Mercurial > repos > nml > verify_map
changeset 0:12f1714f7716 draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
| author | nml |
|---|---|
| date | Tue, 27 Aug 2019 12:33:47 -0400 |
| parents | |
| children | 80b7566e62ec |
| files | test-data/sample1.bam test-data/sample2.bam test-data/sample4.bam test-data/test_percent_log.txt verify_map.xml |
| diffstat | 5 files changed, 68 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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
--- /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>