Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/lib/help/mlst.nf @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 def mlstHelp(params) { |
| kkonganti@1 | 2 |
| kkonganti@1 | 3 Map tool = [:] |
| kkonganti@1 | 4 Map toolspecs = [:] |
| kkonganti@1 | 5 tool.text = [:] |
| kkonganti@1 | 6 tool.helpparams = [:] |
| kkonganti@1 | 7 |
| kkonganti@1 | 8 toolspecs = [ |
| kkonganti@1 | 9 'mlst_run': [ |
| kkonganti@1 | 10 clihelp: "Run MLST tool. Default: ${params.mlst_run}", |
| kkonganti@1 | 11 cliflag: null, |
| kkonganti@1 | 12 clivalue: null |
| kkonganti@1 | 13 ], |
| kkonganti@1 | 14 'mlst_minid': [ |
| kkonganti@1 | 15 clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " + |
| kkonganti@1 | 16 "Default: ${params.mlst_minid}", |
| kkonganti@1 | 17 cliflag: '--minid', |
| kkonganti@1 | 18 clivalue: (params.mlst_minid ?: 95) |
| kkonganti@1 | 19 ], |
| kkonganti@1 | 20 'mlst_mincov': [ |
| kkonganti@1 | 21 clihelp: 'DNA %cov to report partial allele at all [?].' + |
| kkonganti@1 | 22 "Default: ${params.mlst_mincov}", |
| kkonganti@1 | 23 cliflag: '--mincov', |
| kkonganti@1 | 24 clivalue: (params.mlst_mincov ?: 10) |
| kkonganti@1 | 25 ], |
| kkonganti@1 | 26 'mlst_minscore': [ |
| kkonganti@1 | 27 clihelp: 'Minumum score out of 100 to match a scheme.' + |
| kkonganti@1 | 28 "Default: ${params.mlst_minscore}", |
| kkonganti@1 | 29 cliflag: '--minscore', |
| kkonganti@1 | 30 clivalue: (params.mlst_minscore ?: 50) |
| kkonganti@1 | 31 ] |
| kkonganti@1 | 32 ] |
| kkonganti@1 | 33 |
| kkonganti@1 | 34 toolspecs.each { |
| kkonganti@1 | 35 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@1 | 36 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@1 | 37 } |
| kkonganti@1 | 38 |
| kkonganti@1 | 39 return tool |
| kkonganti@1 | 40 } |