Mercurial > repos > iuc > featurecounts
comparison featurecounts.xml @ 27:ce44c6f2ba38 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2db6daac834eea9b88388aed840d484544f0786"
author | iuc |
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date | Tue, 13 Jul 2021 12:14:05 +0000 |
parents | ea04b737afa0 |
children | 7db9d3ea71c9 |
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26:ea04b737afa0 | 27:ce44c6f2ba38 |
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1 <tool id="featurecounts" name="featureCounts" version="2.0.1" profile="16.04"> | 1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
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> | |
4 <token name="@TOOL_VERSION@">2.0.1</token> | |
5 <token name="@VERSION_SUFFIX@">1</token> | |
6 </macros> | |
7 | |
3 <requirements> | 8 <requirements> |
4 <requirement type="package" version="2.0.1">subread</requirement> | 9 <requirement type="package" version="@TOOL_VERSION@">subread</requirement> |
5 <requirement type="package" version="1.11">samtools</requirement> | 10 <requirement type="package" version="1.11">samtools</requirement> |
6 <requirement type="package" version="8.31">coreutils</requirement> | 11 <requirement type="package" version="8.31">coreutils</requirement> |
7 </requirements> | 12 </requirements> |
8 | 13 |
9 <version_command>featureCounts -v 2>&1 | grep .</version_command> | 14 <version_command>featureCounts -v 2>&1 | grep .</version_command> |
118 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": | 123 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": |
119 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}' | 124 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}' |
120 #end if | 125 #end if |
121 | 126 |
122 #if $extended_parameters.R: | 127 #if $extended_parameters.R: |
123 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam | 128 && samtools sort --no-PG -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam |
124 #end if | 129 #end if |
125 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}' | 130 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}' |
126 ]]></command> | 131 ]]></command> |
127 <inputs> | 132 <inputs> |
128 <param name="alignment" | 133 <param name="alignment" |