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

planemo upload

rev	line source
kkonganti@105	1 def amrfinderplusHelp(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 'amrfinderplus_run': [
kkonganti@105	10 clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}",
kkonganti@105	11 cliflag: null,
kkonganti@105	12 clivalue: null
kkonganti@105	13 ],
kkonganti@105	14 'amrfinderplus_db': [
kkonganti@105	15 clihelp: 'Path to AMRFinderPlus database. Please note that ' +
kkonganti@105	16 ' the databases should be ready and formatted with blast for use. ' +
kkonganti@105	17 'Please read more at: ' +
kkonganti@105	18 'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' +
kkonganti@105	19 "Default: ${params.amrfinderplus_db}",
kkonganti@105	20 cliflag: '--database',
kkonganti@105	21 clivalue: (params.amrfinderplus_db ?: '')
kkonganti@105	22 ],
kkonganti@105	23 'amrfinderplus_genes': [
kkonganti@105	24 clihelp: 'Add the plus genes to the report',
kkonganti@105	25 cliflag: '--plus',
kkonganti@105	26 clivalue: (params.amrfinderplus_genes ? ' ' : '')
kkonganti@105	27 ]
kkonganti@105	28 ]
kkonganti@105	29
kkonganti@105	30 toolspecs.each {
kkonganti@105	31 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@105	32 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@105	33 }
kkonganti@105	34
kkonganti@105	35 return tool
kkonganti@105	36 }

Mercurial > repos > kkonganti > cfsan_centriflaken