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1 // Help text for checkm2 predict within CPIPES.
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2
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3 def checkm2predictHelp(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 'checkm2predict_run': [
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12 clihelp: 'Run `checkm2 predict` tool. Default: ' +
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13 (params.checkm2predict_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 'checkm2predict_quiet': [
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18 clihelp: 'Only output errors. ' +
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19 "Default: ${params.checkm2predict_quiet}",
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20 cliflag: '--quiet',
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21 clivalue: (params.checkm2predict_quiet ? ' ' : '')
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22 ],
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23 'checkm2predict_lowmem': [
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24 clihelp: 'Low memory mode. Reduces DIAMOND blocksize to ' +
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25 'significantly reduce RAM usage at the expense of longer runtime. ' +
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26 "Default: ${params.checkm2predict_lowmem}",
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27 cliflag: '--lowmem',
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28 clivalue: (params.checkm2predict_lowmem ? ' ' : '')
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29 ],
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30 'checkm2predict_general': [
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31 clihelp: 'Force the use of the general quality prediction model (gradient boost). ' +
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32 "Default: ${params.checkm2predict_general}",
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33 cliflag: '--general',
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34 clivalue: (params.checkm2predict_general ? ' ' : '')
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35 ],
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36 'checkm2predict_specific': [
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37 clihelp: "Force the use of the specific quality prediction model (neural network) " +
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38 "Default: ${params.checkm2predict_specific}",
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39 cliflag: '--specific',
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40 clivalue: (params.checkm2predict_specific ? ' ' : '')
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41 ],
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42 'checkm2predict_allmodels': [
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43 clihelp: 'Output quality prediction for both models for each genome. ' +
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44 "Default: ${params.checkm2predict_allmodels}",
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45 cliflag: '--allmodels',
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46 clivalue: (params.checkm2predict_allmodels ? ' ' : '')
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47 ],
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48 'checkm2predict_genes': [
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49 clihelp: 'Treat input files as protein files. ' +
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50 "Default: ${params.checkm2predict_genes}",
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51 cliflag: '--genes',
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52 clivalue: (params.checkm2predict_genes ? ' ' : '')
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53 ],
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54 'checkm2predict_x': [
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55 clihelp: 'Extension of input files. ' +
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56 "Default: ${params.checkm2predict_x}",
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57 cliflag: '-x',
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58 clivalue: (params.checkm2predict_x ?: '')
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59 ],
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60 'checkm2predict_tmpdir': [
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61 clihelp: 'Specify an alternate directory for temporary files. ' +
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62 "Default: ${params.checkm2predict_tmpdir}",
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63 cliflag: '--tmpdir',
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64 clivalue: (params.checkm2predict_tmpdir ?: '')
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65 ],
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66 'checkm2predict_rminterfiles': [
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67 clihelp: 'Remove all intermediate files (protein files, diamond output). ' +
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68 "Default: ${params.checkm2predict_rminterfiles}",
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69 cliflag: '--remove_intermediates',
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70 clivalue: (params.checkm2predict_rminterfiles ? ' ' : '')
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71 ],
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72 'checkm2predict_ttable': [
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73 clihelp: 'Provide a specific progidal translation table for bins. The default ' +
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74 'value of false will automatically determine either 11 or 4. ' +
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75 "Default: ${params.checkm2predict_ttable}",
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76 cliflag: '--ttable',
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77 clivalue: (params.checkm2predict_ttable ? ' ' : '')
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78 ],
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79 'checkm2predict_dbg_cos': [
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80 clihelp: 'DEBUG: Write cosine similarity values to a file. ' +
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81 "Default: ${params.checkm2predict_dbg_cos}",
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82 cliflag: '--dbg_cos',
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83 clivalue: (params.checkm2predict_dbg_cos ? ' ' : '')
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84 ],
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85 'checkm2predict_dbg_vectors': [
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86 clihelp: 'DEBUG: Write Dump pickled feature vectors to a file. ' +
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87 "Default: ${params.checkm2predict_dbg_vectors}",
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88 cliflag: '--dbg_vectors',
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89 clivalue: (params.checkm2predict_dbg_vectors ? ' ' : '')
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90 ]
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91 ]
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92
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93 toolspecs.each {
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94 k, v -> tool.text['--' + k] = "${v.clihelp}"
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95 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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96 }
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97
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98 return tool
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99 } |
