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comparison featurecounts.xml @ 14:85aaf50ad9dc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca
author iuc
date Fri, 01 Jun 2018 15:48:47 -0400
parents 386220cf6877
children a8dc8dabf0f3
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13:386220cf6877 14:85aaf50ad9dc
1 <tool id="featurecounts" name="featureCounts" version="1.6.0.5" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.0.6" profile="16.04">
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 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.0">subread</requirement> 4 <requirement type="package" version="1.6.0">subread</requirement>
5 </requirements> 5 </requirements>
6 6
26 #end if 26 #end if
27 27
28 -o "output" 28 -o "output"
29 -T \${GALAXY_SLOTS:-2} 29 -T \${GALAXY_SLOTS:-2}
30 30
31 -s $strand_specificity
31 -t '$extended_parameters.gff_feature_type' 32 -t '$extended_parameters.gff_feature_type'
32 -g '$extended_parameters.gff_feature_attribute' 33 -g '$extended_parameters.gff_feature_attribute'
33 $extended_parameters.summarization_level 34 $extended_parameters.summarization_level
34 $extended_parameters.contribute_to_multiple_features 35 $extended_parameters.contribute_to_multiple_features
35 -s $extended_parameters.strand_specificity
36 $extended_parameters.multimapping_enabled.multimapping_counts 36 $extended_parameters.multimapping_enabled.multimapping_counts
37 37
38 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M": 38 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
39 $extended_parameters.multimapping_enabled.fraction 39 $extended_parameters.multimapping_enabled.fraction
40 #end if 40 #end if
115 type="data" 115 type="data"
116 multiple="false" 116 multiple="false"
117 format="bam,sam" 117 format="bam,sam"
118 label="Alignment file" 118 label="Alignment file"
119 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" > 119 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" >
120 </param>
121
122 <param name="strand_specificity"
123 type="select"
124 label="Specify strand information"
125 argument="-s"
126 help="Indicate if the data is stranded and if strand-specific read counting should be performed. Strand setting must be the same as the strand settings used to produce the mapped BAM input(s)">
127 <option value="0" selected="true">Unstranded</option>
128 <option value="1">Stranded (Forward)</option>
129 <option value="2">Stranded (Reverse)</option>
120 </param> 130 </param>
121 131
122 <conditional name="anno"> 132 <conditional name="anno">
123 <param name="anno_select" type="select" label="Gene annotation file"> 133 <param name="anno_select" type="select" label="Gene annotation file">
124 <option value="builtin">featureCounts built-in</option> 134 <option value="builtin">featureCounts built-in</option>
255 falsevalue="" 265 falsevalue=""
256 argument="-O" 266 argument="-O"
257 label="Allow read to contribute to multiple features" 267 label="Allow read to contribute to multiple features"
258 help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" /> 268 help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" />
259 269
260 <param name="strand_specificity"
261 type="select"
262 label="Strand specificity of the protocol"
263 argument="-s"
264 help="Indicate if strand-specific read counting should be performed.">
265 <option value="0" selected="true">Unstranded</option>
266 <option value="1">Stranded (forwards)</option>
267 <option value="2">Stranded (reverse)</option>
268 </param>
269
270 <conditional name="multimapping_enabled"> 270 <conditional name="multimapping_enabled">
271 <param name="multimapping_counts" 271 <param name="multimapping_counts"
272 type="select" 272 type="select"
273 argument="-M" 273 argument="-M"
274 label="Count multi-mapping reads/fragments" 274 label="Count multi-mapping reads/fragments"
542 Annotations for gene regions should be provided in the GFF/GTF format: 542 Annotations for gene regions should be provided in the GFF/GTF format:
543 543
544 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3 544 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
545 - http://www.ensembl.org/info/website/upload/gff.html 545 - http://www.ensembl.org/info/website/upload/gff.html
546 546
547 Alternatively, the featureCounts built-in annotations for genomes hg38, hg19, mm10 and mm9 can be used through selecting the built-in option above. These 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. 547 Alternatively, the featureCounts built-in annotations for genomes hg38, hg19, mm10 and mm9 can be used through selecting the built-in option above. These annotation files are in simplified annotation format (SAF) as shown below. The GeneID column contains Entrez gene identifiers and each entry (row) is taken as a feature (e.g. an exon).
548
549 Example - **Built-in annotation format**:
550
551 ====== ==== ======= ======= ======
552 GeneID Chr Start End Strand
553 ====== ==== ======= ======= ======
554 497097 chr1 3204563 3207049 -
555 497097 chr1 3411783 3411982 -
556 497097 chr1 3660633 3661579 -
557 ====== ==== ======= ======= ======
558
559 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.
548 560
549 Output format 561 Output format
550 ------------- 562 -------------
551 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. 563 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.
552 564
553 .. _Subread: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf 565 .. _Subread: http://subread.sourceforge.net/
566 .. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
567 .. _`Subread package`: https://sourceforge.net/projects/subread/files/
554 ]]></help> 568 ]]></help>
555 <citations> 569 <citations>
556 <citation type="doi">10.1093/bioinformatics/btt656</citation> 570 <citation type="doi">10.1093/bioinformatics/btt656</citation>
557 </citations> 571 </citations>
558 </tool> 572 </tool>