Mercurial > repos > iuc > featurecounts
comparison featurecounts.xml @ 28:7db9d3ea71c9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6ad844a722ddf6a71cae4c77bc43d3051376d891"
| author | iuc |
|---|---|
| date | Mon, 30 Aug 2021 13:47:52 +0000 |
| parents | ce44c6f2ba38 |
| children | 38b6d12edc68 |
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| 27:ce44c6f2ba38 | 28:7db9d3ea71c9 |
|---|---|
| 279 label="On feature level" | 279 label="On feature level" |
| 280 help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level." /> | 280 help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level." /> |
| 281 | 281 |
| 282 <conditional name = "multifeatures"> | 282 <conditional name = "multifeatures"> |
| 283 <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction"> | 283 <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction"> |
| 284 <option value="" selected="true">Disabled; reads that align to multiple features or overlapping features are excluded</option> | 284 <option value="" selected="true">Disabled: reads that align to multiple features or overlapping features are excluded</option> |
| 285 <option value="-M">Enabled; multi-mapping reads are included (-M)</option> | 285 <option value="-M">Enabled: multi-mapping reads are included (-M)</option> |
| 286 <option value="-O">Enabled: multi-overlapping features are included (-O)</option> | 286 <option value="-O">Enabled: multi-overlapping features are included (-O)</option> |
| 287 <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option> | 287 <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option> |
| 288 </param> | 288 </param> |
| 289 <when value=""/> | 289 <when value=""/> |
| 290 <when value="-M"> | 290 <when value="-M"> |
| 291 <param name="fraction" | 291 <param name="fraction" |
| 292 type="boolean" | 292 type="boolean" |
| 293 truevalue="--fraction" | 293 truevalue="--fraction" |
| 294 falsevalue="" | 294 falsevalue="" |
| 295 argument="--fraction" | 295 argument="--fraction" |
| 296 label="Assign fractions to multimapping reads" | 296 label="Assign fractions to multi-mapping reads" |
| 297 help="If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> | 297 help="If specified, a fractional count 1/x will be generated for each multi-mapping read, where x is the number of alignments (indicated by 'NH' tag) reported for the read."/> |
| 298 </when> | 298 </when> |
| 299 <when value="-O"> | 299 <when value="-O"> |
| 300 <param name="fraction" | 300 <param name="fraction" |
| 301 type="boolean" | 301 type="boolean" |
| 302 truevalue="--fraction" | 302 truevalue="--fraction" |
| 303 falsevalue="" | 303 falsevalue="" |
| 304 argument="--fraction" | 304 argument="--fraction" |
| 305 label="Assign fractions to multimapping reads" | 305 label="Assign fractions to multi-overlapping features" |
| 306 help="If specified, a fractional count 1/n will be generated for each multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> | 306 help="If specified, a fractional count 1/y will be generated for each multi-overlapping feature, where y is the number of features overlapping with the read."/> |
| 307 </when> | 307 </when> |
| 308 <when value="-O -M"> | 308 <when value="-O -M"> |
| 309 <param name="fraction" | 309 <param name="fraction" |
| 310 type="boolean" | 310 type="boolean" |
| 311 truevalue="--fraction" | 311 truevalue="--fraction" |
| 312 falsevalue="" | 312 falsevalue="" |
| 313 argument="--fraction" | 313 argument="--fraction" |
| 314 label="Assign fractions to multimapping reads" | 314 label="Assign fractions to both multi-mapping reads and multi-overlapping features" |
| 315 help="If specified, a fractional count 1/n will be generated for each multi-mapping or multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/> | 315 help="If specified, a fractional count 1/(x*y) will be generated, where x is the number of alignments (indicated by 'NH' tag) and y the number of overlapping features."/> |
| 316 </when> | 316 </when> |
| 317 </conditional> | 317 </conditional> |
| 318 | 318 |
| 319 <param name="mapping_quality" | 319 <param name="mapping_quality" |
| 320 type="integer" | 320 type="integer" |