Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.1.0/lib/help/polypolish.nf @ 1:c6327baca625
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Nov 2023 14:18:16 -0500 |
| parents | c8597e9e1a97 |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 // Help text for `polypolish within CPIPES. |
| kkonganti@0 | 2 |
| kkonganti@0 | 3 def polypolishHelp(params) { |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 Map tool = [:] |
| kkonganti@0 | 6 Map toolspecs = [:] |
| kkonganti@0 | 7 tool.text = [:] |
| kkonganti@0 | 8 tool.helpparams = [:] |
| kkonganti@0 | 9 |
| kkonganti@0 | 10 toolspecs = [ |
| kkonganti@0 | 11 'polypolish_run': [ |
| kkonganti@0 | 12 clihelp: 'Run polypolish tool. Default: ' + |
| kkonganti@0 | 13 (params.polypolish_run ?: false), |
| kkonganti@0 | 14 cliflag: null, |
| kkonganti@0 | 15 clivalue: null |
| kkonganti@0 | 16 ], |
| kkonganti@0 | 17 'polypolish_d': [ |
| kkonganti@0 | 18 clihelp: 'A base must occur at least this many times in the pileup to be considered valid. ' + |
| kkonganti@0 | 19 "Default: ${params.polypolish_d}", |
| kkonganti@0 | 20 cliflag: '-d', |
| kkonganti@0 | 21 clivalue: (params.polypolish_d ?: '') |
| kkonganti@0 | 22 ], |
| kkonganti@0 | 23 'polypolish_i': [ |
| kkonganti@0 | 24 clihelp: 'A base must make up less than this fraction of the read depth to be considered invalid. ' + |
| kkonganti@0 | 25 "Default: ${params.polypolish_i}", |
| kkonganti@0 | 26 cliflag: '-i', |
| kkonganti@0 | 27 clivalue: (params.polypolish_i ?: '') |
| kkonganti@0 | 28 ], |
| kkonganti@0 | 29 'polypolish_m': [ |
| kkonganti@0 | 30 clihelp: 'Ignore alignments with more than this many mismatches and indels. ' + |
| kkonganti@0 | 31 "Default: ${params.polypolish_m}", |
| kkonganti@0 | 32 cliflag: '-m', |
| kkonganti@0 | 33 clivalue: (params.polypolish_m ?: '') |
| kkonganti@0 | 34 ], |
| kkonganti@0 | 35 'polypolish_v': [ |
| kkonganti@0 | 36 clihelp: 'A base must make up at least this fraction of the read depth to be considered valid. ' + |
| kkonganti@0 | 37 "Default: ${params.polypolish_v}", |
| kkonganti@0 | 38 cliflag: '-v', |
| kkonganti@0 | 39 clivalue: (params.polypolish_v ?: '') |
| kkonganti@0 | 40 ] |
| kkonganti@0 | 41 ] |
| kkonganti@0 | 42 |
| kkonganti@0 | 43 toolspecs.each { |
| kkonganti@0 | 44 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@0 | 45 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@0 | 46 } |
| kkonganti@0 | 47 |
| kkonganti@0 | 48 return tool |
| kkonganti@0 | 49 } |