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1 // Help text for dl_pubmlst_profiles_and_schemes.py (dpubmlstpy) within CPIPES.
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2
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3 def dpubmlstpyHelp(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 'dpubmlstpy_run': [
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12 clihelp: 'Run the dl_pubmlst_profiles_and_schemes.py ' +
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13 'script. Default: ' +
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14 (params.dpubmlstpy_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 'dpubmlstpy_org': [
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19 clihelp: 'The organism name to download the MLST alleles ' +
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20 'FASTA and profile CSV for. ' +
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21 " Default: ${params.dpubmlstpy_org}",
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22 cliflag: '-org',
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23 clivalue: (params.dpubmlstpy_org ?: '')
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24 ],
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25 'dpubmlstpy_mlsts': [
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26 clihelp: 'The MLST scheme ID to download. ' +
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27 " Default: ${params.dpubmlstpy_mlsts}",
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28 cliflag: '-mlsts',
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29 clivalue: (params.dpubmlstpy_mlsts ?: '')
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30 ],
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31 'dpubmlstpy_profile': [
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32 clihelp: 'The MLST profile name in the scheme. ' +
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33 " Default: ${params.dpubmlstpy_profile}",
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34 cliflag: '-profile',
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35 clivalue: (params.dpubmlstpy_profile ?: '')
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36 ],
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37 'dpubmlstpy_loci': [
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38 clihelp: 'The key name in the JSON response which lists the ' +
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39 'allele URLs to download. ' +
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40 " Default: ${params.dpubmlstpy_loci}",
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41 cliflag: '-loci',
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42 clivalue: (params.dpubmlstpy_loci ?: '')
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43 ],
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44 'dpubmlstpy_suffix': [
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45 clihelp: 'What should be the suffix of the downloaded allele ' +
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46 'FASTA. ' +
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47 " Default: ${params.dpubmlstpy_suffix}",
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48 cliflag: '-suffix',
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49 clivalue: (params.dpubmlstpy_suffix ?: '')
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50 ],
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51 'dpubmlstpy_akey': [
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52 clihelp: 'What is the key in the JSON response that contains ' +
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53 'the URL for allele FASTA. ' +
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54 " Default: ${params.dpubmlstpy_akey}",
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55 cliflag: '-akey',
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56 clivalue: (params.dpubmlstpy_akey ?: '')
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57 ],
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58 'dpubmlstpy_id': [
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59 clihelp: 'What is the key in the JSON response that contains ' +
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60 'the name of the allele FASTA. ' +
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61 " Default: ${params.dpubmlstpy_id}",
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62 cliflag: '-id',
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63 clivalue: (params.dpubmlstpy_id ?: '')
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64 ]
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65 ]
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66
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67 toolspecs.each {
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68 k, v -> tool.text['--' + k] = "${v.clihelp}"
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69 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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70 }
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71
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72 return tool
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73 } |
