Mercurial > repos > kkonganti > hfp_nowayout
annotate 0.5.0/lib/help/sfhpy.nf @ 0:97cd2f532efe
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 31 Mar 2025 14:50:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 // Help text for sourmash_filter_hits.py (sfhpy) within CPIPES. |
| kkonganti@0 | 2 def sfhpyHelp(params) { |
| kkonganti@0 | 3 |
| kkonganti@0 | 4 Map tool = [:] |
| kkonganti@0 | 5 Map toolspecs = [:] |
| kkonganti@0 | 6 tool.text = [:] |
| kkonganti@0 | 7 tool.helpparams = [:] |
| kkonganti@0 | 8 |
| kkonganti@0 | 9 toolspecs = [ |
| kkonganti@0 | 10 'sfhpy_run': [ |
| kkonganti@0 | 11 clihelp: 'Run the sourmash_filter_hits.py ' + |
| kkonganti@0 | 12 'script. Default: ' + |
| kkonganti@0 | 13 (params.sfhpy_run ?: false), |
| kkonganti@0 | 14 cliflag: null, |
| kkonganti@0 | 15 clivalue: null |
| kkonganti@0 | 16 ], |
| kkonganti@0 | 17 'sfhpy_fcn': [ |
| kkonganti@0 | 18 clihelp: 'Column name by which filtering of rows should be applied. ' + |
| kkonganti@0 | 19 "Default: ${params.sfhpy_fcn}", |
| kkonganti@0 | 20 cliflag: '-fcn', |
| kkonganti@0 | 21 clivalue: (params.sfhpy_fcn ?: '') |
| kkonganti@0 | 22 ], |
| kkonganti@0 | 23 'sfhpy_fcv': [ |
| kkonganti@0 | 24 clihelp: 'Remove genomes whose match with the query FASTQ is less than ' + |
| kkonganti@0 | 25 'this much. ' + |
| kkonganti@0 | 26 "Default: ${params.sfhpy_fcv}", |
| kkonganti@0 | 27 cliflag: '-fcv', |
| kkonganti@0 | 28 clivalue: (params.sfhpy_fcv ?: '') |
| kkonganti@0 | 29 ], |
| kkonganti@0 | 30 'sfhpy_gt': [ |
| kkonganti@0 | 31 clihelp: 'Apply greather than or equal to condition on numeric values of ' + |
| kkonganti@0 | 32 '--sfhpy_fcn column. ' + |
| kkonganti@0 | 33 "Default: ${params.sfhpy_gt}", |
| kkonganti@0 | 34 cliflag: '-gt', |
| kkonganti@0 | 35 clivalue: (params.sfhpy_gt ? ' ' : '') |
| kkonganti@0 | 36 ], |
| kkonganti@0 | 37 'sfhpy_lt': [ |
| kkonganti@0 | 38 clihelp: 'Apply less than or equal to condition on numeric values of ' + |
| kkonganti@0 | 39 '--sfhpy_fcn column. ' + |
| kkonganti@0 | 40 "Default: ${params.sfhpy_lt}", |
| kkonganti@0 | 41 cliflag: '-gt', |
| kkonganti@0 | 42 clivalue: (params.sfhpy_lt ? ' ' : '') |
| kkonganti@0 | 43 ], |
| kkonganti@0 | 44 'sfhpy_all': [ |
| kkonganti@0 | 45 clihelp: 'Instead of just the column value, print entire row. ' + |
| kkonganti@0 | 46 "Default: ${params.sfhpy_all}", |
| kkonganti@0 | 47 cliflag: '-all', |
| kkonganti@0 | 48 clivalue: (params.sfhpy_all ? ' ' : '') |
| kkonganti@0 | 49 ], |
| kkonganti@0 | 50 ] |
| kkonganti@0 | 51 |
| kkonganti@0 | 52 toolspecs.each { |
| kkonganti@0 | 53 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@0 | 54 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@0 | 55 } |
| kkonganti@0 | 56 |
| kkonganti@0 | 57 return tool |
| kkonganti@0 | 58 } |