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1 // Help text for gunc run within CPIPES.
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2
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3 def guncrunHelp(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 'guncrun_run': [
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12 clihelp: 'Run `gunc run` tool. Default: ' +
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13 (params.guncrun_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 'guncrun_in_is_fasta': [
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18 clihelp: 'Is input a file in FASTA format. ' +
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19 "Default: ${params.guncrun_in_is_fasta}",
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20 cliflag: null,
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21 clivalue: null
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22 ],
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23 'guncrun_in_is_fofn': [
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24 clihelp: 'Is input a file of file names. ' +
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25 "Default: ${params.guncrun_in_is_fofn}",
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26 cliflag: null,
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27 clivalue: null
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28 ],
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29 'guncrun_in_is_dir': [
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30 clihelp: 'Is input a directory of FASTA files. ' +
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31 "Default: ${params.guncrun_in_is_dir}",
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32 cliflag: null,
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33 clivalue: null
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34 ],
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35 'guncrun_file_suffix': [
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36 clihelp: "Suffix of files if input is a directory. " +
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37 "Default: ${params.guncrun_file_suffix}",
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38 cliflag: '--file_suffix',
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39 clivalue: (params.guncrun_file_suffix ?: '')
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40 ],
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41 'guncrun_gene_calls': [
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42 clihelp: 'Input files are in FASTA faa format. ' +
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43 "Default: ${params.guncrun_gene_calls}",
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44 cliflag: '--gene_calls',
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45 clivalue: (params.guncrun_gene_calls ? ' ' : '')
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46 ],
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47 'guncrun_temp_dir': [
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48 clihelp: 'Path to directory to store temp files. ' +
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49 "Default: ${params.guncrun_temp_dir}",
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50 cliflag: '--temp_dir',
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51 clivalue: (params.guncrun_temp_dir ?: '')
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52 ],
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53 'guncrun_sensitive': [
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54 clihelp: 'Run with high sensitivity. ' +
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55 "Default: ${params.guncrun_sensitive}",
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56 cliflag: '--sensitive',
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57 clivalue: (params.guncrun_sensitive ? ' ' : '')
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58 ],
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59 'guncrun_detailed_output': [
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60 clihelp: 'Output scores for every taxa level. ' +
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61 "Default: ${params.guncrun_detailed_output}",
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62 cliflag: '--detailed_output',
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63 clivalue: (params.guncrun_detailed_output ? ' ' : '')
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64 ],
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65 'guncrun_ctg_tax_output': [
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66 clihelp: 'Output assignments for each contig. ' +
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67 "Default: ${params.guncrun_ctg_tax_output}",
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68 cliflag: '--contig_taxonomy_output',
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69 clivalue: (params.guncrun_ctg_tax_output ? ' ' : '')
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70 ],
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71 'guncrun_use_species_lvl': [
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72 clihelp: 'Allow species level to be picked as maxCSS. ' +
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73 "Default: ${params.guncrun_use_species_lvl}",
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74 cliflag: '--use_species_level',
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75 clivalue: (params.guncrun_use_species_lvl ? ' ' : '')
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76 ],
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77 'guncrun_min_mapped_genes': [
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78 clihelp: 'Do not calculate GUNC score if number of mapped ' +
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79 'genes is below this value. ' +
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80 "Default: ${params.guncrun_min_mapped_genes}",
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81 cliflag: '--min_mapped_genes',
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82 clivalue: (params.guncrun_min_mapped_genes ?: '')
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83 ]
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84 ]
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85
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86 toolspecs.each {
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87 k, v -> tool.text['--' + k] = "${v.clihelp}"
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88 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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89 }
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90
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91 return tool
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92 } |
