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