kkonganti@17: // Help text for seqkit rmdup within CPIPES. kkonganti@17: kkonganti@17: def seqkitrmdupHelp(params) { kkonganti@17: kkonganti@17: Map tool = [:] kkonganti@17: Map toolspecs = [:] kkonganti@17: tool.text = [:] kkonganti@17: tool.helpparams = [:] kkonganti@17: kkonganti@17: toolspecs = [ kkonganti@17: 'seqkit_rmdup_run': [ kkonganti@17: clihelp: 'Remove duplicate sequences using seqkit rmdup. Default: ' + kkonganti@17: (params.seqkit_rmdup_run ?: false), kkonganti@17: cliflag: null, kkonganti@17: clivalue: null kkonganti@17: ], kkonganti@17: 'seqkit_rmdup_n': [ kkonganti@17: clihelp: 'Match and remove duplicate sequences by full name instead of just ID. ' + kkonganti@17: "Default: ${params.seqkit_rmdup_n}", kkonganti@17: cliflag: '-n', kkonganti@17: clivalue: (params.seqkit_rmdup_n ? ' ' : '') kkonganti@17: ], kkonganti@17: 'seqkit_rmdup_s': [ kkonganti@17: clihelp: 'Match and remove duplicate sequences by sequence content. ' + kkonganti@17: "Default: ${params.seqkit_rmdup_s}", kkonganti@17: cliflag: '-s', kkonganti@17: clivalue: (params.seqkit_rmdup_s ? ' ' : '') kkonganti@17: ], kkonganti@17: 'seqkit_rmdup_d': [ kkonganti@17: clihelp: 'Save the duplicated sequences to a file. ' + kkonganti@17: "Default: ${params.seqkit_rmdup_d}", kkonganti@17: cliflag: null, kkonganti@17: clivalue: null kkonganti@17: ], kkonganti@17: 'seqkit_rmdup_D': [ kkonganti@17: clihelp: 'Save the number and list of duplicated sequences to a file. ' + kkonganti@17: "Default: ${params.seqkit_rmdup_D}", kkonganti@17: cliflag: null, kkonganti@17: clivalue: null kkonganti@17: ], kkonganti@17: 'seqkit_rmdup_i': [ kkonganti@17: clihelp: 'Ignore case while using seqkit rmdup. ' + kkonganti@17: "Default: ${params.seqkit_rmdup_i}", kkonganti@17: cliflag: '-i', kkonganti@17: clivalue: (params.seqkit_rmdup_i ? ' ' : '') kkonganti@17: ], kkonganti@17: 'seqkit_rmdup_P': [ kkonganti@17: clihelp: "Only consider positive strand (i.e. 5') when comparing by sequence content. " + kkonganti@17: "Default: ${params.seqkit_rmdup_P}", kkonganti@17: cliflag: '-P', kkonganti@17: clivalue: (params.seqkit_rmdup_P ? ' ' : '') kkonganti@17: ] kkonganti@17: ] kkonganti@17: kkonganti@17: toolspecs.each { kkonganti@17: k, v -> tool.text['--' + k] = "${v.clihelp}" kkonganti@17: tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] kkonganti@17: } kkonganti@17: kkonganti@17: return tool kkonganti@17: }