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1 // Help text for waterfall_per_computed_serotype.pl (wcomp) within CPIPES.
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2
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3 def wcompHelp(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 'wcomp_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.wcomp_serocol}",
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15 cliflag: '--serocol',
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16 clivalue: (params.wcomp_serocol ?: '')
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17 ],
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18 'wcomp_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.wcomp_seronamecol}",
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22 cliflag: '--seronamecol',
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23 clivalue: (params.wcomp_seronamecol ?: '')
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24 ],
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25 'wcomp_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.wcomp_seronamecol}",
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29 cliflag: '--acc_col',
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30 clivalue: (params.wcomp_acc_col ?: '')
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31 ],
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32 'wcomp_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.wcomp_seronamecol}",
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36 cliflag: '--target_acc_col',
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37 clivalue: (params.wcomp_target_acc_col ?: '')
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38 ],
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39 'wcomp_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.wcomp_complete_sero}",
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47 cliflag: '--complete_serotype_name',
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48 clivalue: (params.wcomp_complete_sero ? ' ' : '')
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49 ],
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50 'wcomp_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.wcomp_not_null_serovar}",
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55 cliflag: '--not_null_serotype_name',
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56 clivalue: (params.wcomp_not_null_serovar ?: '')
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57 ],
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58 'wcomp_i': [
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59 clihelp: 'Force include this serovar. Ignores ' +
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60 '--wcomp_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: --wcomp_complete_sero I 4,[5],12:i:-!Agona' +
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63 " Default: ${params.wcomp_i}",
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64 cliflag: '-i',
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65 clivalue: (params.wcomp_i ? params.wcomp_i.split(/\!/).join(' -i ').trim().replace(/^\-i\s+/, '') : '')
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66 ],
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67 'wcomp_num': [
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68 clihelp: 'Number of genome accessions to be collected per serotype.' +
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69 " Default: ${params.wcomp_num}",
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70 cliflag: '-num',
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71 clivalue: (params.wcomp_num ?: '')
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72 ],
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73 'wcomp_min_contig_size': [
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74 clihelp: 'Minimum contig size to consider a genome for indexing.' +
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75 " Default: ${params.wcomp_min_contig_size}",
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76 cliflag: '--min_contig_size',
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77 clivalue: (params.wcomp_min_contig_size ?: '')
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78 ]
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79 ]
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80
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81 toolspecs.each {
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82 k, v -> tool.text['--' + k] = "${v.clihelp}"
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83 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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84 }
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85
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86 return tool
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87 } |
