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1 // Help text for mashtree within CPIPES.
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2
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3 def mashtreeHelp(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 'mashtree_run': [
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12 clihelp: 'Run mashtree tool. Default: ' +
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13 (params.mashtree_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 'mashtree_fofn': [
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18 clihelp: 'Input is a file of file names. ' +
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19 "Default: ${params.mashtree_fofn}",
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20 cliflag: '--file-of-files',
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21 clivalue: (params.mashtree_fofn ? ' ' : '')
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22 ],
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23 'mashtree_trunclength': [
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24 clihelp: 'How many characters to keep in filename. ' +
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25 "Default: ${params.mashtree_trunclength}",
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26 cliflag: '--truncLength',
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27 clivalue: (params.mashtree_trunclength ?: '')
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28 ],
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29 'mashtree_mindepth': [
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30 clihelp: 'If mindepth is zero, then it will be chosen in a smart but slower method, ' +
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31 'to discard lower-abundance kmers. ' +
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32 "Default: ${params.mashtree_mindepth}",
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33 cliflag: '--mindepth',
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34 clivalue: (params.mashtree_mindepth ?: '')
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35 ],
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36 'mashtree_kmerlength': [
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37 clihelp: "The minimum k-mer length. " +
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38 "Default: ${params.mashtree_kmerlength}",
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39 cliflag: '--kmerlength',
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40 clivalue: (params.mashtree_kmerlength ?: '')
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41 ],
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42 'mashtree_sketchsize': [
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43 clihelp: "The minimum `mash` sketch size. " +
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44 "Default: ${params.mashtree_sketchsize}",
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45 cliflag: '--sketchsize',
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46 clivalue: (params.mashtree_sketchsize ?: '')
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47 ],
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48 'mashtree_seed': [
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49 clihelp: "Seed for `mash` sketch. " +
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50 "Default: ${params.mashtree_seed}",
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51 cliflag: '--seed',
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52 clivalue: (params.mashtree_seed ? ' ' : '')
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53 ],
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54 'mashtree_genomesize': [
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55 clihelp: 'Define genome size. ' +
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56 "Default: ${params.mashtree_genomesize}",
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57 cliflag: '--genomesize',
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58 clivalue: (params.mashtree_genomesize ?: '')
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59 ],
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60 'mashtree_sigfigs': [
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61 clihelp: "How many decimal places to use in mash distances. " +
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62 "Default: ${params.mashtree_sigfigs}",
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63 cliflag: '--sigfigs',
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64 clivalue: (params.mashtree_sigfigs ?: '')
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65 ],
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66 'mashtree_sortorder': [
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67 clihelp: 'For neighbor-joining, the sort order can make a difference. ' +
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68 'Options include: ABC (alphabetical), random, input-order. ' +
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69 "Default: ${params.mashtree_sortorder}",
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70 cliflag: '--sort-order',
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71 clivalue: (params.mashtree_sortorder ?: '')
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72 ]
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73 ]
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74
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75 toolspecs.each {
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76 k, v -> tool.text['--' + k] = "${v.clihelp}"
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77 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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78 }
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79
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80 return tool
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81 } |
