Mercurial > repos > iuc > featurecounts
diff 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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--- a/featurecounts.xml Fri Sep 06 11:08:21 2019 -0400 +++ b/featurecounts.xml Fri Aug 14 04:28:55 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy1" profile="16.04"> +<tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy2" profile="16.04"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> <requirement type="package" version="1.6.4">subread</requirement> @@ -34,12 +34,19 @@ -t '$extended_parameters.gff_feature_type' -g '$extended_parameters.gff_feature_attribute' $extended_parameters.summarization_level - $extended_parameters.contribute_to_multiple_features - $extended_parameters.multimapping_enabled.multimapping_counts + + $extended_parameters.multifeatures.multifeat + #if $extended_parameters.multifeatures.multifeat != "": + $extended_parameters.multifeatures.fraction + #end if + - #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M": - $extended_parameters.multimapping_enabled.fraction - #end if + ## $extended_parameters.contribute_to_multiple_features + ## $extended_parameters.multimapping_enabled.multimapping_counts + + ###if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M": + ## $extended_parameters.multimapping_enabled.fraction + ###end if --> $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": @@ -267,33 +274,41 @@ label="On feature level" 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." /> - <param name="contribute_to_multiple_features" - type="boolean" - truevalue=" -O" - falsevalue="" - argument="-O" - label="Allow read to contribute to multiple features" - 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)" /> - - <conditional name="multimapping_enabled"> - <param name="multimapping_counts" - type="select" - argument="-M" - label="Count multi-mapping reads/fragments" - 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."> - <option value="" selected="true">Disabled; multi-mapping reads are excluded (default)</option> - <option value=" -M">Enabled; multi-mapping reads are included</option> + <conditional name = "multifeatures"> + <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction"> + <option value="" selected="true">Disabled; reads that align to multiple features or overlapping features are excluded</option> + <option value="-M">Enabled; multi-mapping reads are included (-M)</option> + <option value="-O">Enabled: multi-overlapping features are included (-O)</option> + <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option> </param> - <when value=" -M"> - <param name="fraction" - type="boolean" - truevalue="--fraction" - falsevalue="" - argument="--fraction" - label="Assign fractions to multimapping reads" - 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." /> + <when value=""/> + <when value="-M"> + <param name="fraction" + type="boolean" + truevalue="--fraction" + falsevalue="" + argument="--fraction" + label="Assign fractions to multimapping reads" + 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."/> </when> - <when value="" /> + <when value="-O"> + <param name="fraction" + type="boolean" + truevalue="--fraction" + falsevalue="" + argument="--fraction" + label="Assign fractions to multimapping reads" + 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."/> + </when> + <when value="-O -M"> + <param name="fraction" + type="boolean" + truevalue="--fraction" + falsevalue="" + argument="--fraction" + label="Assign fractions to multimapping reads" + 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."/> + </when> </conditional> <param name="mapping_quality"