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1 // Help text for waterfall_per_snp_cluster.pl (wsnp) within CPIPES.
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2
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3 def wsnpHelp(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 'wsnp_serocol': [
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12 clihelp: 'Column number (non 0-based index) of the PDG metadata file ' +
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13 'by which the serotypes are collected.' +
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14 " Default: ${params.wsnp_serocol}",
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15 cliflag: '--serocol',
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16 clivalue: (params.wsnp_serocol ?: '')
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17 ],
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18 'wsnp_seronamecol': [
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19 clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
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20 'name is "serovar". ' +
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21 " Default: ${params.wsnp_seronamecol}",
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22 cliflag: '--seronamecol',
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23 clivalue: (params.wsnp_seronamecol ?: '')
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24 ],
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25 'wsnp_acc_col': [
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26 clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
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27 'name is "acc". ' +
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28 " Default: ${params.wsnp_seronamecol}",
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29 cliflag: '--acc_col',
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30 clivalue: (params.wsnp_acc_col ?: '')
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31 ],
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32 'wsnp_target_acc_col': [
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33 clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
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34 'name is "target_acc". ' +
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35 " Default: ${params.wsnp_seronamecol}",
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36 cliflag: '--target_acc_col',
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37 clivalue: (params.wsnp_target_acc_col ?: '')
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38 ],
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39 'wsnp_complete_sero': [
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40 clihelp: 'Skip indexing serotypes when the serotype name in the column ' +
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41 'number 49 (non 0-based) of PDG metadata file consists a "-". For example, if ' +
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42 'an accession has a serotype= string as such in column ' +
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43 'number 49 (non 0-based): ' +
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44 '"serotype=- 13:z4,z23:-" ' +
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45 'then, the indexing of that accession is skipped.' +
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46 " Default: ${params.wsnp_complete_sero}",
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47 cliflag: '--complete_serotype_name',
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48 clivalue: (params.wsnp_complete_sero ? ' ' : '')
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49 ],
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50 'wsnp_not_null_serovar': [
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51 clihelp: 'Only index the computed_serotype column ' +
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52 'i.e. column number 49 (non 0-based), if the serovar column' +
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53 ' is not NULL. ' +
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54 " Default: ${params.wsnp_not_null_serovar}",
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55 cliflag: '--not_null_serotype_name',
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56 clivalue: (params.wsnp_not_null_serovar ?: '')
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57 ],
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58 'wsnp_i': [
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59 clihelp: 'Force include this serovar. Ignores ' +
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60 '--wsnp_complete_sero for only this serovar. ' +
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61 'Mention multiple serovars separated by a ! (Exclamation mark). ' +
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62 'Ex: --wsnp_complete_sero I 4,[5],12:i:-!Agona' +
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63 " Default: ${params.wsnp_i}",
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64 cliflag: '-i',
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65 clivalue: (params.wsnp_i ? params.wsnp_i.split(/\!/).join(' -i ').trim().replace(/^\-i\s+/, '') : '')
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66 ],
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67 'wsnp_num': [
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68 clihelp: 'Number of genome accessions to collect per SNP cluster.' +
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69 " Default: ${params.wsnp_num}",
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70 cliflag: '-num',
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71 clivalue: (params.wsnp_num ?: '')
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72 ]
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73 ]
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74
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75 toolspecs.each {
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76 k, v -> tool.text['--' + k] = "${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 } |
