kkonganti@101: def seqsero2Help(params) {
kkonganti@101: 
kkonganti@101:     Map tool = [:]
kkonganti@101:     Map toolspecs = [:]
kkonganti@101:     tool.text = [:]
kkonganti@101:     tool.helpparams = [:]
kkonganti@101: 
kkonganti@101:     toolspecs = [
kkonganti@101:         'seqsero2_run': [
kkonganti@101:             clihelp: "Run SeqSero2 tool. Default: ${params.seqsero2_run}",
kkonganti@101:             cliflag: null,
kkonganti@101:             clivalue: null
kkonganti@101:         ],
kkonganti@101:         'seqsero2_t': [
kkonganti@101:             clihelp: "'1' for interleaved paired-end reads, '2' for " +
kkonganti@101:                 "separated paired-end reads, '3' for single reads, '4' for " +
kkonganti@101:                 "genome assembly, '5' for nanopore reads (fasta/fastq). " +
kkonganti@101:                 "Default: ${params.seqsero2_t}",
kkonganti@101:             cliflag: '-t',
kkonganti@101:             clivalue: (params.seqsero2_t ?: '')
kkonganti@101:         ],
kkonganti@101:         'seqsero2_m': [
kkonganti@101:             clihelp: "Which workflow to apply, 'a'(raw reads allele " +
kkonganti@101:                 "micro-assembly), 'k'(raw reads and genome assembly k-mer). " +
kkonganti@101:                 "Default: ${params.seqsero2_m}",
kkonganti@101:             cliflag: '-m',
kkonganti@101:             clivalue: (params.seqsero2_m ?: '')
kkonganti@101:         ],
kkonganti@101:         'seqsero2_c': [
kkonganti@101:             clihelp: 'SeqSero2 will only output serotype prediction without the directory ' +
kkonganti@101:                 'containing log files. ' +
kkonganti@101:                 "Default: ${params.seqsero2_c}",
kkonganti@101:             cliflag: '-c',
kkonganti@101:             clivalue: (params.seqsero2_c ? ' ' : '')
kkonganti@101:         ],
kkonganti@101:         'seqsero2_s': [
kkonganti@101:             clihelp: 'SeqSero2 will not output header in SeqSero_result.tsv. ' +
kkonganti@101:                 "Default: ${params.seqsero2_s}",
kkonganti@101:             cliflag: '-l',
kkonganti@101:             clivalue: (params.seqsero2_s ? ' ' : '')
kkonganti@101:         ]
kkonganti@101:     ]
kkonganti@101: 
kkonganti@101:     toolspecs.each {
kkonganti@101:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@101:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@101:     }
kkonganti@101: 
kkonganti@101:     return tool
kkonganti@101: }