Mercurial > repos > yhoogstrate > fuma

annotate fuma.xml @ 3:4966079d474b 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/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
author yhoogstrate
date Tue, 20 Oct 2015 10:12:08 -0400
parents 86526900cb8f
children cb0543909e83
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
2 <tool id="fuma" name="FuMa" version="2.10.0.a">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
3 <description>match detected fusion genes based on gene names (in particular for RNA-Seq).</description>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
4
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
5 <requirements>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
6 <requirement type="package" version="2.7">python</requirement>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
7 <requirement type="package" version="2.10.0">fuma</requirement>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
8 </requirements>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
9
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
10 <version_command>fuma --version 2>&amp;1 | head -n 1</version_command><!-- -V also works, but is not GNU standard -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
11
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
12 <command><![CDATA[
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
13 #import pipes
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
14
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
15 #set $gene_annotations = []
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
16 #set $samples = []
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
17 #set $links = []
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
18
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
19 #for $i, $d in enumerate( $datasets )
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
20 #set $sample_name = pipes.quote(str($d['sample'].name))
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
21
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
22 #set $gene_annotations = $gene_annotations + [ "ga_" + str($i) + ":" + str($d['gene_annotation'].file_name) ]
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
23
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
24 #set $samples = $samples + [ $sample_name + ":" + str($d['format']) + ":" + str($d['sample'].file_name) ]
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
25 #set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
26 #end for
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
27
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
28 #set $gene_annotations_str = " ".join(gene_annotations)
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
29 #set $samples_str = " ".join(samples)
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
30 #set $links_str = " ".join(links)
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
31
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
32 fuma
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
33 -m
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
34 $params.matching_method
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
35
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
36 $params.strand_specific_matching
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
37 $params.acceptor_donor_order_specific_matchig
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
38
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
39 -a
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
40 $gene_annotations_str
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
41 -s
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
42 $samples_str
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
43 -l
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
44 $links_str
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
45 #if $params.output_format.value == "list_boolean"
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
46 -f list
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
47 #else
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
48 -f $params.output_format.value
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
49 #end if
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
50 -o $fuma_overview ;
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
51
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
52
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
53 #if $params.output_format.value == "list_boolean"
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
54 fuma-list-to-boolean-list -o tmp.txt $fuma_overview ;
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
55 mv tmp.txt $fuma_overview
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
56 #end if
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
57 ]]></command>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
58
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
59 <inputs>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
60 <repeat name="datasets" title="FusionGene Datasets" min="2">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
61 <param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
62 <param name="format" type="select" label="Format of dataset">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
63 <option value="chimera">Chimera prettyPrint()</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
64 <option value="chimerascan">ChimeraScan</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
65 <option value="defuse">DeFuse</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
66 <option value="complete-genomics">Complete Genomics var/mastervar</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
67 <option value="fusion-catcher_final">Fusion Catcher (final-list file)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
68 <option value="fusionmap">FusionMap</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
69 <option value="trinity-gmap">GMAP (As step after Trinity)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
70 <option value="oncofuse">OncoFuse</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
71 <option value="rna-star_chimeric">STAR (chimeric file)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
72 <option value="star-fusion_final">STAR-Fusion (candidates.final)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
73 <option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
74 <option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
75 <option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
76 <option value="tophat-fusion_post_result_html">Tophat Fusion Post (result.html)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
77 </param>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
78 <param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene annotations! Gene annotations should only be different if different reference genome builds were used." />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
79 </repeat>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
80
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
81 <conditional name="params">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
82 <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any FuMa parameter.">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
83 <option value="preSet" selected="true">Use Defaults</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
84 <option value="full">Full parameter list</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
85 </param>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
86 <when value="preSet">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
87 <param name="strand_specific_matching" type="hidden" value="--strand-specific-matching" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
88 <param name="acceptor_donor_order_specific_matchig" type="hidden" value="--acceptor-donor-order-specific-matching" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
89 </when>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
90 <when value="full">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
91 <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets" help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative.">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
92 <option value="overlap">Overlap</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
93 <option value="subset" selected="True">Subset</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
94 <option value="egm">Exact Geneset Matching (EGM)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
95 </param>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
96
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
97 <param name="strand_specific_matching" type="boolean" checked="True" truevalue="--strand-specific-matching" falsevalue="" label="Consider fusion genes distinct when the breakpoints have different strands" help="Only a limited number of file formats support this feature." />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
98 <param name="acceptor_donor_order_specific_matchig" type="boolean" checked="True" truevalue="--acceptor-donor-order-specific-matching" falsevalue="" label="Consider fusion genes distinct when the donor and acceptor sites are swapped (A,B) != (B,A)" help="This settings is not recommended when fusion genes detected in DNA-Seq are used" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
99
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
100 <param name="output_format" type="select" label="Output format">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
101 <option value="list_boolean" selected="true">List (Boolean)</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
102 <option value="list">List</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
103 <option value="summary">Count summary</option>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
104 </param>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
105 </when>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
106 </conditional>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
107 </inputs>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
108
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
109 <outputs>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
110 <data format="tabular" name="fuma_overview" label="${tool.name} on ${', '.join([ str(d['sample'].hid)+': '+d['sample'].name for d in $datasets ])}" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
111 </outputs>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
112
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
113 <tests>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
114 <test>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
115 <!-- <repeat name="datasets"> -->
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
116 <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
117 <param name="datasets_0|format" value="chimerascan" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
118 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
119 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
120 <!-- <repeat name="datasets"> -->
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
121 <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
122 <param name="datasets_1|format" value="defuse" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
123 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
124 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
125 <!-- <repeat name="datasets"> -->
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
126 <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
127 <param name="datasets_2|format" value="fusionmap" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
128 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
129 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
130 <!-- <repeat name="datasets"> -->
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
131 <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
132 <param name="datasets_3|format" value="fusionmap" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
133 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
134 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
135
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
136 <param name="settingsType" value="full" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
137
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
138 <param name="matching_method" value="subset" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
139 <param name="strand_specific_matching" value="--strand-specific-matching" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
140 <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
141 <param name="output_format" value="list_boolean" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
142
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
143 <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
144 </test>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
145 <test>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
146 <!-- <repeat name="datasets"> -->
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
147 <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
148 <param name="datasets_0|format" value="chimerascan" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
149 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
150 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
151 <!-- <repeat name="datasets"> -->
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
152 <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
153 <param name="datasets_1|format" value="defuse" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
154 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
155 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
156 <!-- <repeat name="datasets"> -->
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
157 <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
158 <param name="datasets_2|format" value="fusionmap" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
159 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
160 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
161 <!-- <repeat name="datasets"> -->
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
162 <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
163 <param name="datasets_3|format" value="fusionmap" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
164 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
165 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
166
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
167 <param name="settingsType" value="full" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
168
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
169 <param name="matching_method" value="subset" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
170 <param name="strand_specific_matching" value="" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
171 <param name="acceptor_donor_order_specific_matchig" value="" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
172 <param name="output_format" value="list_boolean" />
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
173
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
174 <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
175 </test>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
176 </tests>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
177
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
178 <help><![CDATA[
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
179 ============
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
180 Introduction
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
181 ============
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
182
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
183 FuMa (Fusion Matcher) matches predicted fusion events (both genomic and transcriptomic) according to chromosomal location or assocatiated gene annotation(s) where the latter should be genome build inspecific.
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
184
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
185 Because RNA-Sequencing deals with samples that may have undergrond splicing, reads may split up because of biological processes. If a fusion event takes place, the same thing may happen. Therefore we hypothesize that using spanning read distances may be unreliable, because there are known introns of > 100kb. Therefore, FuMa translates the breakpoint to gene names, and only overlaps breakpoints with the same genename(s).
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
186
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
187 =====
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
188 Usage
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
189 =====
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
190
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
191 After you have uploaded the results of your Fusion Gene detection experiment, and selected the format to be *tabular*, you can start the FuMa wrapper. For each dataset you simply have to add another repeat. Then you have to select a corresponding format:
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
192
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
193 *******
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
194 Formats
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
195 *******
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
196
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
197 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
198 |Tools | File | Format string |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
199 +===================+=======================+=====================================+
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
200 |Chimera | prettyPrint() output | chimera |
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
201 +-------------------+-----------------------+-------------------------------------+
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
202 |ChimeraScan | chimeras.bedpe | chimerascan |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
203 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
204 |Complete Genomics | highConfidenceJu*.tsv | complete-genomics |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
205 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
206 |Complete Genomics | allJunctionsBeta*.tsv | complete-genomics |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
207 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
208 |DeFuse | results.txt | defuse |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
209 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
210 |DeFuse | results.classify.txt | defuse |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
211 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
212 |DeFuse | results.filtered.txt | defuse |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
213 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
214 |Fusion Catcher | final-list_cand*.txt | fusion-catcher_final |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
215 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
216 |FusionMap | | fusionmap |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
217 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
218 |Trinity + GMAP | | trinity-gmap |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
219 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
220 |OncoFuse | | oncofuse |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
221 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
222 |RNA STAR | Chimeric.out.junction | rna-star_chimeric |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
223 +-------------------+-----------------------+-------------------------------------+
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
224 |STAR Fusion | _candidates.final | star-fusion_final |
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
225 +-------------------+-----------------------+-------------------------------------+
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
226 |TopHat Fusion pre | fusions.out | tophat-fusion_pre |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
227 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
228 |TopHat Fusion post | potential_fusion.txt | tophat-fusion_post_potential_fusion |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
229 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
230 |TopHat Fusion post | result.txt | tophat-fusion_post_result |
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
231 +-------------------+-----------------------+-------------------------------------+
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
232 |TopHat Fusion post | result.html | tophat-fusion_post_result_html |
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
233 +-------------------+-----------------------+-------------------------------------+
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
234
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
235 To annotate genes upon the breakpoints you must provide a BED file that contains gene annotations for the user genome build. Make sure **your BED file contains one gene per line**. You should use BED files that contain one exon per line only if you want restrict your analysis to fusion genes detected within exons.
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
236
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
237 UCSC genome browser provides a very simple way of obtaining BED files with one gene per line by selecting their *RefSeq Genes*-track and *knownGene*-table and putting the export format to BED. Galaxy should have a built-in UCSC table browser.
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
238
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
239 ]]></help>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
240
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
241 <citations>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
242 <citation type="bibtex">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
243 @unpublished{fuma,
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
244 author = {Youri Hoogstrate},
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
245 title = {FuMa: reporting overlap in RNA-seq detected fusion genes},
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
246 url = { https://github.com/yhoogstrate/fuma }
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
247 }
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
248 </citation>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
249 </citations>
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
250 </tool>