cfsan_centriflaken: 0.2.1/lib/help/mlst.nf annotate

"planemo upload"

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

Mercurial > repos > kkonganti > cfsan_centriflaken