kkonganti@0: // Help text for prodigal within CPIPES.
kkonganti@0: 
kkonganti@0: def prodigalHelp(params) {
kkonganti@0: 
kkonganti@0:     Map tool = [:]
kkonganti@0:     Map toolspecs = [:]
kkonganti@0:     tool.text = [:]
kkonganti@0:     tool.helpparams = [:]
kkonganti@0: 
kkonganti@0:     toolspecs = [
kkonganti@0:         'prodigal_run': [
kkonganti@0:             clihelp: 'Run prodigal tool. Default: ' +
kkonganti@0:                 (params.prodigal_run ?: false),
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'prodigal_c': [
kkonganti@0:             clihelp: 'Closed ends. Do not allow genes to run off edges. ' +
kkonganti@0:                 "Default: ${params.prodigal_c}",
kkonganti@0:             cliflag: '--c',
kkonganti@0:             clivalue: (params.prodigal_c ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prodigal_f': [
kkonganti@0:             clihelp: "Select output format (gbk, gff, or sco). " +
kkonganti@0:                 "Default: ${params.prodigal_f}",
kkonganti@0:             cliflag: '-f',
kkonganti@0:             clivalue: (params.prodigal_f ?: '')
kkonganti@0:         ],
kkonganti@0:         'prodigal_g': [
kkonganti@0:             clihelp: "Specify translation table to use." +
kkonganti@0:                 "Default: ${params.prodigal_g}",
kkonganti@0:             cliflag: '-g',
kkonganti@0:             clivalue: (params.prodigal_g ?: '')
kkonganti@0:         ],
kkonganti@0:         'prodigal_m': [
kkonganti@0:             clihelp: "Treat runs of N as masked sequence; don't build genes " +
kkonganti@0:                 'across them. ' +
kkonganti@0:                 "Default: ${params.prodigal_m}",
kkonganti@0:             cliflag: '-m',
kkonganti@0:             clivalue: (params.prodigal_m ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prodigal_n': [
kkonganti@0:             clihelp: 'Bypass Shine-Dalgarno trainer and force a full motif scan. ' +
kkonganti@0:                 "Default: ${params.prodigal_n}",
kkonganti@0:             cliflag: '-n',
kkonganti@0:             clivalue: (params.prodigal_n ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'prodigal_p': [
kkonganti@0:             clihelp: "Select procedure (single or meta). " +
kkonganti@0:                 "Default: ${params.prodigal_p}",
kkonganti@0:             cliflag: '-p',
kkonganti@0:             clivalue: (params.prodigal_p ?: '')
kkonganti@0:         ],
kkonganti@0:         'prodigal_t': [
kkonganti@0:             clihelp: 'Write a training file (if none exists) ending in suffix `.trnd`; ' +
kkonganti@0:                 'otherwise, read and use the specified training file. ' +
kkonganti@0:                 "Default: ${params.prodigal_t}",
kkonganti@0:             cliflag: '-t',
kkonganti@0:             clivalue: (params.prodigal_t ? ' ' : '')
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }