Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.6.1/lib/help/gsrpy.nf @ 15:1972677994a6
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 07 Sep 2023 10:27:12 -0400 |
| parents | 749faef1caa9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 // Help text for gen_salmon_res_table.py (gsrpy) within CPIPES. |
| kkonganti@11 | 2 |
| kkonganti@11 | 3 def gsrpyHelp(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 'gsrpy_run': [ |
| kkonganti@11 | 12 clihelp: 'Run the gen_salmon_res_table.py script. Default: ' + |
| kkonganti@11 | 13 (params.gsrpy_run ?: false), |
| kkonganti@11 | 14 cliflag: null, |
| kkonganti@11 | 15 clivalue: null |
| kkonganti@11 | 16 ], |
| kkonganti@11 | 17 'gsrpy_url': [ |
| kkonganti@11 | 18 clihelp: 'Generate an additional column in final results table ' + |
| kkonganti@11 | 19 'which links out to NCBI Pathogens Isolate Browser. ' + |
| kkonganti@11 | 20 " Default: ${params.gsrpy_url}", |
| kkonganti@11 | 21 cliflag: '-url', |
| kkonganti@11 | 22 clivalue: (params.gsrpy_url ? ' ' : '') |
| kkonganti@11 | 23 ] |
| kkonganti@11 | 24 ] |
| kkonganti@11 | 25 |
| kkonganti@11 | 26 toolspecs.each { |
| kkonganti@11 | 27 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@11 | 28 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@11 | 29 } |
| kkonganti@11 | 30 |
| kkonganti@11 | 31 return tool |
| kkonganti@11 | 32 } |