Mercurial > repos > kkonganti > cfsan_bettercallsal
view 0.5.0/lib/help/seqsero2.nf @ 4:fa1d249ca172
"planemo upload"
author | kkonganti |
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date | Tue, 06 Jun 2023 09:51:44 -0400 |
parents | 365849f031fd |
children |
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def seqsero2Help(params) { Map tool = [:] Map toolspecs = [:] tool.text = [:] tool.helpparams = [:] toolspecs = [ 'seqsero2_run': [ clihelp: "Run SeqSero2 tool. Default: ${params.seqsero2_run}", cliflag: null, clivalue: null ], 'seqsero2_t': [ clihelp: "'1' for interleaved paired-end reads, '2' for " + "separated paired-end reads, '3' for single reads, '4' for " + "genome assembly, '5' for nanopore reads (fasta/fastq). " + "Default: ${params.seqsero2_t}", cliflag: '-t', clivalue: (params.seqsero2_t ?: '') ], 'seqsero2_m': [ clihelp: "Which workflow to apply, 'a'(raw reads allele " + "micro-assembly), 'k'(raw reads and genome assembly k-mer). " + "Default: ${params.seqsero2_m}", cliflag: '-m', clivalue: (params.seqsero2_m ?: '') ], 'seqsero2_c': [ clihelp: 'SeqSero2 will only output serotype prediction without the directory ' + 'containing log files. ' + "Default: ${params.seqsero2_c}", cliflag: '-c', clivalue: (params.seqsero2_c ? ' ' : '') ], 'seqsero2_s': [ clihelp: 'SeqSero2 will not output header in SeqSero_result.tsv. ' + "Default: ${params.seqsero2_s}", cliflag: '-l', clivalue: (params.seqsero2_s ? ' ' : '') ] ] toolspecs.each { k, v -> tool.text['--' + k] = "${v.clihelp}" tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] } return tool }