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1 def mlstHelp(params) {
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2
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3 Map tool = [:]
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4 Map toolspecs = [:]
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5 tool.text = [:]
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6 tool.helpparams = [:]
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7
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8 toolspecs = [
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9 'mlst_run': [
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10 clihelp: "Run MLST tool. Default: ${params.mlst_run}",
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11 cliflag: null,
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12 clivalue: null
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13 ],
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14 'mlst_legacy': [
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15 clihelp: "Use old legacy output with allele header row (requires --mlst_scheme). " +
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16 "Default: ${params.mlst_legacy}",
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17 cliflag: '--legacy',
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18 clivalue: (params.mlst_legacy ? ' ' : '')
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19 ],
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20 'mlst_scheme': [
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21 clihelp: "Don't autodetect, force this scheme on all inputs. " +
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22 "Default: ${params.mlst_scheme}",
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23 cliflag: '--scheme',
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24 clivalue: (params.mlst_scheme ?: null)
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25 ],
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26 'mlst_minid': [
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27 clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " +
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28 "Default: ${params.mlst_minid}",
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29 cliflag: '--minid',
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30 clivalue: (params.mlst_minid ?: 95)
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31 ],
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32 'mlst_mincov': [
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33 clihelp: 'DNA %cov to report partial allele at all [?].' +
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34 "Default: ${params.mlst_mincov}",
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35 cliflag: '--mincov',
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36 clivalue: (params.mlst_mincov ?: 10)
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37 ],
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38 'mlst_minscore': [
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39 clihelp: 'Minumum score out of 100 to match a scheme.' +
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40 "Default: ${params.mlst_minscore}",
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41 cliflag: '--minscore',
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42 clivalue: (params.mlst_minscore ?: 50)
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43 ],
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44 'mlst_datadir': [
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45 clihelp: 'PubMLST data directory. ' +
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46 "Default: ${params.mlst_datadir}",
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47 cliflag: '--datadir',
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48 clivalue: (params.mlst_datadir ?: null)
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49 ],
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50 'mlst_blastdb': [
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51 clihelp: 'BLAST database directory. ' +
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52 "Default: ${params.mlst_blastdb}",
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53 cliflag: '--blastdb',
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54 clivalue: (params.mlst_blastdb ?: null)
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55 ]
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56 ]
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57
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58 toolspecs.each {
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59 k, v -> tool.text['--' + k] = "${v.clihelp}"
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60 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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61 }
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62
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63 return tool
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64 } |
