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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 <<<<<<< HEAD
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20 "Defaut: ${params.kmaindex_t_db}",
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21 =======
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22 "Default: ${params.kmaindex_t_db}",
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23 >>>>>>> 0.5.0
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24 cliflag: '-t_db',
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25 clivalue: (params.kmaindex_t_db ? ' ' : '')
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26 ],
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27 'kmaindex_k': [
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28 clihelp: 'k-mer size. ' +
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29 "Default: ${params.kmaindex_k}",
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30 cliflag: '-k',
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31 clivalue: (params.kmaindex_k ?: '')
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32 ],
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33 'kmaindex_m': [
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34 clihelp: 'Minimizer size. ' +
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35 "Default: ${params.kmaindex_m}",
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36 cliflag: '-m',
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37 clivalue: (params.kmaindex_m ?: '')
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38 ],
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39 'kmaindex_hc': [
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40 clihelp: 'Homopolymer compression. ' +
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41 "Default: ${params.kmaindex_hc}",
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42 cliflag: '-hc',
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43 clivalue: (params.kmaindex_hc ? ' ' : '')
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44 ],
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45 'kmaindex_ML': [
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46 clihelp: 'Minimum length of templates. Defaults to --kmaindex_k ' +
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47 "Default: ${params.kmaindex_ML}",
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48 cliflag: '-ML',
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49 clivalue: (params.kmaindex_ML ?: '')
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50 ],
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51 'kmaindex_ME': [
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52 clihelp: 'Mega DB. ' +
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53 "Default: ${params.kmaindex_ME}",
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54 cliflag: '-ME',
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55 clivalue: (params.kmaindex_ME ? ' ' : '')
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56 ],
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57 'kmaindex_Sparse': [
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58 clihelp: 'Make Sparse DB. ' +
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59 "Default: ${params.kmaindex_Sparse}",
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60 cliflag: '-Sparse',
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61 clivalue: (params.kmaindex_Sparse ? ' ' : '')
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62 ],
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63 'kmaindex_ht': [
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64 clihelp: 'Homology template. ' +
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65 "Default: ${params.kmaindex_ht}",
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66 cliflag: '-ht',
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67 clivalue: (params.kmaindex_ht ?: '')
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68 ],
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69 'kmaindex_hq': [
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70 clihelp: 'Homology query. ' +
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71 "Default: ${params.kmaindex_hq}",
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72 cliflag: '-hq',
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73 clivalue: (params.kmaindex_hq ?: '')
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74 ],
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75 'kmaindex_and': [
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76 clihelp: 'Both homology thresholds have to reach. ' +
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77 "Default: ${params.kmaindex_and}",
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78 cliflag: '-and',
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79 clivalue: (params.kmaindex_and ? ' ' : '')
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80 ],
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81 'kmaindex_nbp': [
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82 clihelp: 'No bias print. ' +
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83 "Default: ${params.kmaindex_nbp}",
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84 cliflag: '-nbp',
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85 clivalue: (params.kmaindex_nbp ? ' ' : '')
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86 ]
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87 ]
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88
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89 toolspecs.each {
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90 k, v -> tool.text['--' + k] = "${v.clihelp}"
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91 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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92 }
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93
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94 return tool
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95 } |
