| Previous changeset 29:38b6d12edc68 (2021-12-04) Next changeset 31:6f66ae7c5f7a (2023-03-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1 |
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modified:
featurecounts.xml |
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| diff -r 38b6d12edc68 -r a56fbe2d6ba7 featurecounts.xml --- a/featurecounts.xml Sat Dec 04 22:18:02 2021 +0000 +++ b/featurecounts.xml Fri Feb 24 14:02:04 2023 +0000 |
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| b'@@ -1,23 +1,26 @@\n-<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">\n+<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">\n <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>\n <macros>\n- <token name="@TOOL_VERSION@">2.0.1</token>\n- <token name="@VERSION_SUFFIX@">2</token>\n+ <token name="@TOOL_VERSION@">2.0.3</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+\n+ <macro name="conditional_gff_opions">\n+ <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."/>\n+ <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\'."/>\n+ <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."/>\n+ </macro>\n </macros>\n <xrefs>\n- <xref type="bio.tools">subread</xref>\n+ <xref type="bio.tools">featurecounts</xref>\n </xrefs>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">subread</requirement>\n- <requirement type="package" version="1.11">samtools</requirement>\n- <requirement type="package" version="8.31">coreutils</requirement>\n+ <requirement type="package" version="1.16.1">samtools</requirement>\n </requirements>\n \n <version_command>featureCounts -v 2>&1 | grep .</version_command>\n <command detect_errors="exit_code"><![CDATA[\n-\n ## Export fc path for its built-in annotation\n-\n export FC_PATH=\\$(command -v featureCounts | sed \'s@/bin/featureCounts$@@\') &&\n \n ## Check whether all alignments are from the same type (bam || sam)\n@@ -27,7 +30,7 @@\n -a \'$anno.reference_gene_sets\'\n -F "GTF"\n #elif $anno.anno_select=="cached":\n- -a \'$anno.reference_gene_sets_builtin.fields.path\'\n+ -a \'$anno.reference_gene_sets_cached.fields.path\'\n -F "GTF"\n #elif $anno.anno_select=="builtin":\n -a \\${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt\n@@ -44,23 +47,17 @@\n $read_filtering_parameters.primary\n $read_filtering_parameters.ignore_dup\n \n- -t \'$extended_parameters.gff_feature_type\'\n- -g \'$extended_parameters.gff_feature_attribute\'\n- $extended_parameters.summarization_level\n+ #if $anno.anno_select!="builtin":\n+ -t \'$anno.gff_feature_type\'\n+ -g \'$anno.gff_feature_attribute\'\n+ $anno.summarization_level\n+ #end if\n \n $extended_parameters.multifeatures.multifeat\n #if $extended_parameters.multifeatures.multifeat != "":\n $extended_parameters.multifeatures.fraction\n #end if\n \n-\n- ## $extended_parameters.contribute_to_multiple_'..b' ftype="gff" dbkey="hg38"/>\n+ <param name="format" value="tabdel_short"/>\n <param name="include_feature_length_file" value="true"/>\n <param name="count_exon_exon_junction_reads" value="-J"/>\n <output name="output_short" file="output_1_short.tab">\n@@ -544,11 +534,14 @@\n </test>\n <!-- Ensure featureCounts built-in annotation works -->\n <test expect_num_outputs="3">\n- <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" />\n+ <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/>\n <param name="anno_select" value="builtin"/>\n- <param name="format" value="tabdel_short" />\n+ <param name="format" value="tabdel_short"/>\n+ <conditional name="pe_parameters">\n+ <param name="paired_end_status" value="PE_individual"/>\n+ </conditional>\n <section name="extended_parameters">\n- <param name="R" value="true" />\n+ <param name="R" value="true"/>\n </section>\n <output name="output_short" file="output_builtin_hg19.tab">\n <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>\n@@ -558,9 +551,9 @@\n </test>\n <!-- Ensure cached GTFs work -->\n <test expect_num_outputs="3">\n- <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />\n+ <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>\n <param name="anno_select" value="cached"/>\n- <param name="format" value="tabdel_medium" />\n+ <param name="format" value="tabdel_medium"/>\n <param name="include_feature_length_file" value="true"/>\n <output name="output_medium" file="output_1_medium.tab">\n <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>\n@@ -571,11 +564,11 @@\n </test>\n <!-- Ensure BAM output works -->\n <test>\n- <param name="alignment" value="subset.sorted.bam" ftype="bam" />\n- <param name="anno_select" value="history" />\n- <param name="reference_gene_sets" value="small.gtf" ftype="gtf" />\n- <section name="extended_parameters" >\n- <param name="R" value="true" />\n+ <param name="alignment" value="subset.sorted.bam" ftype="bam"/>\n+ <param name="anno_select" value="history"/>\n+ <param name="reference_gene_sets" value="small.gtf" ftype="gtf"/>\n+ <section name="extended_parameters">\n+ <param name="R" value="true"/>\n </section>\n <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>\n </test>\n@@ -609,8 +602,8 @@\n GeneID Chr Start End Strand\n ====== ==== ======= ======= ======\n 497097 chr1 3204563 3207049 -\n- 497097 chr1 3411783 3411982 -\n- 497097 chr1 3660633 3661579 -\n+ 497098 chr1 3411783 3411982 -\n+ 497099 chr1 3660633 3661579 -\n ====== ==== ======= ======= ======\n \n 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.\n@@ -627,3 +620,4 @@\n <citation type="doi">10.1093/bioinformatics/btt656</citation>\n </citations>\n </tool>\n+\n' |