Mercurial > repos > iuc > featurecounts
changeset 35:30f6985f0ac7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c43e4b51d4b0a46eeba363fa4061d4af03a677a4
| author | iuc |
|---|---|
| date | Wed, 07 May 2025 09:59:27 +0000 |
| parents | 5dbff3a5845a |
| children | |
| files | featurecounts.xml test-data/output.bam test-data/output_1_jcounts.tab test-data/subset.sorted.featurecounts.bam |
| diffstat | 4 files changed, 3 insertions(+), 4 deletions(-) [+] |
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--- a/featurecounts.xml Sun Dec 22 10:55:10 2024 +0000 +++ b/featurecounts.xml Wed May 07 09:59:27 2025 +0000 @@ -1,9 +1,8 @@ -<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> +<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> <macros> - <token name="@TOOL_VERSION@">2.0.8</token> + <token name="@TOOL_VERSION@">2.1.1</token> <token name="@VERSION_SUFFIX@">0</token> - <macro name="conditional_gff_opions"> <param name="gff_feature_type" type="text" value="exon" argument="-t" label="GFF feature type filter" help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default."/> <param name="gff_feature_attribute" type="text" value="gene_id" argument="-g" label="GFF gene identifier" help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization. Ex: if the 9th column is 'gene_id "ENSG00000223972"; gene_name "DDX11L1" gene_source "havana"' (GTF) or 'gene_id=ENSG00000223972; gene_name=DDX11L1; gene_source=havana' (GFF), the available attributes for this feature are 'gene_id', 'gene_name' and 'gene_source'."/>
--- a/test-data/output_1_jcounts.tab Sun Dec 22 10:55:10 2024 +0000 +++ b/test-data/output_1_jcounts.tab Wed May 07 09:59:27 2025 +0000 @@ -1,1 +1,1 @@ -PrimaryGene SecondaryGenes Site1_chr Site1_location Site1_strand Site2_chr Site2_location Site2_strand featureCounts_input1.bam +Gene_SP1 Gene_SP2 Transcript Status Donor Acceptor Chr_SP1 Location_SP1 Strand_SP1 Chr_SP2 Location_SP2 Strand_SP2 NearestExonBoundary_SP1 NearestExonBoundary_SP2 featureCounts_input1.bam