Mercurial > repos > scottx611x > qualimap2_bamqc
changeset 42:c53375e61b33 draft
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 9fafbbc012490e70d06fcef4704a1e4a45b382c5-dirty
author | scottx611x |
---|---|
date | Sun, 29 Jul 2018 13:53:35 -0400 |
parents | e856fda6f375 |
children | 2395818cb1f1 |
files | qualimap_bamqc.py qualimap_bamqc.xml |
diffstat | 2 files changed, 6 insertions(+), 30 deletions(-) [+] |
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--- a/qualimap_bamqc.py Fri Jul 27 11:53:29 2018 -0400 +++ b/qualimap_bamqc.py Sun Jul 29 13:53:35 2018 -0400 @@ -7,11 +7,10 @@ import sys -def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size): +def qualimap_bamqc(bam_filename, out_dir, jv_mem_size): qualimap_command = [ "qualimap", "bamqc", "-bam " + bam_filename, - "-oc " + genomecov_file, "-outdir " + out_dir, "--java-mem-size=" + jv_mem_size ] @@ -27,11 +26,9 @@ description="Generate Bam Quality Statistics" ) parser.add_argument('--input_file') - parser.add_argument('--out_genome_file') parser.add_argument('--out_dir') parser.add_argument('--out_zip') parser.add_argument('--out_html') - parser.add_argument('--out_results') parser.add_argument('--java_mem_size') args = parser.parse_args() @@ -39,7 +36,6 @@ qualimap_bamqc( args.input_file, - args.out_genome_file, args.out_dir, args.java_mem_size ) @@ -47,7 +43,7 @@ shutil.make_archive( 'raw_data_qualimapReport', 'zip', - os.path.join(args.out_dir,'raw_data_qualimapReport') + os.path.join(args.out_dir, 'raw_data_qualimapReport') ) shutil.move("raw_data_qualimapReport.zip", args.out_zip) @@ -55,10 +51,6 @@ os.path.join(args.out_dir, "genome_results.txt"), args.out_results ) - shutil.move( - os.path.join(args.out_dir, "qualimapReport.html"), - args.out_html - ) if __name__ == "__main__": main()
--- a/qualimap_bamqc.xml Fri Jul 27 11:53:29 2018 -0400 +++ b/qualimap_bamqc.xml Sun Jul 29 13:53:35 2018 -0400 @@ -12,9 +12,7 @@ qualimap_bamqc.py --input_file $input_realigned_bam_file --out_dir qualimap_results - --out_genome_file $genome_coverage --out_zip $raw_data_qualimapReport - --out_html $qualimapReport --out_results $genome_results --java_mem_size $mem_size </command> @@ -23,35 +21,21 @@ <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/> </inputs> <outputs> - <data format="txt" name="genome_coverage" label="Qualimap BamQC Coverage Report for: ${on_string}"></data> - <data format="txt" name="genome_results" label="Qualimap BamQC Results for: ${on_string}"></data> - <data format="html" name="qualimapReport" label="Qualimap BamQC HTML Report for: ${on_string}"></data> - <data format="zip" name="raw_data_qualimapReport" label="Qualimap Raw Data Results for: ${on_string}"></data> + <data format="txt" name="genome_results" label="Qualimap BamQC Results for: ${input_realigned_bam_file}"></data> + <data format="zip" name="raw_data_qualimapReport" label="Qualimap Raw Data Results for: ${input_realigned_bam_file}"></data> </outputs> <tests> <test> <param name="mem_size" value="2G"></param> <param name="input_realigned_bam_file" value="test.bam"></param> - <output name="genome_coverage"> - <assert_contents> - <has_text text="#chr pos coverage" /> - </assert_contents> - </output> <output name="genome_results"> <assert_contents> <has_text text="BamQC report" /> </assert_contents> </output> - <output name="qualimapReport"> - <assert_contents> - <has_text text="Qualimap Report: BAM QC" /> - </assert_contents> - </output> - <output name="qualimap_raw_data_results"> - <assert_contents> - <has_text text="" /> - </assert_contents> + <output name="raw_data_qualimapReport" ftype="zip"> + <metadata name="name" value="raw_data_qualimapReport.zip" /> </output> </test> </tests>