Mercurial > repos > iuc > featurecounts
changeset 33:1b851f87fbe0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit eb563889f227d5c473e2bad2cf9a513e41d03fca
| author | iuc |
|---|---|
| date | Thu, 24 Oct 2024 05:46:38 +0000 |
| parents | f9d49f5cb597 |
| children | 5dbff3a5845a |
| files | featurecounts.xml |
| diffstat | 1 files changed, 4 insertions(+), 5 deletions(-) [+] |
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--- a/featurecounts.xml Sat Sep 09 21:18:37 2023 +0000 +++ b/featurecounts.xml Thu Oct 24 05:46:38 2024 +0000 @@ -1,8 +1,8 @@ <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> <macros> - <token name="@TOOL_VERSION@">2.0.3</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">2.0.6</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."/> @@ -15,7 +15,7 @@ </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">subread</requirement> - <requirement type="package" version="1.16.1">samtools</requirement> + <requirement type="package" version="1.21">samtools</requirement> </requirements> <version_command>featureCounts -v 2>&1 | grep .</version_command> @@ -627,7 +627,7 @@ 497099 chr1 3660633 3661579 - ====== ==== ======= ======= ====== -These annotation files can be found in the `Subread package`_. You can see the version of Subread used by this wrapper in the tool form above under `Options > Requirements`. To create the files, the annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the `Subread User's Guide`_ for more information. Gene names can be obtained for these Entrez identifiers with the Galaxy **annotateMyIDs** tool. +These annotation files can be found in the _`Subread package`_. You can see the version of Subread used by this wrapper in the tool form above under `Options > Requirements`. To create the files, the annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the `Subread User's Guide`_ for more information. Gene names can be obtained for these Entrez identifiers with the Galaxy **annotateMyIDs** tool. Output format ------------- @@ -635,7 +635,6 @@ .. _Subread: http://subread.sourceforge.net/ .. _`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>