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comparison featurecounts.xml @ 18:34b78acbad1d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
author iuc
date Wed, 04 Jul 2018 17:32:31 -0400
parents 5c20eb47f759
children 834c6a106740
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17:5c20eb47f759 18:34b78acbad1d
1 <tool id="featurecounts" name="featureCounts" version="1.6.0.7" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.1.0" 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="1.6.0">subread</requirement> 4 <requirement type="package" version="1.6.1">subread</requirement>
5 <requirement type="package" version="1.7">samtools</requirement> 5 <requirement type="package" version="1.7">samtools</requirement>
6 </requirements> 6 </requirements>
7 7
8 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command> 8 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
543 </output> 543 </output>
544 <output name="output_summary" file="output_1_summary.tab"> 544 <output name="output_summary" file="output_1_summary.tab">
545 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> 545 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
546 </output> 546 </output>
547 </test> 547 </test>
548 <!-- Ensure BAM output works -->
549 <test>
550 <param name="alignment" value="subset.sorted.bam" ftype="bam" />
551 <param name="anno_select" value="history" />
552 <param name="reference_gene_sets" value="small.gtf" ftype="gtf" />
553 <section name="extended_parameters" >
554 <param name="R" value="true" />
555 </section>
556 <output name="output_bam" value="subset.sorted.featurecounts.bam" />
557 </test>
548 </tests> 558 </tests>
549 559
550 <help><![CDATA[ 560 <help><![CDATA[
551 featureCounts 561 featureCounts
552 ############# 562 #############