kkonganti@0: // Help text for mashtree within CPIPES.
kkonganti@0: 
kkonganti@0: def mashtreeHelp(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:         'mashtree_run': [
kkonganti@0:             clihelp: 'Run mashtree tool. Default: ' +
kkonganti@0:                 (params.mashtree_run ?: false),
kkonganti@0:             cliflag: null,
kkonganti@0:             clivalue: null
kkonganti@0:         ],
kkonganti@0:         'mashtree_fofn': [
kkonganti@0:             clihelp: 'Input is a file of file names. ' +
kkonganti@0:                 "Default: ${params.mashtree_fofn}",
kkonganti@0:             cliflag: '--file-of-files',
kkonganti@0:             clivalue: (params.mashtree_fofn ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'mashtree_trunclength': [
kkonganti@0:             clihelp: 'How many characters to keep in filename. ' +
kkonganti@0:                 "Default: ${params.mashtree_trunclength}",
kkonganti@0:             cliflag: '--truncLength',
kkonganti@0:             clivalue: (params.mashtree_trunclength ?: '')
kkonganti@0:         ],
kkonganti@0:         'mashtree_mindepth': [
kkonganti@0:             clihelp: 'If mindepth is zero, then it will be chosen in a smart but slower method, ' +
kkonganti@0:                 'to discard lower-abundance kmers. ' +
kkonganti@0:                 "Default: ${params.mashtree_mindepth}",
kkonganti@0:             cliflag: '--mindepth',
kkonganti@0:             clivalue: (params.mashtree_mindepth ?: '')
kkonganti@0:         ],
kkonganti@0:         'mashtree_kmerlength': [
kkonganti@0:             clihelp: "The minimum k-mer length. " +
kkonganti@0:                 "Default: ${params.mashtree_kmerlength}",
kkonganti@0:             cliflag: '--kmerlength',
kkonganti@0:             clivalue: (params.mashtree_kmerlength ?: '')
kkonganti@0:         ],
kkonganti@0:         'mashtree_sketchsize': [
kkonganti@0:             clihelp: "The minimum `mash` sketch size. " +
kkonganti@0:                 "Default: ${params.mashtree_sketchsize}",
kkonganti@0:             cliflag: '--sketchsize',
kkonganti@0:             clivalue: (params.mashtree_sketchsize ?: '')
kkonganti@0:         ],
kkonganti@0:         'mashtree_seed': [
kkonganti@0:             clihelp: "Seed for `mash` sketch. " +
kkonganti@0:                 "Default: ${params.mashtree_seed}",
kkonganti@0:             cliflag: '--seed',
kkonganti@0:             clivalue: (params.mashtree_seed ? ' ' : '')
kkonganti@0:         ],
kkonganti@0:         'mashtree_genomesize': [
kkonganti@0:             clihelp: 'Define genome size. ' +
kkonganti@0:                 "Default: ${params.mashtree_genomesize}",
kkonganti@0:             cliflag: '--genomesize',
kkonganti@0:             clivalue: (params.mashtree_genomesize ?: '')
kkonganti@0:         ],
kkonganti@0:         'mashtree_sigfigs': [
kkonganti@0:             clihelp: "How many decimal places to use in mash distances. " +
kkonganti@0:                 "Default: ${params.mashtree_sigfigs}",
kkonganti@0:             cliflag: '--sigfigs',
kkonganti@0:             clivalue: (params.mashtree_sigfigs ?: '')
kkonganti@0:         ],
kkonganti@0:         'mashtree_sortorder': [
kkonganti@0:             clihelp: 'For neighbor-joining, the sort order can make a difference. ' +
kkonganti@0:                 'Options include: ABC (alphabetical), random, input-order. ' +
kkonganti@0:                 "Default: ${params.mashtree_sortorder}",
kkonganti@0:             cliflag: '--sort-order',
kkonganti@0:             clivalue: (params.mashtree_sortorder ?: '')
kkonganti@0:         ]
kkonganti@0:     ]
kkonganti@0: 
kkonganti@0:     toolspecs.each {
kkonganti@0:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@0:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     return tool
kkonganti@0: }