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1 // Help text for sourmash sketch dna within CPIPES.
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2
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3 def sourmashsketchHelp(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 'sourmashsketch_run': [
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12 clihelp: 'Run `sourmash sketch dna` tool. Default: ' +
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13 (params.sourmashsketch_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 'sourmashsketch_mode': [
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18 clihelp: "Select which type of signatures to be created: dna, protein, fromfile or translate. "
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19 + "Default: ${params.sourmashsketch_mode}",
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20 cliflag: "${params.sourmashsketch_mode}",
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21 clivalue: ' '
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22 ],
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23 'sourmashsketch_p': [
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24 clihelp: 'Signature parameters to use. ' +
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25 "Default: ${params.sourmashsketch_p}",
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26 cliflag: '-p',
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27 clivalue: (params.sourmashsketch_p ?: '')
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28 ],
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29 'sourmashsketch_file': [
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30 clihelp: '<path> A text file containing a list of sequence files to load. ' +
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31 "Default: ${params.sourmashsketch_file}",
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32 cliflag: '--from-file',
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33 clivalue: (params.sourmashsketch_file ?: '')
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34 ],
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35 'sourmashsketch_f': [
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36 clihelp: 'Recompute signatures even if the file exists. ' +
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37 "Default: ${params.sourmashsketch_f}",
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38 cliflag: '-f',
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39 clivalue: (params.sourmashsketch_f ? ' ' : '')
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40 ],
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41 'sourmashsketch_merge': [
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42 clihelp: 'Merge all input files into one signature file with the specified name. ' +
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43 "Default: ${params.sourmashsketch_merge}",
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44 cliflag: '--merge',
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45 clivalue: (params.sourmashsketch_merge ? ' ' : '')
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46 ],
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47 'sourmashsketch_singleton': [
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48 clihelp: 'Compute a signature for each sequence record individually. ' +
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49 "Default: ${params.sourmashsketch_singleton}",
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50 cliflag: '--singleton',
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51 clivalue: (params.sourmashsketch_singleton ? ' ' : '')
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52 ],
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53 'sourmashsketch_name': [
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54 clihelp: 'Name the signature generated from each file after the first record in the file. ' +
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55 "Default: ${params.sourmashsketch_name}",
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56 cliflag: '--name-from-first',
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57 clivalue: (params.sourmashsketch_name ? ' ' : '')
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58 ],
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59 'sourmashsketch_randomize': [
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60 clihelp: 'Shuffle the list of input files randomly. ' +
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61 "Default: ${params.sourmashsketch_randomize}",
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62 cliflag: '--randomize',
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63 clivalue: (params.sourmashsketch_randomize ? ' ' : '')
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64 ]
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65 ]
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66
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67 toolspecs.each {
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68 k, v -> tool.text['--' + k] = "${v.clihelp}"
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69 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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70 }
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71
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72 return tool
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73 } |
