kkonganti@11: // Help text for kma index within CPIPES.
kkonganti@11: 
kkonganti@11: def kmaindexHelp(params) {
kkonganti@11: 
kkonganti@11:     Map tool = [:]
kkonganti@11:     Map toolspecs = [:]
kkonganti@11:     tool.text = [:]
kkonganti@11:     tool.helpparams = [:]
kkonganti@11: 
kkonganti@11:     toolspecs = [
kkonganti@11:         'kmaindex_run': [
kkonganti@11:             clihelp: 'Run kma index tool. Default: ' +
kkonganti@11:                 (params.kmaindex_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'kmaindex_t_db': [
kkonganti@11:             clihelp: 'Add to existing DB. ' +
kkonganti@11:                 "Default: ${params.kmaindex_t_db}",
kkonganti@11:             cliflag: '-t_db',
kkonganti@11:             clivalue: (params.kmaindex_t_db ? ' ' : '')
kkonganti@11:         ], 
kkonganti@11:         'kmaindex_k': [
kkonganti@11:             clihelp: 'k-mer size. ' +
kkonganti@11:                 "Default: ${params.kmaindex_k}",
kkonganti@11:             cliflag: '-k',
kkonganti@11:             clivalue: (params.kmaindex_k ?: '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_m': [
kkonganti@11:             clihelp: 'Minimizer size. ' +
kkonganti@11:                 "Default: ${params.kmaindex_m}",
kkonganti@11:             cliflag: '-m',
kkonganti@11:             clivalue: (params.kmaindex_m ?: '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_hc': [
kkonganti@11:             clihelp: 'Homopolymer compression. ' +
kkonganti@11:                 "Default: ${params.kmaindex_hc}",
kkonganti@11:             cliflag: '-hc',
kkonganti@11:             clivalue: (params.kmaindex_hc ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_ML': [
kkonganti@11:             clihelp: 'Minimum length of templates. Defaults to --kmaindex_k ' +
kkonganti@11:                 "Default: ${params.kmaindex_ML}",
kkonganti@11:             cliflag: '-ML',
kkonganti@11:             clivalue: (params.kmaindex_ML ?: '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_ME': [
kkonganti@11:             clihelp: 'Mega DB. ' +
kkonganti@11:                 "Default: ${params.kmaindex_ME}",
kkonganti@11:             cliflag: '-ME',
kkonganti@11:             clivalue: (params.kmaindex_ME ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_Sparse': [
kkonganti@11:             clihelp: 'Make Sparse DB. ' +
kkonganti@11:                 "Default: ${params.kmaindex_Sparse}",
kkonganti@11:             cliflag: '-Sparse',
kkonganti@11:             clivalue: (params.kmaindex_Sparse ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_ht': [
kkonganti@11:             clihelp: 'Homology template. ' +
kkonganti@11:                 "Default: ${params.kmaindex_ht}",
kkonganti@11:             cliflag: '-ht',
kkonganti@11:             clivalue: (params.kmaindex_ht ?: '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_hq': [
kkonganti@11:             clihelp: 'Homology query. ' +
kkonganti@11:                 "Default: ${params.kmaindex_hq}",
kkonganti@11:             cliflag: '-hq',
kkonganti@11:             clivalue: (params.kmaindex_hq ?: '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_and': [
kkonganti@11:             clihelp: 'Both homology thresholds have to reach. ' +
kkonganti@11:                 "Default: ${params.kmaindex_and}",
kkonganti@11:             cliflag: '-and',
kkonganti@11:             clivalue: (params.kmaindex_and ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'kmaindex_nbp': [
kkonganti@11:             clihelp: 'No bias print. ' +
kkonganti@11:                 "Default: ${params.kmaindex_nbp}",
kkonganti@11:             cliflag: '-nbp',
kkonganti@11:             clivalue: (params.kmaindex_nbp ? ' ' : '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }