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kkonganti@11
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1 // Help text for megahit within CPIPES.
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2
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3 def megahitHelp(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 'megahit_run': [
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12 clihelp: 'Run MEGAHIT assembler. Default: ' +
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13 (params.megahit_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 'megahit_min_count': [
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18 clihelp: '<int>. Minimum multiplicity for filtering (k_min+1)-mers. ' +
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19 "Default: ${params.megahit_min_count}",
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20 cliflag: '--min-count',
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21 clivalue: (params.megahit_min_count ?: '')
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22 ],
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23 'megahit_k_list': [
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24 clihelp: 'Comma-separated list of kmer size. All values must be odd, in ' +
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25 "the range 15-255, increment should be <= 28. Ex: '21,29,39,59,79,99,119,141'. " +
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26 "Default: ${params.megahit_k_list}",
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27 cliflag: '--k-list',
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28 clivalue: (params.megahit_k_list ?: '')
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29 ],
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30 'megahit_no_mercy': [
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31 clihelp: 'Do not add mercy k-mers. ' +
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32 "Default: ${params.megahit_no_mercy}",
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33 cliflag: '--no-mercy',
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34 clivalue: (params.megahit_no_mercy ? ' ' : '')
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35 ],
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36 'megahit_bubble_level': [
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37 clihelp: '<int>. Intensity of bubble merging (0-2), 0 to disable. ' +
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38 "Default: ${params.megahit_bubble_level}",
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39 cliflag: '--bubble-level',
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40 clivalue: (params.megahit_bubble_level ?: '')
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41 ],
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42 'megahit_merge_level': [
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43 clihelp: '<l,s>. Merge complex bubbles of length <= l*kmer_size and ' +
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44 "similarity >= s. Default: ${params.megahit_merge_level}",
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45 cliflag: '--merge-level',
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46 clivalue: (params.megahit_merge_level ?: '')
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47 ],
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48 'megahit_prune_level': [
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49 clihelp: '<int>. Strength of low depth pruning (0-3). ' +
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50 "Default: ${params.megahit_prune_level}",
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51 cliflag: '--prune-level',
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52 clivalue: (params.megahit_prune_level ?: '')
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53 ],
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54 'megahit_prune_depth': [
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55 clihelp: '<int>. Remove unitigs with avg k-mer depth less than this value. ' +
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56 "Default: ${params.megahit_prune_depth}",
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57 cliflag: '--prune-depth',
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58 clivalue: (params.megahit_prune_depth ?: '')
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59 ],
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60 'megahit_low_local_ratio': [
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61 clihelp: '<float>. Ratio threshold to define low local coverage contigs. ' +
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62 "Default: ${params.megahit_low_local_ratio}",
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63 cliflag: '--low-local-ratio',
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64 clivalue: (params.megahit_low_local_ratio ?: '')
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65 ],
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66 'megahit_max_tip_len': [
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67 clihelp: '<int>. remove tips less than this value [<int> * k]. ' +
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68 "Default: ${params.megahit_max_tip_len}",
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69 cliflag: '--max-tip-len',
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70 clivalue: (params.megahit_max_tip_len ?: '')
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71 ],
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72 'megahit_no_local': [
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73 clihelp: 'Disable local assembly. ' +
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74 "Default: ${params.megahit_no_local}",
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75 cliflag: '--no-local',
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76 clivalue: (params.megahit_no_local ? ' ' : '')
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77 ],
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78 'megahit_kmin_1pass': [
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79 clihelp: 'Use 1pass mode to build SdBG of k_min. ' +
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80 "Default: ${params.megahit_kmin_1pass}",
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81 cliflag: '--kmin-1pass',
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82 clivalue: (params.megahit_kmin_1pass ? ' ' : '')
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83 ],
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84 'megahit_preset': [
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85 clihelp: '<str>. Override a group of parameters. Valid values are '+
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86 "meta-sensitive which enforces '--min-count 1 --k-list 21,29,39,49,...,129,141', " +
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87 'meta-large (large & complex metagenomes, like soil) which enforces ' +
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88 "'--k-min 27 --k-max 127 --k-step 10'. " +
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89 "Default: ${params.megahit_preset}",
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90 cliflag: '--preset',
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91 clivalue: (params.megahit_preset ?: '')
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92 ],
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93 'megahit_mem_flag': [
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94 clihelp: '<int>. SdBG builder memory mode. 0: minimum; 1: moderate; 2: use all memory specified. ' +
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95 "Default: ${params.megahit_mem_flag}",
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96 cliflag: '--mem-flag',
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97 clivalue: (params.megahit_mem_flag ?: '')
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98 ],
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99 'megahit_min_contig_len': [
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100 clihelp: '<int>. Minimum length of contigs to output. ' +
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101 "Default: ${params.megahit_min_contig_len}",
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102 cliflag: '--use-gpu',
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103 clivalue: (params.megahit_min_contig_len ?: '')
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104 ]
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105 ]
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106
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107 toolspecs.each {
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108 k, v -> tool.text['--' + k] = "${v.clihelp}"
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109 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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110 }
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111
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112 return tool
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113 } |
