Mercurial > repos > scottx611x > qualimap2_bamqc
comparison qualimap_bamqc.py @ 35:a3e9c80894dd draft
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
| author | scottx611x |
|---|---|
| date | Thu, 26 Jul 2018 16:55:10 -0400 |
| parents | 7e359370b5a2 |
| children | 0e6aeed62025 |
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| 34:7e359370b5a2 | 35:a3e9c80894dd |
|---|---|
| 33 parser.add_argument('--out_dir') | 33 parser.add_argument('--out_dir') |
| 34 parser.add_argument('--java_mem_size') | 34 parser.add_argument('--java_mem_size') |
| 35 | 35 |
| 36 args = parser.parse_args() | 36 args = parser.parse_args() |
| 37 | 37 |
| 38 print(os.listdir(args.out_dir)) | |
| 39 | |
| 40 qualimap_bamqc( | 38 qualimap_bamqc( |
| 41 args.input_file, | 39 args.input_file, |
| 42 args.out_genome_file, | 40 args.out_genome_file, |
| 43 args.out_dir, | 41 args.out_dir, |
| 44 args.java_mem_size | 42 args.java_mem_size |
| 45 ) | 43 ) |
| 44 | |
| 45 print(os.listdir(args.out_dir)) | |
| 46 | 46 |
| 47 shutil.move(args.out_dir + "/genome_results.txt", "./genome_results.txt") | 47 shutil.move(args.out_dir + "/genome_results.txt", "./genome_results.txt") |
| 48 shutil.move(args.out_dir + "/qualimapReport.html", "./qualimapReport.html") | 48 shutil.move(args.out_dir + "/qualimapReport.html", "./qualimapReport.html") |
| 49 shutil.make_archive( | 49 shutil.make_archive( |
| 50 './raw_data_qualimapReport', | 50 './raw_data_qualimapReport', |