Mercurial > repos > iuc > qualimap_rnaseq

comparison qualimap_rnaseq.xml @ 1:ce0da6c9f49e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
author iuc
date Tue, 29 Oct 2019 09:14:03 -0400
parents 613e6446ea5d
children 35e00077ba61
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0:613e6446ea5d 1:ce0da6c9f49e
1 <tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" version="@VERSION@"> 1 <tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" version="@VERSION@+galaxy1">
2 <macros> 2 <macros>
3 <import>qualimap_macros.xml</import> 3 <import>qualimap_macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="requirements" /> 5 <expand macro="requirements" />
6 <expand macro="version_command" /> 6 <expand macro="version_command" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @SET_JAVA_OPTS@ && 8 @SET_JAVA_OPTS@ &&
9 9
10 ## Have qualimap detect file format by suffix
11 ## since its autodetection is unreliable.
12 ln -s '$features' features.gtf &&
13
10 qualimap rnaseq 14 qualimap rnaseq
11 -bam '${seq_info.input}' 15 -bam '${seq_info.input}'
12 -gtf '$features' 16 -gtf features.gtf
13 ${seq_info.treat_as_pe} 17 ${seq_info.treat_as_pe}
14 ${seq_info.sorted} 18 ${seq_info.sorted}
15 ${counts_out.report_counts} 19 ${counts_out.report_counts}
16 --sequencing-protocol ${read_filtering.library_type} 20 --sequencing-protocol ${read_filtering.library_type}
17 --algorithm ${read_filtering.treat_multimappers} 21 --algorithm ${read_filtering.treat_multimappers}