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1 // Help text for `masurca's polca.sh` within CPIPES.
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2
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3 def masurcapolcaHelp(params) {
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4
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5 Map tool = [:]
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6 Map toolspecs = [:]
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7 tool.text = [:]
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8 tool.helpparams = [:]
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9
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10 toolspecs = [
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11 'masurcapolca_run': [
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12 clihelp: 'Run `polca.sh` from masurca. Default: ' +
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13 (params.masurcapolca_run ?: false),
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14 cliflag: null,
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15 clivalue: null
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16 ],
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17 'masurcapolca_n': [
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18 clihelp: 'Do not polish, just create vcf file, evaluate the assembly and exit. ' +
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19 "Default: ${params.masurcapolca_n}",
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20 cliflag: '-n',
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21 clivalue: (params.masurcapolca_n ? ' ' : '')
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22 ]
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23 ]
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24
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25 toolspecs.each {
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26 k, v -> tool.text['--' + k] = "${v.clihelp}"
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27 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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28 }
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29
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30 return tool
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31 } |
