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comparison featurecounts.xml @ 26:48a5ee6c175c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4"
author iuc
date Fri, 14 Aug 2020 08:28:31 +0000
parents 9f24599f93e5
children 55cdfc5bb826
comparison
equal deleted inserted replaced
25:9f24599f93e5 26:48a5ee6c175c
1 <tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy1" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy2" profile="16.04">
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 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.4">subread</requirement> 4 <requirement type="package" version="1.6.4">subread</requirement>
5 <requirement type="package" version="1.9">samtools</requirement> 5 <requirement type="package" version="1.9">samtools</requirement>
6 <requirement type="package" version="8.31">coreutils</requirement> 6 <requirement type="package" version="8.31">coreutils</requirement>
32 32
33 -s $strand_specificity 33 -s $strand_specificity
34 -t '$extended_parameters.gff_feature_type' 34 -t '$extended_parameters.gff_feature_type'
35 -g '$extended_parameters.gff_feature_attribute' 35 -g '$extended_parameters.gff_feature_attribute'
36 $extended_parameters.summarization_level 36 $extended_parameters.summarization_level
37 $extended_parameters.contribute_to_multiple_features 37
38 $extended_parameters.multimapping_enabled.multimapping_counts 38 $extended_parameters.multifeatures.multifeat
39 39 #if $extended_parameters.multifeatures.multifeat != "":
40 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M": 40 $extended_parameters.multifeatures.fraction
41 $extended_parameters.multimapping_enabled.fraction
42 #end if 41 #end if
42
43
44 ## $extended_parameters.contribute_to_multiple_features
45 ## $extended_parameters.multimapping_enabled.multimapping_counts
46
47 ###if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
48 ## $extended_parameters.multimapping_enabled.fraction
49 ###end if -->
43 50
44 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads 51 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
45 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": 52 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
46 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome: 53 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:
47 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome' 54 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
265 falsevalue="" 272 falsevalue=""
266 argument="-f" 273 argument="-f"
267 label="On feature level" 274 label="On feature level"
268 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." /> 275 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." />
269 276
270 <param name="contribute_to_multiple_features" 277 <conditional name = "multifeatures">
271 type="boolean" 278 <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction">
272 truevalue=" -O" 279 <option value="" selected="true">Disabled; reads that align to multiple features or overlapping features are excluded</option>
273 falsevalue="" 280 <option value="-M">Enabled; multi-mapping reads are included (-M)</option>
274 argument="-O" 281 <option value="-O">Enabled: multi-overlapping features are included (-O)</option>
275 label="Allow read to contribute to multiple features" 282 <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option>
276 help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" />
277
278 <conditional name="multimapping_enabled">
279 <param name="multimapping_counts"
280 type="select"
281 argument="-M"
282 label="Count multi-mapping reads/fragments"
283 help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads.">
284 <option value="" selected="true">Disabled; multi-mapping reads are excluded (default)</option>
285 <option value=" -M">Enabled; multi-mapping reads are included</option>
286 </param> 283 </param>
287 <when value=" -M"> 284 <when value=""/>
288 <param name="fraction" 285 <when value="-M">
289 type="boolean" 286 <param name="fraction"
290 truevalue="--fraction" 287 type="boolean"
291 falsevalue="" 288 truevalue="--fraction"
292 argument="--fraction" 289 falsevalue=""
293 label="Assign fractions to multimapping reads" 290 argument="--fraction"
294 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. This option must be used together with the '-M' option." /> 291 label="Assign fractions to multimapping reads"
292 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."/>
295 </when> 293 </when>
296 <when value="" /> 294 <when value="-O">
295 <param name="fraction"
296 type="boolean"
297 truevalue="--fraction"
298 falsevalue=""
299 argument="--fraction"
300 label="Assign fractions to multimapping reads"
301 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."/>
302 </when>
303 <when value="-O -M">
304 <param name="fraction"
305 type="boolean"
306 truevalue="--fraction"
307 falsevalue=""
308 argument="--fraction"
309 label="Assign fractions to multimapping reads"
310 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."/>
311 </when>
297 </conditional> 312 </conditional>
298 313
299 <param name="mapping_quality" 314 <param name="mapping_quality"
300 type="integer" 315 type="integer"
301 value="0" 316 value="0"