cfsan_centriflaken: 0.4.2/lib/help/mlst.nf annotate

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rev	line source
kkonganti@105	1 def mlstHelp(params) {
kkonganti@105	2
kkonganti@105	3 Map tool = [:]
kkonganti@105	4 Map toolspecs = [:]
kkonganti@105	5 tool.text = [:]
kkonganti@105	6 tool.helpparams = [:]
kkonganti@105	7
kkonganti@105	8 toolspecs = [
kkonganti@105	9 'mlst_run': [
kkonganti@105	10 clihelp: "Run MLST tool. Default: ${params.mlst_run}",
kkonganti@105	11 cliflag: null,
kkonganti@105	12 clivalue: null
kkonganti@105	13 ],
kkonganti@105	14 'mlst_minid': [
kkonganti@105	15 clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " +
kkonganti@105	16 "Default: ${params.mlst_minid}",
kkonganti@105	17 cliflag: '--minid',
kkonganti@105	18 clivalue: (params.mlst_minid ?: 95)
kkonganti@105	19 ],
kkonganti@105	20 'mlst_mincov': [
kkonganti@105	21 clihelp: 'DNA %cov to report partial allele at all [?].' +
kkonganti@105	22 "Default: ${params.mlst_mincov}",
kkonganti@105	23 cliflag: '--mincov',
kkonganti@105	24 clivalue: (params.mlst_mincov ?: 10)
kkonganti@105	25 ],
kkonganti@105	26 'mlst_minscore': [
kkonganti@105	27 clihelp: 'Minumum score out of 100 to match a scheme.' +
kkonganti@105	28 "Default: ${params.mlst_minscore}",
kkonganti@105	29 cliflag: '--minscore',
kkonganti@105	30 clivalue: (params.mlst_minscore ?: 50)
kkonganti@105	31 ]
kkonganti@105	32 ]
kkonganti@105	33
kkonganti@105	34 toolspecs.each {
kkonganti@105	35 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@105	36 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@105	37 }
kkonganti@105	38
kkonganti@105	39 return tool
kkonganti@105	40 }

Mercurial > repos > kkonganti > cfsan_centriflaken