Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/lib/help/seqsero2.nf @ 20:133571bf891f
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 11:42:00 -0400 |
| parents | 0e7a0053e4a6 |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 def seqsero2Help(params) { |
| kkonganti@17 | 2 |
| kkonganti@17 | 3 Map tool = [:] |
| kkonganti@17 | 4 Map toolspecs = [:] |
| kkonganti@17 | 5 tool.text = [:] |
| kkonganti@17 | 6 tool.helpparams = [:] |
| kkonganti@17 | 7 |
| kkonganti@17 | 8 toolspecs = [ |
| kkonganti@17 | 9 'seqsero2_run': [ |
| kkonganti@17 | 10 clihelp: "Run SeqSero2 tool. Default: ${params.seqsero2_run}", |
| kkonganti@17 | 11 cliflag: null, |
| kkonganti@17 | 12 clivalue: null |
| kkonganti@17 | 13 ], |
| kkonganti@17 | 14 'seqsero2_t': [ |
| kkonganti@17 | 15 clihelp: "'1' for interleaved paired-end reads, '2' for " + |
| kkonganti@17 | 16 "separated paired-end reads, '3' for single reads, '4' for " + |
| kkonganti@17 | 17 "genome assembly, '5' for nanopore reads (fasta/fastq). " + |
| kkonganti@17 | 18 "Default: ${params.seqsero2_t}", |
| kkonganti@17 | 19 cliflag: '-t', |
| kkonganti@17 | 20 clivalue: (params.seqsero2_t ?: '') |
| kkonganti@17 | 21 ], |
| kkonganti@17 | 22 'seqsero2_m': [ |
| kkonganti@17 | 23 clihelp: "Which workflow to apply, 'a'(raw reads allele " + |
| kkonganti@17 | 24 "micro-assembly), 'k'(raw reads and genome assembly k-mer). " + |
| kkonganti@17 | 25 "Default: ${params.seqsero2_m}", |
| kkonganti@17 | 26 cliflag: '-m', |
| kkonganti@17 | 27 clivalue: (params.seqsero2_m ?: '') |
| kkonganti@17 | 28 ], |
| kkonganti@17 | 29 'seqsero2_c': [ |
| kkonganti@17 | 30 clihelp: 'SeqSero2 will only output serotype prediction without the directory ' + |
| kkonganti@17 | 31 'containing log files. ' + |
| kkonganti@17 | 32 "Default: ${params.seqsero2_c}", |
| kkonganti@17 | 33 cliflag: '-c', |
| kkonganti@17 | 34 clivalue: (params.seqsero2_c ? ' ' : '') |
| kkonganti@17 | 35 ], |
| kkonganti@17 | 36 'seqsero2_s': [ |
| kkonganti@17 | 37 clihelp: 'SeqSero2 will not output header in SeqSero_result.tsv. ' + |
| kkonganti@17 | 38 "Default: ${params.seqsero2_s}", |
| kkonganti@17 | 39 cliflag: '-l', |
| kkonganti@17 | 40 clivalue: (params.seqsero2_s ? ' ' : '') |
| kkonganti@17 | 41 ] |
| kkonganti@17 | 42 ] |
| kkonganti@17 | 43 |
| kkonganti@17 | 44 toolspecs.each { |
| kkonganti@17 | 45 k, v -> tool.text['--' + k] = "${v.clihelp}" |
| kkonganti@17 | 46 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ] |
| kkonganti@17 | 47 } |
| kkonganti@17 | 48 |
| kkonganti@17 | 49 return tool |
| kkonganti@17 | 50 } |