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comparison featurecounts.xml @ 24:dfa29fefb36a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:36:53 -0400
parents 944deba3eb6a
children 9f24599f93e5
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23:944deba3eb6a 24:dfa29fefb36a
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"