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comparison featurecounts.xml @ 28:db82f928d25e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2db6daac834eea9b88388aed840d484544f0786"
author iuc
date Tue, 13 Jul 2021 12:13:34 +0000
parents 55cdfc5bb826
children 3cd88f5c9d4c
comparison
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27:55cdfc5bb826 28:db82f928d25e
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&gt;&amp;1 | grep .</version_command> 14 <version_command>featureCounts -v 2&gt;&amp;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"