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1 // Help text for `gen_salmon_tph_and_krona_tsv.py` (gsalkronapy) within CPIPES.
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2
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3 def gsalkronapyHelp(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 'gsalkronapy_run': [
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12 clihelp: 'Run the `gen_salmon_tph_and_krona_tsv.py` script. Default: ' +
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13 (params.gsalkronapy_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 'gsalkronapy_sf': [
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18 clihelp: 'Set the scaling factor by which TPM values ' +
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19 'are scaled down.' +
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20 " Default: ${params.gsalkronapy_sf}",
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21 cliflag: '-sf',
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22 clivalue: (params.gsalkronapy_sf ?: '')
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23 ],
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24 'gsalkronapy_smres_suffix': [
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25 clihelp: 'Find the `sourmash gather` result files ' +
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26 'ending in this suffix.' +
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27 " Default: ${params.gsalkronapy_smres_suffix}",
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28 cliflag: '-smres-suffix',
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29 clivalue: (params.gsalkronapy_smres_suffix ?: '')
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30 ],
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31 'gsalkronapy_failed_suffix': [
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32 clihelp: 'Find the sample names which failed classification stored ' +
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33 'inside the files ending in this suffix.' +
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34 " Default: ${params.gsalkronapy_failed_suffix}",
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35 cliflag: '-failed-suffix',
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36 clivalue: (params.gsalkronapy_failed_suffix ?: '')
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37 ],
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38 'gsalkronapy_num_lin_cols': [
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39 clihelp: 'Number of columns expected in the lineages CSV file. ' +
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40 " Default: ${params.gsalkronapy_num_lin_cols}",
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41 cliflag: '-num-lin-cols',
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42 clivalue: (params.gsalkronapy_num_lin_cols ?: '')
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43 ],
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44 'gsalkronapy_lin_regex': [
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45 clihelp: 'Number of columns expected in the lineages CSV file. ' +
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46 " Default: ${params.gsalkronapy_num_lin_cols}",
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47 cliflag: '-num-lin-cols',
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48 clivalue: (params.gsalkronapy_num_lin_cols ?: '')
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49 ]
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50 ]
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51
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52 toolspecs.each {
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53 k, v -> tool.text['--' + k] = "${v.clihelp}"
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54 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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55 }
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56
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57 return tool
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58 } |
