Mercurial > repos > nml > verify_map
changeset 1:80b7566e62ec draft default tip
"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 | |
| files | macros.xml verify_map.xml |
| diffstat | 2 files changed, 22 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 23 10:28:13 2020 -0400 @@ -0,0 +1,16 @@ +<macros> + <token name="@VERSION@">1.8.2</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">snvphyl-tools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1099/mgen.0.000116</citation> + <yield/> + </citations> + </xml> +</macros>
--- a/verify_map.xml Tue Aug 27 12:33:47 2019 -0400 +++ b/verify_map.xml Tue Jun 23 10:28:13 2020 -0400 @@ -1,8 +1,9 @@ -<tool id="verify_map" name="Verify Mapping Quality" version="1.8.2"> +<tool id="verify_map" name="Verify Mapping Quality" version="@VERSION@+galaxy1"> <description>Checks the mapping quality of all BAM files generated in the core SNV pipeline.</description> - <requirements> - <requirement type="package" version="1.8.2">snvphyl-tools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"> verify_mapping_quality.pl #for $f in $bams.keys# --bam "$f=$bams[$f]" #end for# @@ -60,5 +61,5 @@ - min-map - The minimum perecent coverage required in each BAM file. </help> - <citations/> + <expand macro="citations"/> </tool>