Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/lib/help/masurcapolca.nf @ 15:7c0407ebbdf3
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 17:55:16 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 // Help text for `masurca's polca.sh` within CPIPES. |
| kkonganti@11 | 2 |
| kkonganti@11 | 3 def masurcapolcaHelp(params) { |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 Map tool = [:] |
| kkonganti@11 | 6 Map toolspecs = [:] |
| kkonganti@11 | 7 tool.text = [:] |
| kkonganti@11 | 8 tool.helpparams = [:] |
| kkonganti@11 | 9 |
| kkonganti@11 | 10 toolspecs = [ |
| kkonganti@11 | 11 'masurcapolca_run': [ |
| kkonganti@11 | 12 clihelp: 'Run `polca.sh` from masurca. Default: ' + |
| kkonganti@11 | 13 (params.masurcapolca_run ?: false), |
| kkonganti@11 | 14 cliflag: null, |
| kkonganti@11 | 15 clivalue: null |
| kkonganti@11 | 16 ], |
| kkonganti@11 | 17 'masurcapolca_n': [ |
| kkonganti@11 | 18 clihelp: 'Do not polish, just create vcf file, evaluate the assembly and exit. ' + |
| kkonganti@11 | 19 "Default: ${params.masurcapolca_n}", |
| kkonganti@11 | 20 cliflag: '-n', |
| kkonganti@11 | 21 clivalue: (params.masurcapolca_n ? ' ' : '') |
| kkonganti@11 | 22 ] |
| kkonganti@11 | 23 ] |
| kkonganti@11 | 24 |
| kkonganti@11 | 25 toolspecs.each { |
| kkonganti@11 | 26 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@11 | 27 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@11 | 28 } |
| kkonganti@11 | 29 |
| kkonganti@11 | 30 return tool |
| kkonganti@11 | 31 } |