Mercurial > repos > iuc > featurecounts
changeset 29:38b6d12edc68 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13"
| author | iuc |
|---|---|
| date | Sat, 04 Dec 2021 22:18:02 +0000 |
| parents | 7db9d3ea71c9 |
| children | a56fbe2d6ba7 |
| files | featurecounts.xml |
| diffstat | 1 files changed, 39 insertions(+), 37 deletions(-) [+] |
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--- a/featurecounts.xml Mon Aug 30 13:47:52 2021 +0000 +++ b/featurecounts.xml Sat Dec 04 22:18:02 2021 +0000 @@ -1,10 +1,12 @@ <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> - <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> + <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> <macros> <token name="@TOOL_VERSION@">2.0.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> - + <xrefs> + <xref type="bio.tools">subread</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">subread</requirement> <requirement type="package" version="1.11">samtools</requirement> @@ -36,6 +38,12 @@ -T \${GALAXY_SLOTS:-2} -s $strand_specificity + + -Q $read_filtering_parameters.mapping_quality + $read_filtering_parameters.splitonly + $read_filtering_parameters.primary + $read_filtering_parameters.ignore_dup + -t '$extended_parameters.gff_feature_type' -g '$extended_parameters.gff_feature_attribute' $extended_parameters.summarization_level @@ -64,14 +72,11 @@ $extended_parameters.by_read_group - -Q $extended_parameters.mapping_quality $extended_parameters.largest_overlap --minOverlap $extended_parameters.min_overlap --fracOverlap $extended_parameters.frac_overlap --fracOverlapFeature $extended_parameters.frac_overlap_feature $extended_parameters.read_reduction - $extended_parameters.primary - $extended_parameters.ignore_dup #if $extended_parameters.R: $extended_parameters.R #end if @@ -256,6 +261,33 @@ help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." /> </section> + <section name="read_filtering_parameters" title="Read filtering options"> + <param name="mapping_quality" + type="integer" + value="0" + argument="-Q" + label="Minimum mapping quality per read" + help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." /> + <param name="splitonly" type="select" display="radio" label="Filter split alignments" help="Split alignments are alignments with CIGAR string containing 'N', e.g. exon spanning reads in RNASeq."> + <option value="">No filtering: count split and non-split alignments</option> + <option value="--splitOnly">Count only split alignments (--splitOnly)</option> + <option value="--nonSplitOnly">Count only non-split alignments (--nonSplitOnly)</option> + </param> + <param type="boolean" + truevalue=" --primary" + falsevalue="" + argument="--primary" + label="Only count primary alignments" + help="If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a dataset will be counted regardless of whether they are from multi-mapping reads or not ('-M' is ignored)." /> + <param name="ignore_dup" + type="boolean" + truevalue=" --ignoreDup" + falsevalue="" + argument="--ignoreDup" + label="Ignore reads marked as duplicate" + help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." /> + </section> + <section name="extended_parameters" title="Advanced options"> <param name="gff_feature_type" type="text" @@ -316,13 +348,6 @@ </when> </conditional> - <param name="mapping_quality" - type="integer" - value="0" - argument="-Q" - label="Minimum mapping quality per read" - help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." /> - <conditional name="exon_exon_junction_read_counting_enabled"> <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue="" label="Exon-exon junctions" @@ -401,22 +426,6 @@ <option value="--read2pos 3">Reduce it to the 3' end</option> </param> - <param name="primary" - type="boolean" - truevalue=" --primary" - falsevalue="" - argument="--primary" - label="Only count primary alignments" - help="If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a dataset will be counted regardless of whether they are from multi-mapping reads or not ('-M' is ignored)." /> - - <param name="ignore_dup" - type="boolean" - truevalue=" --ignoreDup" - falsevalue="" - argument="--ignoreDup" - label="Ignore reads marked as duplicate" - help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." /> - <param type="boolean" truevalue="-R BAM" falsevalue="" @@ -424,13 +433,6 @@ label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)." help="" /> - <param name="count_split_alignments_only" - type="boolean" - truevalue=" --countSplitAlignmentsOnly" - falsevalue="" - argument="--countSplitAlignmentsOnly" - label="Ignore unspliced alignments" - help="If specified, only split alignments (CIGAR strings containing the letter `N') will be counted. All the other alignments will be ignored. An example of split alignments are exon-spanning reads in RNA-seq data." /> </section> </inputs> <outputs> @@ -618,7 +620,7 @@ FeatureCounts produces a table containing counted reads, per gene, per row. Optionally the last column can be set to be the effective gene-length. These tables are compatible with the DESeq2, edgeR and limma-voom Galaxy wrappers by IUC. .. _Subread: http://subread.sourceforge.net/ -.. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf +.. _`Subread User's Guide`: https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf .. _`Subread package`: https://sourceforge.net/projects/subread/files/ ]]></help> <citations>