Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/lib/help/mlst.nf @ 0:082e0091e813 draft default tip

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author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 def mlstHelp(params) {
2
3 Map tool = [:]
4 Map toolspecs = [:]
5 tool.text = [:]
6 tool.helpparams = [:]
7
8 toolspecs = [
9 'mlst_run': [
10 clihelp: "Run MLST tool. Default: ${params.mlst_run}",
11 cliflag: null,
12 clivalue: null
13 ],
14 'mlst_minid': [
15 clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " +
16 "Default: ${params.mlst_minid}",
17 cliflag: '--minid',
18 clivalue: (params.mlst_minid ?: 95)
19 ],
20 'mlst_mincov': [
21 clihelp: 'DNA %cov to report partial allele at all [?].' +
22 "Default: ${params.mlst_mincov}",
23 cliflag: '--mincov',
24 clivalue: (params.mlst_mincov ?: 10)
25 ],
26 'mlst_minscore': [
27 clihelp: 'Minumum score out of 100 to match a scheme.' +
28 "Default: ${params.mlst_minscore}",
29 cliflag: '--minscore',
30 clivalue: (params.mlst_minscore ?: 50)
31 ]
32 ]
33
34 toolspecs.each {
35 k, v -> tool.text['--' + k] = "${v.clihelp}"
36 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
37 }
38
39 return tool
40 }