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1 // Help text for prodigal within CPIPES.
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2
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3 def prodigalHelp(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 'prodigal_run': [
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12 clihelp: 'Run prodigal tool. Default: ' +
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13 (params.prodigal_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 'prodigal_c': [
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18 clihelp: 'Closed ends. Do not allow genes to run off edges. ' +
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19 "Default: ${params.prodigal_c}",
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20 cliflag: '--c',
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21 clivalue: (params.prodigal_c ? ' ' : '')
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22 ],
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23 'prodigal_f': [
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24 clihelp: "Select output format (gbk, gff, or sco). " +
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25 "Default: ${params.prodigal_f}",
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26 cliflag: '-f',
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27 clivalue: (params.prodigal_f ?: '')
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28 ],
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29 'prodigal_g': [
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30 clihelp: "Specify translation table to use." +
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31 "Default: ${params.prodigal_g}",
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32 cliflag: '-g',
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33 clivalue: (params.prodigal_g ?: '')
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34 ],
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35 'prodigal_m': [
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36 clihelp: "Treat runs of N as masked sequence; don't build genes " +
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37 'across them. ' +
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38 "Default: ${params.prodigal_m}",
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39 cliflag: '-m',
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40 clivalue: (params.prodigal_m ? ' ' : '')
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41 ],
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42 'prodigal_n': [
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43 clihelp: 'Bypass Shine-Dalgarno trainer and force a full motif scan. ' +
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44 "Default: ${params.prodigal_n}",
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45 cliflag: '-n',
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46 clivalue: (params.prodigal_n ? ' ' : '')
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47 ],
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48 'prodigal_p': [
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49 clihelp: "Select procedure (single or meta). " +
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50 "Default: ${params.prodigal_p}",
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51 cliflag: '-p',
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52 clivalue: (params.prodigal_p ?: '')
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53 ],
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54 'prodigal_t': [
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55 clihelp: 'Write a training file (if none exists) ending in suffix `.trnd`; ' +
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56 'otherwise, read and use the specified training file. ' +
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57 "Default: ${params.prodigal_t}",
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58 cliflag: '-t',
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59 clivalue: (params.prodigal_t ? ' ' : '')
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60 ]
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61 ]
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62
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63 toolspecs.each {
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64 k, v -> tool.text['--' + k] = "${v.clihelp}"
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65 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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66 }
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67
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68 return tool
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69 } |
