Mercurial > repos > yhoogstrate > fuma

annotate fuma.xml @ 7:ec04b7552167 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 811623bf945377481ed49f83e4dc4d08e83103c5
author yhoogstrate
date Wed, 09 Dec 2015 09:56:41 -0500
parents a5f10935f9ab
children 8366a8c82a7a
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"?>
4
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
2 <tool id="fuma" name="FuMa" version="2.11.0.a">
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
3 <description>match detected fusion genes based on gene names (in particular for RNA-Seq)</description>
2
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>
4
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
7 <requirement type="package" version="2.11.0">fuma</requirement>
2
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
5
a5f10935f9ab planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
yhoogstrate
parents: 4
diff changeset
39 --long-gene-size $params.long_gene_size
a5f10935f9ab planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
yhoogstrate
parents: 4
diff changeset
40
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
41 -a
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
42 $gene_annotations_str
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
43 -s
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
44 $samples_str
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
45 -l
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
46 $links_str
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
47 #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
48 -f list
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
49 #else
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
50 -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
51 #end if
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
52 -o $fuma_overview ;
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
53
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
54
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
55 #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
56 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
57 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
58 #end if
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
59 ]]></command>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
60
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
61 <inputs>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
62 <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
63 <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
64 <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
65 <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
66 <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
67 <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
68 <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
69 <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
70 <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
71 <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
72 <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
73 <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
74 <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
75 <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
76 <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
77 <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
78 <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
79 </param>
4
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
80 <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" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
81 </repeat>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
82
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
83 <conditional name="params">
4
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
84 <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any FuMa parameter">
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
85 <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
86 <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
87 </param>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
88 <when value="preSet">
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
89 <param name="strand_specific_matching" type="hidden" value="--strand-specific-matching" />
5
a5f10935f9ab planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
yhoogstrate
parents: 4
diff changeset
90 <param name="acceptor_donor_order_specific_matchig" type="hidden" value="--no-acceptor-donor-order-specific-matching" />
a5f10935f9ab planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
yhoogstrate
parents: 4
diff changeset
91 <param name="long_gene_size" type="hidden" value="200000" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
92 </when>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
93 <when value="full">
4
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
94 <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">
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
95 <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
96 <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
97 <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
98 </param>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
99
4
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
100 <param name="strand_specific_matching" type="boolean" checked="True"
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
101 truevalue="--strand-specific-matching"
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
102 falsevalue="--no-strand-specific-matching"
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
103 label="Consider fusion genes distinct when the breakpoints have different strands: (A&lt;-,B&lt;-) != (-&gt;A,B&lt;-); default"
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
104 help="Only a limited number of file formats support this feature" />
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
105 <param name="acceptor_donor_order_specific_matchig" type="boolean" checked="False"
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
106 truevalue="--acceptor-donor-order-specific-matching"
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
107 falsevalue="--no-acceptor-donor-order-specific-matching"
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
108 label="Consider fusion genes distinct when the donor and acceptor sites are swapped (A,B) != (B,A)"
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
109 help="This settings is not recommended when fusion genes detected in DNA-Seq are used" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
110
5
a5f10935f9ab planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
yhoogstrate
parents: 4
diff changeset
111 <param name="long_gene_size" type="integer" min="0" value="200000" label="Long gene size" help="Gene-name based matching is more sensitive to long genes. This is the gene size used to mark fusion genes spanning a 'long gene' as reported the output. Use 0 to disable this feature (--long-gene-size)" />
a5f10935f9ab planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
yhoogstrate
parents: 4
diff changeset
112
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
113 <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
114 <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
115 <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
116 <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
117 </param>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
118 </when>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
119 </conditional>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
120 </inputs>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
121
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
122 <outputs>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
123 <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
124 </outputs>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
125
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
126 <tests>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
127 <test>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
128 <!-- <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
129 <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
130 <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
131 <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
132 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
133 <!-- <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
134 <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
135 <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
136 <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
137 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
138 <!-- <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
139 <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
140 <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
141 <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
142 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
143 <!-- <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
144 <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
145 <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
146 <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
147 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
148
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
149 <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
150
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
151 <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
152 <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
153 <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" />
5
a5f10935f9ab planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
yhoogstrate
parents: 4
diff changeset
154 <param name="long_gene_size" value="200000" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
155 <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
156
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
157 <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
158 </test>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
159 <test>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
160 <!-- <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
161 <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
162 <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
163 <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
164 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
165 <!-- <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
166 <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
167 <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
168 <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
169 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
170 <!-- <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
171 <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
172 <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
173 <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
174 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
175 <!-- <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
176 <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
177 <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
178 <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
179 <!-- </repeat> -->
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
180
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
181 <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
182
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
183 <param name="matching_method" value="subset" />
4
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
184 <param name="strand_specific_matching" value="False" /><!-- Set to false, automatically sets the false value -->
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
185 <param name="acceptor_donor_order_specific_matchig" value="False" /><!-- Set to false, automatically sets the false value -->
5
a5f10935f9ab planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
yhoogstrate
parents: 4
diff changeset
186 <param name="long_gene_size" value="200000" />
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
187 <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
188
3
4966079d474b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
yhoogstrate
parents: 2
diff changeset
189 <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
190 </test>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
191 </tests>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
192
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
193 <help><![CDATA[
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
194 ============
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
195 Introduction
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
4
cb0543909e83 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 36132cfcfe9203c499b73a2f0eea570c05e07ab8
yhoogstrate
parents: 3
diff changeset
198 A new generation of tools that identify fusion genes in RNA-seq data is limited in either sensitivity and or specificity. To allow further downstream analysis and to estimate performance, predicted fusion genes from different tools have to be compared. However, the transcriptomic context complicates genomic location-based matching. FusionMatcher (FuMa) is a program that reports identical fusion genes based on gene-name annotations. FuMa automatically compares and summarizes all combinations of two or more datasets in a single run, without additional programming necessary. FuMa uses one gene annotation, avoiding mismatches caused by tool specific gene annotations. FuMa matches 10% more fusion genes compared to exact gene matching (EGM) due to overlapping genes and accepts intermediate output files that allow a step wise analysis of corresponding tools.
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
199
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
200 =====
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
201 Usage
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
202 =====
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 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
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 *******
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
207 Formats
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
208 *******
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 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
211 |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
212 +===================+=======================+=====================================+
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
213 |Chimera | prettyPrint() output | chimera |
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
214 +-------------------+-----------------------+-------------------------------------+
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
215 |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
216 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
217 |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
218 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
219 |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
220 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
221 |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
222 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
223 |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
224 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
225 |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
226 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
227 |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
228 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
229 |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
230 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
231 |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
232 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
233 |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
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 |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
236 +-------------------+-----------------------+-------------------------------------+
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
237 |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
238 +-------------------+-----------------------+-------------------------------------+
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
239 |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
240 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
241 |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
242 +-------------------+-----------------------+-------------------------------------+
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
243 |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
244 +-------------------+-----------------------+-------------------------------------+
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
245 |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
246 +-------------------+-----------------------+-------------------------------------+
0
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
247
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
248 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
249
a4cfaa0e3e5d planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty
yhoogstrate
parents:
diff changeset
250 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
251
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
252 ]]></help>
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
253
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
254 <citations>
7
ec04b7552167 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 811623bf945377481ed49f83e4dc4d08e83103c5
yhoogstrate
parents: 5
diff changeset
255 <citation type="doi">10.1093/bioinformatics/btv721</citation>
2
86526900cb8f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
yhoogstrate
parents: 1
diff changeset
256 </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
257 </tool>