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1 // Help text for kma index within CPIPES.
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2
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3 def kmaindexHelp(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 'kmaindex_run': [
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12 clihelp: 'Run kma index tool. Default: ' +
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13 (params.kmaindex_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 'kmaindex_t_db': [
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18 clihelp: 'Add to existing DB. ' +
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19 "Default: ${params.kmaindex_t_db}",
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20 cliflag: '-t_db',
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21 clivalue: (params.kmaindex_t_db ? ' ' : '')
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22 ],
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23 'kmaindex_k': [
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24 clihelp: 'k-mer size. ' +
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25 "Default: ${params.kmaindex_k}",
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26 cliflag: '-k',
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27 clivalue: (params.kmaindex_k ?: '')
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28 ],
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29 'kmaindex_m': [
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30 clihelp: 'Minimizer size. ' +
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31 "Default: ${params.kmaindex_m}",
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32 cliflag: '-m',
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33 clivalue: (params.kmaindex_m ?: '')
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34 ],
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35 'kmaindex_hc': [
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36 clihelp: 'Homopolymer compression. ' +
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37 "Default: ${params.kmaindex_hc}",
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38 cliflag: '-hc',
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39 clivalue: (params.kmaindex_hc ? ' ' : '')
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40 ],
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41 'kmaindex_ML': [
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42 clihelp: 'Minimum length of templates. Defaults to --kmaindex_k ' +
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43 "Default: ${params.kmaindex_ML}",
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44 cliflag: '-ML',
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45 clivalue: (params.kmaindex_ML ?: '')
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46 ],
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47 'kmaindex_ME': [
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48 clihelp: 'Mega DB. ' +
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49 "Default: ${params.kmaindex_ME}",
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50 cliflag: '-ME',
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51 clivalue: (params.kmaindex_ME ? ' ' : '')
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52 ],
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53 'kmaindex_Sparse': [
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54 clihelp: 'Make Sparse DB. ' +
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55 "Default: ${params.kmaindex_Sparse}",
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56 cliflag: '-Sparse',
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57 clivalue: (params.kmaindex_Sparse ? ' ' : '')
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58 ],
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59 'kmaindex_ht': [
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60 clihelp: 'Homology template. ' +
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61 "Default: ${params.kmaindex_ht}",
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62 cliflag: '-ht',
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63 clivalue: (params.kmaindex_ht ?: '')
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64 ],
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65 'kmaindex_hq': [
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66 clihelp: 'Homology query. ' +
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67 "Default: ${params.kmaindex_hq}",
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68 cliflag: '-hq',
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69 clivalue: (params.kmaindex_hq ?: '')
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70 ],
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71 'kmaindex_and': [
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72 clihelp: 'Both homology thresholds have to reach. ' +
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73 "Default: ${params.kmaindex_and}",
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74 cliflag: '-and',
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75 clivalue: (params.kmaindex_and ? ' ' : '')
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76 ],
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77 'kmaindex_nbp': [
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78 clihelp: 'No bias print. ' +
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79 "Default: ${params.kmaindex_nbp}",
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80 cliflag: '-nbp',
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81 clivalue: (params.kmaindex_nbp ? ' ' : '')
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82 ]
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83 ]
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84
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85 toolspecs.each {
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86 k, v -> tool.text['--' + k] = "${v.clihelp}"
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87 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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88 }
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89
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90 return tool
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91 } |
