Mercurial > repos > iuc > featurecounts
comparison featurecounts.xml @ 12:e270d0978616 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 5c013729eeb48f723f7d436c4ded998c8d9291eb
| author | iuc |
|---|---|
| date | Mon, 07 May 2018 06:21:38 -0400 |
| parents | d0beb2753aba |
| children | c7085a3028ef |
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| 11:d0beb2753aba | 12:e270d0978616 |
|---|---|
| 1 <tool id="featurecounts" name="featureCounts" version="1.6.0.3" profile="16.04"> | 1 <tool id="featurecounts" name="featureCounts" version="1.6.0.4" 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 |
| 130 <param name="alignment" | 130 <param name="alignment" |
| 131 type="data" | 131 type="data" |
| 132 multiple="false" | 132 multiple="false" |
| 133 format="bam,sam" | 133 format="bam,sam" |
| 134 label="Alignment file" | 134 label="Alignment file" |
| 135 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. These files must have the database/genome attribute already specified e.g. hg38, not the default: ?" > | 135 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: ?" > |
| 136 <validator type="unspecified_build"/> | |
| 137 </param> | 136 </param> |
| 138 | 137 |
| 139 <conditional name="anno"> | 138 <conditional name="anno"> |
| 140 <param name="anno_select" type="select" label="Gene annotation file"> | 139 <param name="anno_select" type="select" label="Gene annotation file"> |
| 141 <option value="builtin">featureCounts built-in</option> | 140 <option value="builtin">featureCounts built-in</option> |
| 161 <param name="reference_gene_sets" | 160 <param name="reference_gene_sets" |
| 162 format="gff,gtf,gff3" | 161 format="gff,gtf,gff3" |
| 163 type="data" | 162 type="data" |
| 164 label="Gene annotation file" | 163 label="Gene annotation file" |
| 165 help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment"> | 164 help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment"> |
| 166 <options> | |
| 167 <filter type="data_meta" key="dbkey" ref="alignment"/> | |
| 168 </options> | |
| 169 <validator type="no_options" message="The current history does not include a dataset with the build associated with the selected input file"/> | |
| 170 </param> | 165 </param> |
| 171 </when> | 166 </when> |
| 172 </conditional> | 167 </conditional> |
| 173 | 168 |
| 174 <param name="format" | 169 <param name="format" |