Wrapper.py #7
Wrapper.py #7
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| parser.add_argument('-if', '--inc-fr', help='including fr1. Default = - ', default="-") | ||
| parser.add_argument('func_filter', help='functionality filter input. Options: productive, unproductive, ' | ||
| 'remove_unknown') | ||
| parser.add_argument('unique', help='Options: "VGene,CDR3.IMGT.AA,best_match_class", "VGene,CDR3.IMGT.AA", ' |
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Argparse has a choices option that allows you to set strictly available options. These should be available in the help output.
| parser.add_argument('-noe', '--naive-output-ce', help=' input naive ce: options path to output history ', default='XXX') | ||
| parser.add_argument('-nol', '--naive-output-all', help=' input naive all: options path to output history ', | ||
| default='XXX') | ||
| parser.add_argument('filter_unique', help='input for unique filter. Options: remove, remove_vjaa, keep, no') |
| default='XXX') | ||
| parser.add_argument('filter_unique', help='input for unique filter. Options: remove, remove_vjaa, keep, no') | ||
| parser.add_argument('-uc', '--unique-count', help='input for the unique count. Default=2', default='2') | ||
| parser.add_argument('class_filter', help='input for class filter. Options: 70_70, 60_55, 70_0, 60_0, 19_0, ' |
| parser.add_argument('class_filter', help='input for class filter. Options: 70_70, 60_55, 70_0, 60_0, 19_0, ' | ||
| '101_101 ') | ||
| parser.add_argument('region_filter', help='input for region filter. Options: leader, CDR1, FR1, FR2') | ||
| parser.add_argument('-fa', '--fast', help='input fast process. input: yes, no. Default=no', default='no') |
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This is a boolean flag. Look at the argparse documentation for store_true or store_const. This way you can use --fast to set the argument to 'yes' or 'no' without using --fast no.
| '"productive CDR3.IMGT.AA,best_match_class", "CDR3.IMGT.AA", "VGene,' | ||
| 'CDR3.IMGT.seq,best_match_class", "VGene,CDR3.IMGT.seq",' | ||
| ' "CDR3.IMGT.seq,best_match_class", "CDR3.IMGT.seq", Sequence.ID ') | ||
| parser.add_argument('-no', '--naive-output', help='New IMGT archives per class in history. Option: no, yes. Default=no', |
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See comment below about storing constants and boolean flags.
| parser.add_argument('result_html', help='Path of the output file') | ||
| parser.add_argument('result_dir', help='Path where the results will be stored') | ||
| parser.add_argument('title', help='Specify the title for the run') | ||
| parser.add_argument('-if', '--inc-fr', help='including fr1. Default = - ', default="-") |
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What are the available options here? Were you able to figure that out?
It looks like it has something to do with the inclusion of the FR1 region.
Maybe this is an argument that is skipped in wrapper.sh? Not all arguments are used I think.
| args = parser.parse_args() | ||
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| subprocess.call(["bash", "wrapper.sh", args.input, args.method, args.result_html, args.result_dir, |
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"wrapper.sh" Might not be in the current working directory. If galaxy executes the tool it is not, because the working directory is separate from the output directory. You need to find a way to always execute the wrapper.sh script that is in the same directory as this wrapper.py script.
calling wrapper.sh with:
bash wrapper.sh tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz custom $PWD/results/output.html $PWD/results "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz" "-" productive Sequence.ID no XXXX XXXX XXXX XXXX XXXX remove 2 70_70 FR1 no
can now be done using wrapper.py and folowwing input:
python wrapper.py tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz $PWD/results/output.html $PWD/results "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz" productive Sequence.ID remove 70_70 FR1