Mercurial > repos > iuc > featurecounts
comparison featurecounts.xml @ 25:90d16db017d7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4"
| author | iuc |
|---|---|
| date | Fri, 14 Aug 2020 04:28:55 -0400 |
| parents | a37612abf7f9 |
| children | ea04b737afa0 |
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| 24:a37612abf7f9 | 25:90d16db017d7 |
|---|---|
| 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" |