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comparison featurecounts.xml @ 23:944deba3eb6a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d
author iuc
date Thu, 06 Jun 2019 17:53:42 -0400
parents 819225afd6b3
children dfa29fefb36a
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22:819225afd6b3 23:944deba3eb6a
1 <tool id="featurecounts" name="featureCounts" version="1.6.3+galaxy2" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.4" 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="1.6.3">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="8.30">coreutils</requirement> 6 <requirement type="package" version="8.31">coreutils</requirement>
7 </requirements> 7 </requirements>
8 8
9 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command> 9 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 11
295 <when value="" /> 295 <when value="" />
296 </conditional> 296 </conditional>
297 297
298 <param name="mapping_quality" 298 <param name="mapping_quality"
299 type="integer" 299 type="integer"
300 value="12" 300 value="0"
301 argument="-Q" 301 argument="-Q"
302 label="Minimum mapping quality per read" 302 label="Minimum mapping quality per read"
303 help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 12 by default." /> 303 help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." />
304 304
305 <conditional name="exon_exon_junction_read_counting_enabled"> 305 <conditional name="exon_exon_junction_read_counting_enabled">
306 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue="" 306 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
307 label="Exon-exon junctions" 307 label="Exon-exon junctions"
308 help="If specified, reads supporting each exon-exon junction will be counted" /> 308 help="If specified, reads supporting each exon-exon junction will be counted" />