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