kkonganti@11: // Help text for seqkit rmdup within CPIPES.
kkonganti@11: 
kkonganti@11: def seqkitrmdupHelp(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:         'seqkit_rmdup_run': [
kkonganti@11:             clihelp: 'Remove duplicate sequences using seqkit rmdup. Default: ' +
kkonganti@11:                 (params.seqkit_rmdup_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'seqkit_rmdup_n': [
kkonganti@11:             clihelp: 'Match and remove duplicate sequences by full name instead of just ID. ' +
kkonganti@11:                 "Default: ${params.seqkit_rmdup_n}",
kkonganti@11:             cliflag: '-n',
kkonganti@11:             clivalue: (params.seqkit_rmdup_n ? ' ' : '')
kkonganti@11:         ], 
kkonganti@11:         'seqkit_rmdup_s': [
kkonganti@11:             clihelp: 'Match and remove duplicate sequences by sequence content. ' +
kkonganti@11:                 "Default: ${params.seqkit_rmdup_s}",
kkonganti@11:             cliflag: '-s',
kkonganti@11:             clivalue: (params.seqkit_rmdup_s ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'seqkit_rmdup_d': [
kkonganti@11:             clihelp: 'Save the duplicated sequences to a file. ' +
kkonganti@11:                 "Default: ${params.seqkit_rmdup_d}",
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'seqkit_rmdup_D': [
kkonganti@11:             clihelp: 'Save the number and list of duplicated sequences to a file. ' +
kkonganti@11:                 "Default: ${params.seqkit_rmdup_D}",
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'seqkit_rmdup_i': [
kkonganti@11:             clihelp: 'Ignore case while using seqkit rmdup. ' +
kkonganti@11:                 "Default: ${params.seqkit_rmdup_i}",
kkonganti@11:             cliflag: '-i',
kkonganti@11:             clivalue: (params.seqkit_rmdup_i ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'seqkit_rmdup_P': [
kkonganti@11:             clihelp: "Only consider positive strand (i.e. 5') when comparing by sequence content. " +
kkonganti@11:                 "Default: ${params.seqkit_rmdup_P}",
kkonganti@11:             cliflag: '-P',
kkonganti@11:             clivalue: (params.seqkit_rmdup_P ? ' ' : '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }