Mercurial > repos > scottx611x > qualimap2_bamqc
changeset 2:5b36882f6455 draft
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
| author | scottx611x |
|---|---|
| date | Wed, 25 Jul 2018 11:32:53 -0400 |
| parents | 716e406ce6ea |
| children | c9afc13316ec |
| files | qualimap_bamqc.py qualimap_bamqc.xml |
| diffstat | 2 files changed, 6 insertions(+), 10 deletions(-) [+] |
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--- a/qualimap_bamqc.py Wed Jul 25 10:59:11 2018 -0400 +++ b/qualimap_bamqc.py Wed Jul 25 11:32:53 2018 -0400 @@ -28,7 +28,7 @@ description="Generate Bam Quality Statistics" ) parser.add_argument('--input_file') - parser.add_argument('--out_genome_file', default="genome_results.txt") + parser.add_argument('--out_genome_file', default="genome_coverage.txt") parser.add_argument('--out_dir') parser.add_argument('--java_mem_size', default="8G")
--- a/qualimap_bamqc.xml Wed Jul 25 10:59:11 2018 -0400 +++ b/qualimap_bamqc.xml Wed Jul 25 11:32:53 2018 -0400 @@ -11,7 +11,6 @@ <command interpreter="python"> qualimap_bamqc.py --input_file $input_realigned_bam_file - --out_genome_file $genome_results --out_dir qualimap_results --java_mem_size $mem_size </command> @@ -23,6 +22,7 @@ <data format="txt" name="genome_results" label="Qualimap BamQC report"> <discover_datasets pattern="genome_results*" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/> </data> + <data format="txt" name="genome_coverage" label="Qualimap BamQC coverage report"></data> <data format="html" name="qualimap_html_results" label="Qualimap BamQC HTML report"> <discover_datasets pattern="qualimapReport*" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/> </data> @@ -31,15 +31,11 @@ <tests> <test> <param name="input_realigned_bam_file" value="test.bam"></param> - <output name="genome_results"> - <assert_contents> - <has_text text="BamQC report" /> - </assert_contents> + <output name="genome_results" file="genome_results.txt" ftype="txt"> </output> - <output name="qualimap_html_results"> - <assert_contents> - <has_text text="Qualimap report: BAM QC" /> - </assert_contents> + <output name="genome_coverage" file="genome_coverage.txt" ftype="txt"> + </output> + <output name="qualimap_html_results" file="qualimapReport.html" ftype="html"> </output> </test> </tests>