Mercurial > repos > jjohnson > defuse8

annotate defuse_trinity_analysis.xml @ 1:e0a835a2f74a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 1a82c0609363fe0541e6dbdd46308a67f30ca9e1-dirty
author jjohnson
date Mon, 20 May 2019 15:30:06 -0400
parents 63f23d5db27c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
1 <?xml version="1.0"?>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
2 <tool id="defuse_trinity_analysis" name="Defuse Trinity" version="@DEFUSE_VERSION@.2">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
3 <description>verify fusions with trinity</description>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
4 <macros>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
5 <import>macros.xml</import>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
6 </macros>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
7 <command detect_errors="default"><![CDATA[
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
8 python $__tool_directory__/defuse_trinity_analysis.py --input $defuse_results --transcripts $trinity_transcripts --peptides $trinity_orfs
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
9 --nbases $nbases --min_pep_len $min_pep_len --ticdist $ticdist --readthrough=$readthrough
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
10 #if 'matched' in str($outputs).split(','):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
11 --matched="$matched_output"
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
12 #end if
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
13 #if 'aligned' in str($outputs).split(','):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
14 --transcript_alignment="$aligned_output"
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
15 #end if
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
16 --output $output
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
17 ]]></command>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
18 <inputs>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
19 <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
20 <param name="trinity_transcripts" type="data" format="fasta" label="TrinityRNAseq: Assembled Transcripts"/>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
21 <param name="trinity_orfs" type="data" format="fasta" label="transcriptsToOrfs: Candidate Peptide Sequences"/>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
22 <param name="nbases" type="integer" value="12" min="1" label="Number of bases on either side of the fusion to compare"/>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
23 <param name="min_pep_len" type="integer" value="100" min="0" label="Minimum length of peptide to report"/>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
24 <param name="ticdist" type="integer" value="1000000" min="0" label="Maximum intrachromosomal distance to be classified a Transcription-induced chimera (TIC)"/>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
25 <param name="readthrough" type="integer" value="4" min="0" label="Number of stop_codons to read through"/>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
26 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
27 <option value="matched">Matched Fusions Trinity Tanscripts and ORFs Tabular</option>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
28 <option value="aligned">Aligned Fusion and Trinity Transcipts Fasta</option>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
29 </param>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
30 </inputs>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
31 <outputs>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
32 <data name="matched_output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusions Trinity Matched ">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
33 <filter>(outputs and 'matched' in outputs)</filter>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
34 </data>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
35 <data name="aligned_output" metadata_source="defuse_results" format="fasta" label="${tool.name} on ${on_string}: Fusion Trinity Sequences">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
36 <filter>(outputs and 'aligned' in outputs)</filter>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
37 </data>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
38 <data name="output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusion Report"/>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
39 </outputs>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
40 <tests>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
41 </tests>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
42 <help>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
43 **Defuse Results**
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
44
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
45 Verifies DeFuse_ fusion predictions in results.tsv with TrinityRNAseq_ assembled transcripts and ORFs.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
46
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
47 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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
48
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
49 This program relies on the header line of the deFuse results.tsv to determine which columns to use for analysis.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
50
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
51 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
52 .. _TrinityRNAseq: http://trinityrnaseq.github.io/
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
53 </help>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
54 <expand macro="citations">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
55 <citation type="doi">10.1038/nbt.1883</citation>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
56 <citation type="doi">10.1038/s41598-018-36840-z</citation>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
57 </expand>
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
parents:
diff changeset
58 </tool>