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1 // Help text for pirate within CPIPES.
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2
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3 def pirateHelp(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 'pirate_run': [
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12 clihelp: 'Run pirate tool. Default: ' +
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13 (params.pirate_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 'pirate_steps': [
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18 clihelp: '% identity thresholds to use for pangenome construction. ' +
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19 "Default: ${params.pirate_steps}",
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20 cliflag: '-s',
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21 clivalue: (params.pirate_steps ?: '')
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22 ],
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23 'pirate_features': [
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24 clihelp: 'Choose features to use for pangenome construction. ' +
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25 'Multiple may be entered, seperated by a comma' +
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26 "Default: ${params.pirate_features}",
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27 cliflag: '-f',
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28 clivalue: (params.pirate_features ?: '')
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29 ],
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30 'pirate_nucl': [
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31 clihelp: 'CDS are not translated to AA sequence. ' +
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32 "Default: ${params.pirate_nucl}",
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33 cliflag: '-n',
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34 clivalue: (params.pirate_nucl ? ' ' : '')
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35 ],
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36 'pirate_pan_opt': [
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37 clihelp: 'Additional arguments to pass to pangenome_contruction. ' +
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38 "Default: ${params.pirate_pan_opt}",
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39 cliflag: '--pan-opt',
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40 clivalue: (params.pirate_pan_opt ?: '')
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41 ],
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42 'pirate_pan_off': [
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43 clihelp: "Don't run pangenome tool. " +
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44 "Default: ${params.pirate_pan_off}",
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45 cliflag: '--pan-off',
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46 clivalue: (params.pirate_pan_off ? ' ' : '')
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47 ],
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48 'pirate_min_len': [
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49 clihelp: 'Minimum length for feature extraction. ' +
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50 "Default: ${params.pirate_min_len}",
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51 cliflag: '--min-len',
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52 clivalue: (params.pirate_min_len ?: '')
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53 ],
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54 'pirate_para_off': [
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55 clihelp: 'Switch off paralog identification. ' +
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56 "Default: ${params.pirate_para_off}",
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57 cliflag: '--para-off',
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58 clivalue: (params.pirate_para_off ?: '')
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59 ],
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60 'pirate_para_args': [
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61 clihelp: 'Options to pass to paralog splitting algorithm. ' +
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62 "Default: ${params.pirate_para_args}",
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63 cliflag: '--para-args',
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64 clivalue: (params.pirate_para_args ?: '')
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65 ],
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66 'pirate_classify_off': [
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67 clihelp: 'Do not classify paralogs, assumes this has been ' +
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68 'run previously. ' +
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69 "Default: ${params.pirate_classify_off}",
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70 cliflag: '--classify-off',
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71 clivalue: (params.pirate_classify_off ? ' ' : '')
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72 ],
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73 'pirate_align': [
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74 clihelp: 'align all genes and produce core/pangenome alignments. ' +
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75 "Default: ${params.pirate_align}",
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76 cliflag: '--align',
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77 clivalue: (params.pirate_align ? ' ' : '')
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78 ],
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79 'pirate_rplots': [
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80 clihelp: 'Plot summaries using R. ' +
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81 "Default: ${params.pirate_rplots}",
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82 cliflag: '--rplots',
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83 clivalue: (params.pirate_rplots ? ' ' : '')
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84 ]
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85 ]
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86
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87 toolspecs.each {
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88 k, v -> tool.text['--' + k] = "${v.clihelp}"
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89 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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90 }
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91
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92 return tool
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93 } |
