Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/lib/help/abricate.nf @ 17:0e7a0053e4a6
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 10:42:02 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 // Help text for abricate within CPIPES. |
| kkonganti@17 | 2 |
| kkonganti@17 | 3 def abricateHelp(params) { |
| kkonganti@17 | 4 |
| kkonganti@17 | 5 Map tool = [:] |
| kkonganti@17 | 6 Map toolspecs = [:] |
| kkonganti@17 | 7 tool.text = [:] |
| kkonganti@17 | 8 tool.helpparams = [:] |
| kkonganti@17 | 9 |
| kkonganti@17 | 10 toolspecs = [ |
| kkonganti@17 | 11 'abricate_run': [ |
| kkonganti@17 | 12 clihelp: 'Run ABRicate tool. Default: ' + |
| kkonganti@17 | 13 (params.abricate_run ?: false), |
| kkonganti@17 | 14 cliflag: null, |
| kkonganti@17 | 15 clivalue: null |
| kkonganti@17 | 16 ], |
| kkonganti@17 | 17 'abricate_minid': [ |
| kkonganti@17 | 18 clihelp: 'Minimum DNA %identity. ' + |
| kkonganti@17 | 19 "Default: " + (params.abricate_minid ?: 80), |
| kkonganti@17 | 20 cliflag: '--minid', |
| kkonganti@17 | 21 clivalue: (params.abricate_minid ?: 80) |
| kkonganti@17 | 22 ], |
| kkonganti@17 | 23 'abricate_mincov': [ |
| kkonganti@17 | 24 clihelp: 'Minimum DNA %coverage. ' + |
| kkonganti@17 | 25 "Default: " + (params.abricate_mincov ?: 80), |
| kkonganti@17 | 26 cliflag: '--mincov', |
| kkonganti@17 | 27 clivalue: (params.abricate_mincov ?: 80) |
| kkonganti@17 | 28 ], |
| kkonganti@17 | 29 'abricate_datadir': [ |
| kkonganti@17 | 30 clihelp: 'ABRicate databases folder. ' + |
| kkonganti@17 | 31 "Default: " + (params.abricate_datadir ?: 'undefined'), |
| kkonganti@17 | 32 cliflag: '--datadir', |
| kkonganti@17 | 33 clivalue: (params.abricate_datadir ?: '') |
| kkonganti@17 | 34 ] |
| kkonganti@17 | 35 ] |
| kkonganti@17 | 36 |
| kkonganti@17 | 37 toolspecs.each { |
| kkonganti@17 | 38 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@17 | 39 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@17 | 40 } |
| kkonganti@17 | 41 |
| kkonganti@17 | 42 return tool |
| kkonganti@17 | 43 } |