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Featurecounts multioverlap/multialign #3156

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merged 3 commits into from Aug 14, 2020
+45 −30
Merged

Featurecounts multioverlap/multialign #3156

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62f3cea
mods
astrovsky01 Jul 31, 2020
cc553fe
featurecounts multialign and multioverlap
astrovsky01 Aug 10, 2020
a937ee2
version bump
astrovsky01 Aug 10, 2020
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75 tools/featurecounts/featurecounts.xml
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@@ -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>
@@ -34,13 +34,20 @@
-t '$extended_parameters.gff_feature_type'
-g '$extended_parameters.gff_feature_attribute'
$extended_parameters.summarization_level
$extended_parameters.contribute_to_multiple_features
$extended_parameters.multimapping_enabled.multimapping_counts
#if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
$extended_parameters.multimapping_enabled.fraction
$extended_parameters.multifeatures.multifeat
#if $extended_parameters.multifeatures.multifeat != "":
$extended_parameters.multifeatures.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":
#if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:
@@ -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="-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>
<when value="" />
</conditional>

<param name="mapping_quality"