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1 // Help text for get_top_unique_mash_hit_genomes.py (tuspy) within CPIPES.
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2
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3 def tuspyHelp(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 'tuspy_run': [
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12 clihelp: 'Run the get_top_unique_mash_hits_genomes.py ' +
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13 'script. Default: ' +
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14 (params.tuspy_run ?: false),
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15 cliflag: null,
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16 clivalue: null
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17 ],
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18 'tuspy_s': [
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19 clihelp: 'Absolute UNIX path to metadata text file with the ' +
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20 'field separator, | and ' +
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21 '5 fields: serotype|asm_lvl|asm_url|snp_cluster_id' +
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22 'Ex: serotype=Derby,antigen_formula=4:f,g:-|Scaffold|402440|ftp://...' +
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23 '|PDS000096654.2. Mentioning this option will create a pickle file for the ' +
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24 'provided metadata and exits.' +
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25 " Default: ${params.tuspy_s}",
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26 cliflag: '-s',
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27 clivalue: (params.tuspy_s ?: '')
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28 ],
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29 'tuspy_m': [
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30 clihelp: 'Absolute UNIX path to mash screen results file.' +
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31 " Default: ${params.tuspy_m}",
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32 cliflag: '-m',
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33 clivalue: (params.tuspy_m ?: '')
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34 ],
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35 'tuspy_ps': [
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36 clihelp: 'Absolute UNIX Path to serialized metadata object ' +
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37 'in a pickle file.' +
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38 " Default: ${params.tuspy_ps}",
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39 cliflag: '-ps',
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40 clivalue: (params.tuspy_ps ?: '')
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41 ],
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42 'tuspy_gd': [
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43 clihelp: 'Absolute UNIX Path to directory containing ' +
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44 'gzipped genome FASTA files.' +
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45 " Default: ${params.tuspy_gd}",
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46 cliflag: '-gd',
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47 clivalue: (params.tuspy_gd ?: '')
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48 ],
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49 'tuspy_gds': [
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50 clihelp: 'Genome FASTA file suffix to search for in the ' +
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51 'genome directory.' +
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52 " Default: ${params.tuspy_gds}",
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53 cliflag: '-gds',
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54 clivalue: (params.tuspy_gds ?: '')
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55 ],
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56 'tuspy_n': [
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57 clihelp: 'Return up to this many number of top N unique ' +
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58 'genome accession hits.' +
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59 " Default: ${params.tuspy_n}",
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60 cliflag: '-n',
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61 clivalue: (params.tuspy_n ?: '')
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62 ],
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63 'tuspy_skip': [
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64 clihelp: 'Skip all hits which belong to the following bioproject ' +
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65 'accession(s). A comma separated list of more than one bioproject. ' +
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66 " Default: ${params.tuspy_skip}",
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67 cliflag: '-skip',
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68 clivalue: (params.tuspy_skip ?: '')
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69 ]
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70 ]
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71
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72 toolspecs.each {
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73 k, v -> tool.text['--' + k] = "${v.clihelp}"
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74 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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75 }
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76
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77 return tool
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78 } |
