kkonganti@1: // Help text for gen_salmon_res_table.py (gsrpy) within CPIPES.
kkonganti@1: 
kkonganti@1: def gsrpyHelp(params) {
kkonganti@1: 
kkonganti@1:     Map tool = [:]
kkonganti@1:     Map toolspecs = [:]
kkonganti@1:     tool.text = [:]
kkonganti@1:     tool.helpparams = [:]
kkonganti@1: 
kkonganti@1:     toolspecs = [
kkonganti@1:         'gsrpy_run': [
kkonganti@1:             clihelp: 'Run the gen_salmon_res_table.py script. Default: ' +
kkonganti@1:                 (params.gsrpy_run ?: false),
kkonganti@1:             cliflag: null,
kkonganti@1:             clivalue: null
kkonganti@1:         ],
kkonganti@1:         'gsrpy_url': [
kkonganti@1:             clihelp: 'Generate an additional column in final results table ' +
kkonganti@1:                 'which links out to NCBI Pathogens Isolate Browser. ' +
kkonganti@1:                 " Default: ${params.gsrpy_url}",
kkonganti@1:             cliflag: '-url',
kkonganti@1:             clivalue: (params.gsrpy_url ? ' ' : '')
kkonganti@1:         ]
kkonganti@1:     ]
kkonganti@1: 
kkonganti@1:     toolspecs.each {
kkonganti@1:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@1:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     return tool
kkonganti@1: }