Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/lib/help/mlst.nf @ 11:a5f31c44f8c9
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 16:11:44 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 def mlstHelp(params) { |
| kkonganti@11 | 2 |
| kkonganti@11 | 3 Map tool = [:] |
| kkonganti@11 | 4 Map toolspecs = [:] |
| kkonganti@11 | 5 tool.text = [:] |
| kkonganti@11 | 6 tool.helpparams = [:] |
| kkonganti@11 | 7 |
| kkonganti@11 | 8 toolspecs = [ |
| kkonganti@11 | 9 'mlst_run': [ |
| kkonganti@11 | 10 clihelp: "Run MLST tool. Default: ${params.mlst_run}", |
| kkonganti@11 | 11 cliflag: null, |
| kkonganti@11 | 12 clivalue: null |
| kkonganti@11 | 13 ], |
| kkonganti@11 | 14 'mlst_legacy': [ |
| kkonganti@11 | 15 clihelp: "Use old legacy output with allele header row (requires --mlst_scheme). " + |
| kkonganti@11 | 16 "Default: ${params.mlst_legacy}", |
| kkonganti@11 | 17 cliflag: '--legacy', |
| kkonganti@11 | 18 clivalue: (params.mlst_legacy ? ' ' : '') |
| kkonganti@11 | 19 ], |
| kkonganti@11 | 20 'mlst_scheme': [ |
| kkonganti@11 | 21 clihelp: "Don't autodetect, force this scheme on all inputs. " + |
| kkonganti@11 | 22 "Default: ${params.mlst_scheme}", |
| kkonganti@11 | 23 cliflag: '--scheme', |
| kkonganti@11 | 24 clivalue: (params.mlst_scheme ?: null) |
| kkonganti@11 | 25 ], |
| kkonganti@11 | 26 'mlst_minid': [ |
| kkonganti@11 | 27 clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " + |
| kkonganti@11 | 28 "Default: ${params.mlst_minid}", |
| kkonganti@11 | 29 cliflag: '--minid', |
| kkonganti@11 | 30 clivalue: (params.mlst_minid ?: 95) |
| kkonganti@11 | 31 ], |
| kkonganti@11 | 32 'mlst_mincov': [ |
| kkonganti@11 | 33 clihelp: 'DNA %cov to report partial allele at all [?].' + |
| kkonganti@11 | 34 "Default: ${params.mlst_mincov}", |
| kkonganti@11 | 35 cliflag: '--mincov', |
| kkonganti@11 | 36 clivalue: (params.mlst_mincov ?: 10) |
| kkonganti@11 | 37 ], |
| kkonganti@11 | 38 'mlst_minscore': [ |
| kkonganti@11 | 39 clihelp: 'Minumum score out of 100 to match a scheme.' + |
| kkonganti@11 | 40 "Default: ${params.mlst_minscore}", |
| kkonganti@11 | 41 cliflag: '--minscore', |
| kkonganti@11 | 42 clivalue: (params.mlst_minscore ?: 50) |
| kkonganti@11 | 43 ], |
| kkonganti@11 | 44 'mlst_datadir': [ |
| kkonganti@11 | 45 clihelp: 'PubMLST data directory. ' + |
| kkonganti@11 | 46 "Default: ${params.mlst_datadir}", |
| kkonganti@11 | 47 cliflag: '--datadir', |
| kkonganti@11 | 48 clivalue: (params.mlst_datadir ?: null) |
| kkonganti@11 | 49 ], |
| kkonganti@11 | 50 'mlst_blastdb': [ |
| kkonganti@11 | 51 clihelp: 'BLAST database directory. ' + |
| kkonganti@11 | 52 "Default: ${params.mlst_blastdb}", |
| kkonganti@11 | 53 cliflag: '--blastdb', |
| kkonganti@11 | 54 clivalue: (params.mlst_blastdb ?: null) |
| kkonganti@11 | 55 ] |
| kkonganti@11 | 56 ] |
| kkonganti@11 | 57 |
| kkonganti@11 | 58 toolspecs.each { |
| kkonganti@11 | 59 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@11 | 60 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@11 | 61 } |
| kkonganti@11 | 62 |
| kkonganti@11 | 63 return tool |
| kkonganti@11 | 64 } |