Mercurial > repos > iuc > nanocompore_sampcomp

comparison NanocomporeDB_process.py @ 2:25abc2c72ff9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
author iuc
date Wed, 17 Jun 2020 13:28:27 -0400
parents c43f4b80f5a9
children b833eff63b10
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1:c43f4b80f5a9 2:25abc2c72ff9
36 parser.add_argument('--annotation-bed', required=False, type=is_valid_file, 36 parser.add_argument('--annotation-bed', required=False, type=is_valid_file,
37 help='BED file containing the annotation of the transcriptome used as reference when mapping') 37 help='BED file containing the annotation of the transcriptome used as reference when mapping')
38 parser.add_argument('--pvalue-types', type=str, 38 parser.add_argument('--pvalue-types', type=str,
39 default='GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue', 39 default='GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue',
40 help='path to the annotations') 40 help='path to the annotations')
41 parser.add_argument('--bedgraph', default=False, 41 parser.add_argument('--bedgraph', action="store_true",
42 help='write output in BEDGRAPH format instead of BED') 42 help='write output in BEDGRAPH format instead of BED')
43 parser.add_argument('--pvalue-threshold', default=1.0, 43 parser.add_argument('--pvalue-threshold', default=1.0,
44 help='Maximum reported p-value.') 44 help='Maximum reported p-value.')
45 parser.add_argument('--out-dir', default="./", type=is_valid_directory, 45 parser.add_argument('--out-dir', default="./", type=is_valid_directory,
46 help='path the plotting output directory.') 46 help='path the plotting output directory.')