Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/lib/help/mashscreen.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 // Help text for mash screen within CPIPES. |
| kkonganti@17 | 2 |
| kkonganti@17 | 3 def mashscreenHelp(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 'mashscreen_run': [ |
| kkonganti@17 | 12 clihelp: 'Run `mash screen` tool. Default: ' + |
| kkonganti@17 | 13 (params.mashscreen_run ?: false), |
| kkonganti@17 | 14 cliflag: null, |
| kkonganti@17 | 15 clivalue: null |
| kkonganti@17 | 16 ], |
| kkonganti@17 | 17 'mashscreen_w': [ |
| kkonganti@17 | 18 clihelp: 'Winner-takes-all strategy for identity estimates. After counting ' + |
| kkonganti@17 | 19 'hashes for each query, hashes that appear in multiple queries will ' + |
| kkonganti@17 | 20 'be removed from all except the one with the best identity (ties ' + |
| kkonganti@17 | 21 'broken by larger query), and other identities will be reduced. This ' + |
| kkonganti@17 | 22 'removes output redundancy, providing a rough compositional outline. ' + |
| kkonganti@17 | 23 " Default: ${params.mashscreen_w}", |
| kkonganti@17 | 24 cliflag: '-w', |
| kkonganti@17 | 25 clivalue: (params.mashscreen_w ? ' ' : '') |
| kkonganti@17 | 26 ], |
| kkonganti@17 | 27 'mashscreen_i': [ |
| kkonganti@17 | 28 clihelp: 'Minimum identity to report. Inclusive unless set to zero, in which ' + |
| kkonganti@17 | 29 'case only identities greater than zero (i.e. with at least one ' + |
| kkonganti@17 | 30 'shared hash) will be reported. Set to -1 to output everything. ' + |
| kkonganti@17 | 31 "(-1-1). Default: ${params.mashscreen_i}", |
| kkonganti@17 | 32 cliflag: '-i', |
| kkonganti@17 | 33 clivalue: (params.mashscreen_i ?: '') |
| kkonganti@17 | 34 ], |
| kkonganti@17 | 35 'mashscreen_v': [ |
| kkonganti@17 | 36 clihelp: 'Maximum p-value to report (0-1). ' + |
| kkonganti@17 | 37 "Default: ${params.mashscreen_v}", |
| kkonganti@17 | 38 cliflag: '-v', |
| kkonganti@17 | 39 clivalue: (params.mashscreen_v ?: '') |
| kkonganti@17 | 40 ] |
| kkonganti@17 | 41 ] |
| kkonganti@17 | 42 |
| kkonganti@17 | 43 toolspecs.each { |
| kkonganti@17 | 44 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@17 | 45 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@17 | 46 } |
| kkonganti@17 | 47 |
| kkonganti@17 | 48 return tool |
| kkonganti@17 | 49 } |