo transcripts from the RNA-seq data are compared with the deFuse fusion sequences using a subsequence around the deFuse indetified fusion breakpoint.  The Trinity transcriptToOrfs output provides potential proteins from the projected fusion transcript.  

This program relies on the header line of the deFuse results.tsv to determine which columns to use for analysis.   

.. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
.. _TrinityRNAseq: http://trinityrnaseq.github.io/
  </help>
    <expand macro="citations">
        <citation type="doi">10.1038/nbt.1883</citation>
        <citation type="doi">10.1038/s41598-018-36840-z</citation>
    </expand>
</tool>