Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/lib/help/amrfinderplus.nf @ 18:75558ffe3e68
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 11:01:13 -0400 |
| parents | 0e7a0053e4a6 |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 def amrfinderplusHelp(params) { |
| kkonganti@17 | 2 |
| kkonganti@17 | 3 Map tool = [:] |
| kkonganti@17 | 4 Map toolspecs = [:] |
| kkonganti@17 | 5 tool.text = [:] |
| kkonganti@17 | 6 tool.helpparams = [:] |
| kkonganti@17 | 7 |
| kkonganti@17 | 8 toolspecs = [ |
| kkonganti@17 | 9 'amrfinderplus_run': [ |
| kkonganti@17 | 10 clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}", |
| kkonganti@17 | 11 cliflag: null, |
| kkonganti@17 | 12 clivalue: null |
| kkonganti@17 | 13 ], |
| kkonganti@17 | 14 'amrfinderplus_db': [ |
| kkonganti@17 | 15 clihelp: 'Path to AMRFinderPlus database. Please note that ' + |
| kkonganti@17 | 16 ' the databases should be ready and formatted with blast for use. ' + |
| kkonganti@17 | 17 'Please read more at: ' + |
| kkonganti@17 | 18 'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' + |
| kkonganti@17 | 19 "Default: ${params.amrfinderplus_db}", |
| kkonganti@17 | 20 cliflag: '--database', |
| kkonganti@17 | 21 clivalue: (params.amrfinderplus_db ?: '') |
| kkonganti@17 | 22 ], |
| kkonganti@17 | 23 'amrfinderplus_genes': [ |
| kkonganti@17 | 24 clihelp: 'Add the plus genes to the report', |
| kkonganti@17 | 25 cliflag: '--plus', |
| kkonganti@17 | 26 clivalue: (params.amrfinderplus_genes ? ' ' : '') |
| kkonganti@17 | 27 ] |
| kkonganti@17 | 28 ] |
| kkonganti@17 | 29 |
| kkonganti@17 | 30 toolspecs.each { |
| kkonganti@17 | 31 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@17 | 32 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@17 | 33 } |
| kkonganti@17 | 34 |
| kkonganti@17 | 35 return tool |
| kkonganti@17 | 36 } |