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comparison featurecounts.xml @ 30:56aa64c23690 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:07:43 +0000
parents 3cd88f5c9d4c
children 83ab9e468b86
comparison
equal deleted inserted replaced
29:3cd88f5c9d4c 30:56aa64c23690
1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> 2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.0.1</token> 4 <token name="@TOOL_VERSION@">2.0.1</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 7 <xrefs>
8 <xref type="bio.tools">subread</xref>
9 </xrefs>
8 <requirements> 10 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">subread</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
10 <requirement type="package" version="1.11">samtools</requirement> 12 <requirement type="package" version="1.11">samtools</requirement>
11 <requirement type="package" version="8.31">coreutils</requirement> 13 <requirement type="package" version="8.31">coreutils</requirement>
12 </requirements> 14 </requirements>
279 label="On feature level" 281 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." /> 282 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." />
281 283
282 <conditional name = "multifeatures"> 284 <conditional name = "multifeatures">
283 <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction"> 285 <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> 286 <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> 287 <option value="-M">Enabled; multi-mapping reads are included (-M)</option>
286 <option value="-O">Enabled: multi-overlapping features are included (-O)</option> 288 <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> 289 <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option>
288 </param> 290 </param>
289 <when value=""/> 291 <when value=""/>
290 <when value="-M"> 292 <when value="-M">
291 <param name="fraction" 293 <param name="fraction"
292 type="boolean" 294 type="boolean"
293 truevalue="--fraction" 295 truevalue="--fraction"
294 falsevalue="" 296 falsevalue=""
295 argument="--fraction" 297 argument="--fraction"
296 label="Assign fractions to multi-mapping reads" 298 label="Assign fractions to multimapping reads"
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."/> 299 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."/>
298 </when> 300 </when>
299 <when value="-O"> 301 <when value="-O">
300 <param name="fraction" 302 <param name="fraction"
301 type="boolean" 303 type="boolean"
302 truevalue="--fraction" 304 truevalue="--fraction"
303 falsevalue="" 305 falsevalue=""
304 argument="--fraction" 306 argument="--fraction"
305 label="Assign fractions to multi-overlapping features" 307 label="Assign fractions to multimapping reads"
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."/> 308 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."/>
307 </when> 309 </when>
308 <when value="-O -M"> 310 <when value="-O -M">
309 <param name="fraction" 311 <param name="fraction"
310 type="boolean" 312 type="boolean"
311 truevalue="--fraction" 313 truevalue="--fraction"
312 falsevalue="" 314 falsevalue=""
313 argument="--fraction" 315 argument="--fraction"
314 label="Assign fractions to both multi-mapping reads and multi-overlapping features" 316 label="Assign fractions to multimapping reads"
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."/> 317 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."/>
316 </when> 318 </when>
317 </conditional> 319 </conditional>
318 320
319 <param name="mapping_quality" 321 <param name="mapping_quality"
320 type="integer" 322 type="integer"