comparison verify_map.xml @ 1:80b7566e62ec draft default tip

"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"

0:12f1714f7716

<tool id="verify_map" name="Verify Mapping Quality" version="1.8.2">
	<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>
	<command detect_errors="exit_code">
		verify_mapping_quality.pl
 		#for $f in $bams.keys# --bam "$f=$bams[$f]" #end for#
 		#if $mindepth :
        	--min-depth $mindepth

**Options**
  - min-depth - The minimum depth of coverage required in each BAM file.
  - min-map - The minimum perecent coverage required in each BAM file.

	</help>
	<citations/>
</tool>

1:80b7566e62ec

<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>
	<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#
 		#if $mindepth :
        	--min-depth $mindepth

**Options**
  - min-depth - The minimum depth of coverage required in each BAM file.
  - min-map - The minimum perecent coverage required in each BAM file.

	</help>
	<expand macro="citations"/>
</tool>