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comparison defuse_trinity_analysis.xml @ 11:b22f8634ff84 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author jjohnson
date Sun, 17 Jan 2016 14:11:06 -0500
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10:f65857c1b92e 11:b22f8634ff84
1 <?xml version="1.0"?>
2 <tool id="defuse_trinity_analysis" name="Defuse Trinity" version="0.6.1">
3 <description>verify fusions with trinity</description>
4 <stdio>
5 <exit_code range="1:" level="fatal" description="Error" />
6 </stdio>
7 <command interpreter="python">defuse_trinity_analysis.py --input $defuse_results --transcripts $trinity_transcripts --peptides $trinity_orfs
8 --nbases $nbases --min_pep_len $min_pep_len --ticdist $ticdist --readthrough=$readthrough
9 #if 'matched' in str($outputs).split(','):
10 --matched="$matched_output"
11 #end if
12 #if 'aligned' in str($outputs).split(','):
13 --transcript_alignment="$aligned_output"
14 #end if
15 --output $output
16 </command>
17 <inputs>
18 <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/>
19 <param name="trinity_transcripts" type="data" format="fasta" label="TrinityRNAseq: Assembled Transcripts"/>
20 <param name="trinity_orfs" type="data" format="fasta" label="transcriptsToOrfs: Candidate Peptide Sequences"/>
21 <param name="nbases" type="integer" value="12" min="1" label="Number of bases on either side of the fusion to compare"/>
22 <param name="min_pep_len" type="integer" value="100" min="0" label="Minimum length of peptide to report"/>
23 <param name="ticdist" type="integer" value="1000000" min="0" label="Maximum intrachromosomal distance to be classified a Transcription-induced chimera (TIC)"/>
24 <param name="readthrough" type="integer" value="4" min="0" label="Number of stop_codons to read through"/>
25 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
26 <option value="matched">Matched Fusions Trinity Tanscripts and ORFs Tabular</option>
27 <option value="aligned">Aligned Fusion and Trinity Transcipts Fasta</option>
28 </param>
29 </inputs>
30 <outputs>
31 <data name="matched_output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusions Trinity Matched ">
32 <filter>(outputs and 'matched' in outputs)</filter>
33 </data>
34 <data name="aligned_output" metadata_source="defuse_results" format="fasta" label="${tool.name} on ${on_string}: Fusion Trinity Sequences">
35 <filter>(outputs and 'aligned' in outputs)</filter>
36 </data>
37 <data name="output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusion Report"/>
38 </outputs>
39 <tests>
40 <test>
41 <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
42 <output name="vcf" file="mm10_results.filtered.vcf"/>
43 </test>
44 </tests>
45 <help>
46 **Defuse Results**
47
48 Verifies DeFuse_ fusion predictions in results.tsv with TrinityRNAseq_ assembled transcripts and ORFs.
49
50 This program relies on the header line of the results.tsv to determine which columns to use for analysis.
51
52 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
53 .. _TrinityRNAseq: http://trinityrnaseq.github.io/
54 </help>
55 </tool>