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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
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32:f9d49f5cb597 33:1b851f87fbe0
1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> 1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> 2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.0.3</token> 4 <token name="@TOOL_VERSION@">2.0.6</token>
5 <token name="@VERSION_SUFFIX@">2</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 6
7 <macro name="conditional_gff_opions"> 7 <macro name="conditional_gff_opions">
8 <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."/> 8 <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."/>
9 <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 &quot;ENSG00000223972&quot;; gene_name &quot;DDX11L1&quot; gene_source &quot;havana&quot;' (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'."/> 9 <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 &quot;ENSG00000223972&quot;; gene_name &quot;DDX11L1&quot; gene_source &quot;havana&quot;' (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'."/>
10 <param name="summarization_level" type="boolean" truevalue=" -f" falsevalue="" argument="-f" 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."/> 10 <param name="summarization_level" type="boolean" truevalue=" -f" falsevalue="" argument="-f" 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."/>
13 <xrefs> 13 <xrefs>
14 <xref type="bio.tools">featurecounts</xref> 14 <xref type="bio.tools">featurecounts</xref>
15 </xrefs> 15 </xrefs>
16 <requirements> 16 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">subread</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
18 <requirement type="package" version="1.16.1">samtools</requirement> 18 <requirement type="package" version="1.21">samtools</requirement>
19 </requirements> 19 </requirements>
20 20
21 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command> 21 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
22 <command detect_errors="exit_code"><![CDATA[ 22 <command detect_errors="exit_code"><![CDATA[
23 ## Export fc path for its built-in annotation 23 ## Export fc path for its built-in annotation
625 497097 chr1 3204563 3207049 - 625 497097 chr1 3204563 3207049 -
626 497098 chr1 3411783 3411982 - 626 497098 chr1 3411783 3411982 -
627 497099 chr1 3660633 3661579 - 627 497099 chr1 3660633 3661579 -
628 ====== ==== ======= ======= ====== 628 ====== ==== ======= ======= ======
629 629
630 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. 630 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.
631 631
632 Output format 632 Output format
633 ------------- 633 -------------
634 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. 634 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.
635 635
636 .. _Subread: http://subread.sourceforge.net/ 636 .. _Subread: http://subread.sourceforge.net/
637 .. _`Subread User's Guide`: https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf 637 .. _`Subread User's Guide`: https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf
638 .. _`Subread package`: https://sourceforge.net/projects/subread/files/
639 ]]></help> 638 ]]></help>
640 <citations> 639 <citations>
641 <citation type="doi">10.1093/bioinformatics/btt656</citation> 640 <citation type="doi">10.1093/bioinformatics/btt656</citation>
642 </citations> 641 </citations>
643 </tool> 642 </tool>