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comparison featurecounts.xml @ 33:dad3302e7b34 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
author iuc
date Thu, 02 Mar 2023 12:50:37 +0000
parents 456cc2927264
children 12b3317716d3
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32:456cc2927264 33:dad3302e7b34
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@">2.0.3</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</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."/>
89 -p 89 -p
90 $pe_parameters.only_both_ends 90 $pe_parameters.only_both_ends
91 $pe_parameters.exclude_chimerics 91 $pe_parameters.exclude_chimerics
92 #if str($pe_parameters.paired_end_status) == "PE_fragments": 92 #if str($pe_parameters.paired_end_status) == "PE_fragments":
93 --countReadPairs 93 --countReadPairs
94 #if $pe_parameters.check_distance_enabled.checkFragLength: 94 #if $pe_parameters.check_distance_enabled.checkFragLength == "true":
95 --checkFragLength 95 --checkFragLength
96 --minFragLength $pe_parameters.check_distance_enabled.minimum_fragment_length 96 --minFragLength $pe_parameters.check_distance_enabled.minimum_fragment_length
97 --maxFragLength $pe_parameters.check_distance_enabled.maximum_fragment_length 97 --maxFragLength $pe_parameters.check_distance_enabled.maximum_fragment_length
98 #end if 98 #end if
99 #end if 99 #end if
547 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 547 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
548 </output> 548 </output>
549 <output name="output_summary" file="output_summary_builtin_hg19.tab"/> 549 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
550 <output name="output_bam" file="output.bam" ftype="bam"/> 550 <output name="output_bam" file="output.bam" ftype="bam"/>
551 </test> 551 </test>
552 <!-- Ensure fragment counting works -->
553 <test expect_num_outputs="3">
554 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/>
555 <param name="anno_select" value="builtin"/>
556 <param name="format" value="tabdel_short"/>
557 <conditional name="pe_parameters">
558 <param name="paired_end_status" value="PE_fragments"/>
559 </conditional>
560 <section name="extended_parameters">
561 <param name="R" value="true"/>
562 </section>
563 <output name="output_short" file="output_builtin_hg19_fragment.tab">
564 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
565 </output>
566 <output name="output_summary" file="output_summary_builtin_hg19_fragments.tab"/>
567 <output name="output_bam" file="output_fragments.bam" ftype="bam"/>
568 </test>
552 <!-- Ensure cached GTFs work --> 569 <!-- Ensure cached GTFs work -->
553 <test expect_num_outputs="3"> 570 <test expect_num_outputs="3">
554 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> 571 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>
555 <param name="anno_select" value="cached"/> 572 <param name="anno_select" value="cached"/>
556 <param name="format" value="tabdel_medium"/> 573 <param name="format" value="tabdel_medium"/>