fuma: fuma.xml annotate

annotate fuma.xml @ 6:b92f986bd0ab draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit a88597518f3715c0b22283f6f31757205efcb8d0-dirty

author	yhoogstrate
date	Mon, 01 Jun 2015 05:18:14 -0400
parents	fb762ef764a9
children	77c5a17f335b

rev	line source
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	1 <?xml version="1.0" encoding="UTF-8"?>
4 c9b1bbe7bdac Fixed if-statement and improved the version command. yhoogstrate parents: 3 diff changeset	2 <tool id="fuma" name="FuMa" version="2.7.1.b">
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	3 <description>FuMa (FusionMatcher) matches detected fusion genes based on gene name subset matching (designed in particular for RNA-Seq).</description>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	4
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	5 <requirements>
3 f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	6 <requirement type="package" version="2.7.1">fuma</requirement>
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	7 </requirements>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	8
4 c9b1bbe7bdac Fixed if-statement and improved the version command. yhoogstrate parents: 3 diff changeset	9 <version_command>fuma --version 2>&1 \| head -n 1</version_command><!-- -V also works, but is not GNU standard -->
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	10
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	11 <command>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	12 #import pipes
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	13
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	14 #set $gene_annotations = []
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	15 #set $samples = []
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	16 #set $links = []
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	17
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	18 #for $i, $d in enumerate( $datasets )
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	19
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	20 #set $sample_name = pipes.quote(str($d['sample'].name))
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	21
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	22 #set $gene_annotations = $gene_annotations + [ "ga_" + str($i) + ":" + str($d['gene_annotation'].file_name) ]
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	23
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	24 #set $samples = $samples + [ $sample_name + ":" + str($d['format']) + ":" + str($d['sample'].file_name) ]
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	25 #set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	26 #end for
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	27
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	28 #set $gene_annotations_str = " ".join(gene_annotations)
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	29 #set $samples_str = " ".join(samples)
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	30 #set $links_str = " ".join(links)
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	31
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	32 fuma
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	33 -a
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	34 $gene_annotations_str
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	35 -s
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	36 $samples_str
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	37 -l
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	38 $links_str
4 c9b1bbe7bdac Fixed if-statement and improved the version command. yhoogstrate parents: 3 diff changeset	39 #if $output_format.value == "list_boolean"
3 f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	40 -f list
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	41 #else
4 c9b1bbe7bdac Fixed if-statement and improved the version command. yhoogstrate parents: 3 diff changeset	42 -f $output_format.value
3 f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	43 #end if
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	44 -o $fuma_overview ;
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	45
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	46
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	47
5 fb762ef764a9 Uploaded yhoogstrate parents: 4 diff changeset	48 #if $output_format.value == "list_boolean"
3 f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	49 fuma-list-to-boolean-list -o tmp.txt $fuma_overview &&
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	50 mv tmp.txt $fuma_overview
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	51 #end if
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	52 </command>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	53
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	54 <inputs>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	55 <repeat name="datasets" title="FusionGene Datasets" min="2">
2 76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	56 <param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" />
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	57 <param name="format" type="select" label="Format of dataset">
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	58 <option value="chimerascan">ChimeraScan</option>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	59 <option value="defuse">DeFuse</option>
3 f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	60 <option value="complete-genomics">Complete Genomics</option>
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	61 <option value="fusion-catcher_final">Fusion Catcher (final-list file)</option>
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	62 <option value="fusionmap">FusionMap</option>
3 f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	63 <option value="trinity-gmap">GMAP (As step after Trinity)</option>
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	64 <option value="oncofuse">OncoFuse</option>
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	65 <option value="rna-star_chimeric">STAR (chimeric file)</option>
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	66 <option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option>
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	67 <option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option>
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	68 <option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option>
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	69 </param>
2 76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	70 <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." />
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	71 </repeat>
2 76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	72
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	73 <param name="output_format" type="select" label="Output format">
3 f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	74 <option value="list_boolean" selected="true">List (Boolean)</option>
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	75 <option value="list">List</option>
2 76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	76 <option value="summary">Count summary</option>
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	77 </param>
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	78 </inputs>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	79
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	80 <outputs>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	81 <data format="tabular" name="fuma_overview" label="${tool.name} on ${', '.join([ str(d['sample'].hid)+': '+d['sample'].name for d in $datasets ])}" />
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	82 </outputs>
267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	83
2 76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	84 <tests>
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	85 <test>
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	86 <!-- <repeat name="datasets"> -->
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	87 <param name="datasets_0\|sample" value="chimerascan.txt" ftype="tabular" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	88 <param name="datasets_0\|format" value="chimerascan" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	89 <param name="datasets_0\|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	90 <!-- </repeat> -->
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	91 <!-- <repeat name="datasets"> -->
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	92 <param name="datasets_1\|sample" value="defuse.txt" ftype="tabular" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	93 <param name="datasets_1\|format" value="defuse" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	94 <param name="datasets_1\|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	95 <!-- </repeat> -->
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	96 <!-- <repeat name="datasets"> -->
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	97 <param name="datasets_2\|sample" value="fusion-map.txt" ftype="tabular" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	98 <param name="datasets_2\|format" value="fusionmap" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	99 <param name="datasets_2\|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	100 <!-- </repeat> -->
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	101 <!-- <repeat name="datasets"> -->
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	102 <param name="datasets_3\|sample" value="edgren_tp.txt" ftype="tabular" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	103 <param name="datasets_3\|format" value="fusionmap" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	104 <param name="datasets_3\|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	105 <!-- </repeat> -->
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	106
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	107 <param name="output_format" value="summary" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	108
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	109 <output name="fuma_overview" file="output.txt" />
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	110 </test>
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	111 </tests>
76293f7745ff Uploaded yhoogstrate parents: 1 diff changeset	112
3 f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	113 <help>============
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	114 Introduction
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	115 ============
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	116
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	117 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.
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	118
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	119 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).
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	120
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	121 =====
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	122 Usage
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	123 =====
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	124
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	125 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:
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	126
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	127 *******
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	128 Formats
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	129 *******
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	130
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	131 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	132 \|Tools \| File \| Format string \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	133 +===================+=======================+=====================================+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	134 \|ChimeraScan \| chimeras.bedpe \| chimerascan \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	135 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	136 \|Complete Genomics \| highConfidenceJu*.tsv \| complete-genomics \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	137 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	138 \|Complete Genomics \| allJunctionsBeta*.tsv \| complete-genomics \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	139 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	140 \|DeFuse \| results.txt \| defuse \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	141 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	142 \|DeFuse \| results.classify.txt \| defuse \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	143 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	144 \|DeFuse \| results.filtered.txt \| defuse \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	145 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	146 \|Fusion Catcher \| final-list_cand*.txt \| fusion-catcher_final \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	147 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	148 \|FusionMap \| \| fusionmap \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	149 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	150 \|Trinity + GMAP \| \| trinity-gmap \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	151 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	152 \|OncoFuse \| \| oncofuse \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	153 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	154 \|RNA STAR \| Chimeric.out.junction \| rna-star_chimeric \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	155 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	156 \|TopHat Fusion pre \| fusions.out \| tophat-fusion_pre \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	157 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	158 \|TopHat Fusion post \| potential_fusion.txt \| tophat-fusion_post_potential_fusion \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	159 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	160 \|TopHat Fusion post \| result.txt \| tophat-fusion_post_result \|
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	161 +-------------------+-----------------------+-------------------------------------+
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	162
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	163 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.
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	164
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	165 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.
f06461883f7b updated to version 2.7.1 and extended wrapper with additional output type and a help section yhoogstrate parents: 2 diff changeset	166
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	167 </help>
6 b92f986bd0ab planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit a88597518f3715c0b22283f6f31757205efcb8d0-dirty yhoogstrate parents: 5 diff changeset	168
b92f986bd0ab planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit a88597518f3715c0b22283f6f31757205efcb8d0-dirty yhoogstrate parents: 5 diff changeset	169 <citations>
b92f986bd0ab planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit a88597518f3715c0b22283f6f31757205efcb8d0-dirty yhoogstrate parents: 5 diff changeset	170 </citations>
0 267d0c2ebe56 Uploaded yhoogstrate parents: diff changeset	171 </tool>

Mercurial > repos > yhoogstrate > fuma

annotate fuma.xml @ 6:b92f986bd0ab draft