Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_detect.xml @ 3:5348cfd3ba5c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
author erasmus-medical-center
date Thu, 10 Aug 2017 05:38:27 -0400
parents 173ca9768e22
children d58d99a070ce
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents: 2
diff changeset
1 <tool id="dr_disco_detect" name="Dr. Disco (detect)" version="@TOOL_VERSION@-g0">
1
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
2 <description>Detects break-points in RNA-seq</description>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
3 <macros>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
4 <import>macros.xml</import>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
5 </macros>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
6
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
7 <expand macro="requirements"/>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
8 <expand macro="version_command"/>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
9
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
11 dr-disco
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
12 detect
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
13 --min-e-score '${min_e_score}'
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
14 '${star_discordant_alignment_fixed}'
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents: 2
diff changeset
15 '${output_fusion_events}'
1
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
16 ]]></command>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
17 <inputs>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
18 <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
19 <param name="min_e_score" argument="--min-e-score" type="integer" value="8" min="0"
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
20 label="Minimal score to initiate pulling sub-graphs" help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." />
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
21 </inputs>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
22
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
23 <outputs>
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents: 2
diff changeset
24 <data name="output_fusion_events" format="tabular" label="${tool.name} on ${star_discordant_alignment_fixed.name}" />
1
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
25 </outputs>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
26
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
27 <tests>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
28 <test>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
29 <param name="star_discordant_alignment_fixed" value="detect.bam" />
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
30 <param name="min_e_score" value="8" />
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
31
3
5348cfd3ba5c planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
erasmus-medical-center
parents: 2
diff changeset
32 <output name="output_fusion_events" file="detect.txt" />
1
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
33 </test>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
34 </tests>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
35
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
36 <help><![CDATA[
2
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
37
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
38 **What it does**
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
39
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
40 Detects junctions in ('dr-disco fix' prepared) Chimeric alignments and tries to reconstruct fusion genes and genomic breakpoints using a Graph data structure.
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
41
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
42 This software is in particular designed for RNA-Seq data prepared with random hexamer priming because of the presence of intronic reads.
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
43
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
44 **Attributions**
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
45
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
46 This work is part of Youri Hoogstrate's PhD thesis.
173ca9768e22 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576
erasmus-medical-center
parents: 1
diff changeset
47
1
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
48 ]]></help>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
49
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
50 <expand macro="citations"/>
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
erasmus-medical-center
parents:
diff changeset
51 </tool>