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

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

<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
	      	#end if

                --cores \${GALAXY_SLOTS:-1}

      		#if $minmap :
        	--min-map $minmap
	      	#end if
		> $output_log
	</command>

	<inputs>
		<param name="bams" type="data_collection" label="Collect of BAM files" format="bam" />
		<param name="mindepth" type="integer" label="The minimum depth of coverage required in each BAM file." format="" optional="true" />
		<param name="minmap" type="integer" label="The minimum percent coverage required in each BAM file." format="" optional="true" />
	</inputs>

	<outputs>
		<data format="txt" name="output_log" from_work_dir="mapping_percentage.log" label="Mapping Percentage Log"/>
	</outputs>

	<tests>
		<test>
			<param name="bams">
				<collection type="list">
					<element name="s1" value="sample1.bam"/>
					<element name="s2" value="sample2.bam"/>
					<element name="s4" value="sample4.bam"/>
				</collection>
			</param>
			<output name="output_log" file="test_percent_log.txt" ftype="txt"/>
		</test>
	</tests>

	<help>
What it does
============

This script checks the mapping quality of all BAM files generated from the SNVPhyl pipeline.


Usage
=====

**Parameters**
  - input - The collection of BAM files in the dataset.


**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>