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1 // Help text for sourmash gather within CPIPES.mashsketch
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2
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3 def sourmashgatherHelp(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 'sourmashgather_run': [
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12 clihelp: 'Run `sourmash gather` tool. Default: ' +
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13 (params.sourmashgather_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 'sourmashgather_n': [
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18 clihelp: 'Number of results to report. ' +
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19 'By default, will terminate at --sourmashgather_thr_bp value. ' +
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20 "Default: ${params.sourmashgather_n}",
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21 cliflag: '-n',
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22 clivalue: (params.sourmashgather_n ?: '')
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23 ],
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24 'sourmashgather_thr_bp': [
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25 clihelp: 'Reporting threshold (in bp) for estimated overlap with remaining query. ' +
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26 "Default: ${params.sourmashgather_thr_bp}",
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27 cliflag: '--threshold-bp',
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28 clivalue: (params.sourmashgather_thr_bp ?: '')
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29 ],
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30 'sourmashgather_ani_ci': [
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31 clihelp: 'Output confidence intervals for ANI estimates. ' +
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32 "Default: ${params.sourmashgather_ani_ci}",
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33 cliflag: '--estimate-ani-ci',
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34 clivalue: (params.sourmashgather_ani_ci ? ' ' : '')
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35 ],
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36 'sourmashgather_k': [
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37 clihelp: 'The k-mer size to select. ' +
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38 "Default: ${params.sourmashgather_k}",
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39 cliflag: '-k',
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40 clivalue: (params.sourmashgather_k ?: '')
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41 ],
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42 'sourmashgather_dna': [
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43 clihelp: 'Choose DNA signature. ' +
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44 "Default: ${params.sourmashgather_dna}",
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45 cliflag: '--dna',
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46 clivalue: (params.sourmashgather_dna ? ' ' : '')
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47 ],
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48 'sourmashgather_rna': [
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49 clihelp: 'Choose RNA signature. ' +
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50 "Default: ${params.sourmashgather_rna}",
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51 cliflag: '--rna',
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52 clivalue: (params.sourmashgather_rna ? ' ' : '')
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53 ],
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54 'sourmashgather_nuc': [
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55 clihelp: 'Choose Nucleotide signature. ' +
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56 "Default: ${params.sourmashgather_nuc}",
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57 cliflag: '--nucleotide',
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58 clivalue: (params.sourmashgather_nuc ? ' ' : '')
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59 ],
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60 'sourmashgather_scaled': [
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61 clihelp: 'Scaled value should be between 100 and 1e6. ' +
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62 "Default: ${params.sourmashgather_scaled}",
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63 cliflag: '--scaled',
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64 clivalue: (params.sourmashgather_scaled ?: '')
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65 ],
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66 'sourmashgather_inc_pat': [
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67 clihelp: 'Search only signatures that match this pattern in name, filename, or md5. ' +
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68 "Default: ${params.sourmashgather_inc_pat}",
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69 cliflag: '--include-db-pattern',
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70 clivalue: (params.sourmashgather_inc_pat ?: '')
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71 ],
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72 'sourmashgather_exc_pat': [
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73 clihelp: 'Search only signatures that do not match this pattern in name, filename, or md5. ' +
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74 "Default: ${params.sourmashgather_exc_pat}",
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75 cliflag: '--exclude-db-pattern',
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76 clivalue: (params.sourmashgather_exc_pat ?: '')
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77 ]
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78 ]
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79
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80 toolspecs.each {
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81 k, v -> tool.text['--' + k] = "${v.clihelp}"
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82 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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83 }
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84
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85 return tool
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86 } |
