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1 // Help text for gen_salmon_res_table.py (gsrpy) within CPIPES.
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2
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3 def gsrpyHelp(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 'gsrpy_run': [
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12 clihelp: 'Run the gen_salmon_res_table.py script. Default: ' +
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13 (params.gsrpy_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 'gsrpy_url': [
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18 clihelp: 'Generate an additional column in final results table ' +
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19 'which links out to NCBI Pathogens Isolate Browser. ' +
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20 " Default: ${params.gsrpy_url}",
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21 cliflag: '-url',
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22 clivalue: (params.gsrpy_url ? ' ' : '')
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23 ]
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24 ]
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25
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26 toolspecs.each {
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27 k, v -> tool.text['--' + k] = "${v.clihelp}"
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28 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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29 }
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30
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31 return tool
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32 } |
