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comparison featurecounts.xml @ 24:a37612abf7f9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08"
author iuc
date Fri, 06 Sep 2019 11:08:21 -0400
parents 9301937c9037
children 90d16db017d7
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23:9301937c9037 24:a37612abf7f9
1 <tool id="featurecounts" name="featureCounts" version="1.6.4" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy1" 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="1.6.4">subread</requirement> 4 <requirement type="package" version="1.6.4">subread</requirement>
5 <requirement type="package" version="1.9">samtools</requirement> 5 <requirement type="package" version="1.9">samtools</requirement>
6 <requirement type="package" version="8.31">coreutils</requirement> 6 <requirement type="package" version="8.31">coreutils</requirement>
111 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": 111 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
112 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}' 112 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
113 #end if 113 #end if
114 114
115 #if $extended_parameters.R: 115 #if $extended_parameters.R:
116 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} *.featureCounts.bam 116 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
117 #end if 117 #end if
118 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}' 118 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
119 ]]></command> 119 ]]></command>
120 <inputs> 120 <inputs>
121 <param name="alignment" 121 <param name="alignment"
143 <option value="history">in your history</option> 143 <option value="history">in your history</option>
144 </param> 144 </param>
145 <when value="builtin"> 145 <when value="builtin">
146 <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts"> 146 <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
147 <options from_data_table="featurecounts_anno"> 147 <options from_data_table="featurecounts_anno">
148 <filter type="data_meta" key="dbkey" ref="alignment" column="0"/> 148 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
149 </options> 149 </options>
150 </param> 150 </param>
151 </when> 151 </when>
152 <when value="cached"> 152 <when value="cached">
153 <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator"> 153 <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
154 <options from_data_table="gene_sets"> 154 <options from_data_table="gene_sets">
155 <filter type="data_meta" key="dbkey" ref="alignment" column="0"/> 155 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
156 <filter type="sort_by" column="2" />
156 </options> 157 </options>
157 <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/> 158 <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
158 </param> 159 </param>
159 </when> 160 </when>
160 <when value="history"> 161 <when value="history">