Mercurial > repos > nml > verify_map
comparison verify_map.xml @ 1:80b7566e62ec draft default tip
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
author | nml |
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date | Tue, 23 Jun 2020 10:28:13 -0400 |
parents | 12f1714f7716 |
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0:12f1714f7716 | 1:80b7566e62ec |
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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> |