featurecounts: featurecounts.xml comparison

comparison featurecounts.xml @ 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

comparison

equal deleted inserted replaced

-:7db9d3ea71c9
+:38b6d12edc68
 <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>
 <requirement type="package" version="8.31">coreutils</requirement>
 </requirements>
 -o "output"
 -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
 $extended_parameters.multifeatures.multifeat
 $extended_parameters.long_reads
 $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:
 $extended_parameters.R
 #end if
 #if str($extended_parameters.read_extension_5p) != "0":
 --readExtension5 $extended_parameters.read_extension_5p
 falsevalue=""
 argument="-C"
 checked="true"
 label="Exclude chimeric fragments"
 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"
 label="Assign fractions to both multi-mapping reads and multi-overlapping features"
 help="If specified, a fractional count 1/(x*y) will be generated, where x is the number of alignments (indicated by 'NH' tag) and y the number of overlapping features."/>
 </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"
 help="If specified, reads supporting each exon-exon junction will be counted" />
 <when value="-J">
 <option value="" selected="true">Leave the read as it is</option>
 <option value="--read2pos 5">Reduce it to the 5' end</option>
 <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=""
 argument="-R"
 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>
 <data format="tabular"
 name="output_medium"
 Output format
 -------------
 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>
 <citation type="doi">10.1093/bioinformatics/btt656</citation>
 </citations>

Mercurial > repos > iuc > featurecounts

comparison featurecounts.xml @ 29:38b6d12edc68 draft