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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
author nml
date Tue, 23 Jun 2020 10:28:13 -0400
parents 12f1714f7716
children
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0:12f1714f7716 1:80b7566e62ec
1 <tool id="verify_map" name="Verify Mapping Quality" version="1.8.2"> 1 <tool id="verify_map" name="Verify Mapping Quality" version="@VERSION@+galaxy1">
2 <description>Checks the mapping quality of all BAM files generated in the core SNV pipeline.</description> 2 <description>Checks the mapping quality of all BAM files generated in the core SNV pipeline.</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.8.2">snvphyl-tools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
7 verify_mapping_quality.pl 8 verify_mapping_quality.pl
8 #for $f in $bams.keys# --bam "$f=$bams[$f]" #end for# 9 #for $f in $bams.keys# --bam "$f=$bams[$f]" #end for#
9 #if $mindepth : 10 #if $mindepth :
10 --min-depth $mindepth 11 --min-depth $mindepth
58 **Options** 59 **Options**
59 - min-depth - The minimum depth of coverage required in each BAM file. 60 - min-depth - The minimum depth of coverage required in each BAM file.
60 - min-map - The minimum perecent coverage required in each BAM file. 61 - min-map - The minimum perecent coverage required in each BAM file.
61 62
62 </help> 63 </help>
63 <citations/> 64 <expand macro="citations"/>
64 </tool> 65 </tool>