--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/defuse_trinity_analysis.xml	Mon May 20 15:25:03 2019 -0400
@@ -0,0 +1,58 @@
+<?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>