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comparison fuma.xml @ 8:8366a8c82a7a draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit d90385601350b4d5fafae3004b470dee4a7f442d-dirty
author yhoogstrate
date Mon, 08 Feb 2016 04:56:40 -0500
parents ec04b7552167
children b21145d59d9c
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7:ec04b7552167 8:8366a8c82a7a
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="fuma" name="FuMa" version="2.11.0.a"> 2 <tool id="fuma" name="FuMa" version="2.11.3-g0">
3 <description>match detected fusion genes based on gene names (in particular for RNA-Seq)</description> 3 <description>match detected fusion genes based on gene names (in particular for RNA-Seq)</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.7">python</requirement> 6 <requirement type="package" version="2.7">python</requirement>
7 <requirement type="package" version="2.11.0">fuma</requirement> 7 <requirement type="package" version="2.11.3">fuma</requirement>
8 </requirements> 8 </requirements>
9 9
10 <version_command>fuma --version 2>&amp;1 | head -n 1</version_command><!-- -V also works, but is not GNU standard --> 10 <version_command>fuma --version 2>&amp;1 | head -n 1</version_command><!-- -V also works, but is not GNU standard -->
11 11
12 <command><![CDATA[ 12 <command><![CDATA[
62 <repeat name="datasets" title="FusionGene Datasets" min="2"> 62 <repeat name="datasets" title="FusionGene Datasets" min="2">
63 <param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" /> 63 <param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" />
64 <param name="format" type="select" label="Format of dataset"> 64 <param name="format" type="select" label="Format of dataset">
65 <option value="chimera">Chimera prettyPrint()</option> 65 <option value="chimera">Chimera prettyPrint()</option>
66 <option value="chimerascan">ChimeraScan</option> 66 <option value="chimerascan">ChimeraScan</option>
67 <option value="complete-genomics">Complete Genomics var/mastervar</option>
67 <option value="defuse">DeFuse</option> 68 <option value="defuse">DeFuse</option>
68 <option value="complete-genomics">Complete Genomics var/mastervar</option> 69 <option value="ericscript">EricScript (.results.total.txt)</option>
69 <option value="fusion-catcher_final">Fusion Catcher (final-list file)</option> 70 <option value="fusion-catcher_final">Fusion Catcher (final-list file)</option>
70 <option value="fusionmap">FusionMap</option> 71 <option value="fusionmap">FusionMap</option>
71 <option value="trinity-gmap">GMAP (As step after Trinity)</option> 72 <option value="trinity-gmap">GMAP (As step after Trinity)</option>
72 <option value="oncofuse">OncoFuse</option> 73 <option value="oncofuse">OncoFuse</option>
74 <option value="soapfuse-final-gene">SOAPFuse (final.*.for.genes.txt)</option>
75 <option value="soapfuse-final-transcript">SOAPFuse (final.*.for.trans.txt)</option>
73 <option value="rna-star_chimeric">STAR (chimeric file)</option> 76 <option value="rna-star_chimeric">STAR (chimeric file)</option>
74 <option value="star-fusion_final">STAR-Fusion (candidates.final)</option> 77 <option value="star-fusion_final">STAR-Fusion (candidates.final)</option>
75 <option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option> 78 <option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option>
76 <option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option> 79 <option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option>
77 <option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option> 80 <option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option>
222 +-------------------+-----------------------+-------------------------------------+ 225 +-------------------+-----------------------+-------------------------------------+
223 |DeFuse | results.classify.txt | defuse | 226 |DeFuse | results.classify.txt | defuse |
224 +-------------------+-----------------------+-------------------------------------+ 227 +-------------------+-----------------------+-------------------------------------+
225 |DeFuse | results.filtered.txt | defuse | 228 |DeFuse | results.filtered.txt | defuse |
226 +-------------------+-----------------------+-------------------------------------+ 229 +-------------------+-----------------------+-------------------------------------+
230 |EricScript | .results.total.txt | ericscript ************* |
231 +-------------------+-----------------------+-------------------------------------+
227 |Fusion Catcher | final-list_cand*.txt | fusion-catcher_final | 232 |Fusion Catcher | final-list_cand*.txt | fusion-catcher_final |
228 +-------------------+-----------------------+-------------------------------------+ 233 +-------------------+-----------------------+-------------------------------------+
229 |FusionMap | | fusionmap | 234 |FusionMap | | fusionmap |
230 +-------------------+-----------------------+-------------------------------------+ 235 +-------------------+-----------------------+-------------------------------------+
231 |Trinity + GMAP | | trinity-gmap | 236 |Trinity + GMAP | | trinity-gmap |
232 +-------------------+-----------------------+-------------------------------------+ 237 +-------------------+-----------------------+-------------------------------------+
233 |OncoFuse | | oncofuse | 238 |OncoFuse | | oncofuse |
234 +-------------------+-----------------------+-------------------------------------+ 239 +-------------------+-----------------------+-------------------------------------+
235 |RNA STAR | Chimeric.out.junction | rna-star_chimeric | 240 |RNA STAR | Chimeric.out.junction | rna-star_chimeric |
236 +-------------------+-----------------------+-------------------------------------+ 241 +-------------------+-----------------------+-------------------------------------+
242 |SOAPFuse | final.*.for.genes.txt | soapfuse-final-gene |
243 +-------------------+-----------------------+-------------------------------------+
244 |SOAPFuse | final.*.for.trans.txt | soapfuse-final-transcript |
245 +-------------------+-----------------------+-------------------------------------+
237 |STAR Fusion | _candidates.final | star-fusion_final | 246 |STAR Fusion | _candidates.final | star-fusion_final |
238 +-------------------+-----------------------+-------------------------------------+ 247 +-------------------+-----------------------+-------------------------------------+
239 |TopHat Fusion pre | fusions.out | tophat-fusion_pre | 248 |TopHat Fusion pre | fusions.out | tophat-fusion_pre |
240 +-------------------+-----------------------+-------------------------------------+ 249 +-------------------+-----------------------+-------------------------------------+
241 |TopHat Fusion post | potential_fusion.txt | tophat-fusion_post_potential_fusion | 250 |TopHat Fusion post | potential_fusion.txt | tophat-fusion_post_potential_fusion |
242 +-------------------+-----------------------+-------------------------------------+ 251 +-------------------+-----------------------+-------------------------------------+
243 |TopHat Fusion post | result.txt | tophat-fusion_post_result | 252 |TopHat Fusion post | result.txt | tophat-fusion_post_result |
244 +-------------------+-----------------------+-------------------------------------+ 253 +-------------------+-----------------------+-------------------------------------+
245 |TopHat Fusion post | result.html | tophat-fusion_post_result_html | 254 |TopHat Fusion post | result.html | tophat-fusion_post_result_html |
246 +-------------------+-----------------------+-------------------------------------+ 255 +-------------------+-----------------------+-------------------------------------+
256
257 ************* EricScript often contains entries with unknown breakpoints.
258 Because no genomic coordinates are given those fusion genes can not be
259 imported into FuMa and only those with breakpoints will be taken into account.
260
261
247 262
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. 263 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.
249 264
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. 265 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.
251 266