# HG changeset patch
# User nml
# Date 1566923627 14400
# Node ID 12f1714f7716aa4395b85605e80a0e6f9353980c

"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"

diff -r 000000000000 -r 12f1714f7716 test-data/sample1.bam
Binary file test-data/sample1.bam has changed
diff -r 000000000000 -r 12f1714f7716 test-data/sample2.bam
Binary file test-data/sample2.bam has changed
diff -r 000000000000 -r 12f1714f7716 test-data/sample4.bam
Binary file test-data/sample4.bam has changed
diff -r 000000000000 -r 12f1714f7716 test-data/test_percent_log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_percent_log.txt	Tue Aug 27 12:33:47 2019 -0400
@@ -0,0 +1,4 @@
+==========Reference Mapping Quality===========
+NUMBER OF BP's IN REFERENCE GENOME: 48502
+MINIMUM DEPTH: 10
+MINIMUM MAPPING: 80
diff -r 000000000000 -r 12f1714f7716 verify_map.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/verify_map.xml	Tue Aug 27 12:33:47 2019 -0400
@@ -0,0 +1,64 @@
+<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
+	      	#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>
+	<citations/>
+</tool>