kkonganti@17: // Help text for waterfall_per_computed_serotype.pl (wcomp) within CPIPES.
kkonganti@17: 
kkonganti@17: def wcompHelp(params) {
kkonganti@17: 
kkonganti@17:     Map tool = [:]
kkonganti@17:     Map toolspecs = [:]
kkonganti@17:     tool.text = [:]
kkonganti@17:     tool.helpparams = [:]
kkonganti@17: 
kkonganti@17:     toolspecs = [
kkonganti@17:         'wcomp_serocol': [
kkonganti@17:             clihelp: 'Column number (non 0-based index) of the PDG metadata file ' +
kkonganti@17:                 'by which the serotypes are collected.' +
kkonganti@17:                 " Default: ${params.wcomp_serocol}",
kkonganti@17:             cliflag: '--serocol',
kkonganti@17:             clivalue: (params.wcomp_serocol ?: '')
kkonganti@17:         ],
kkonganti@17:         'wcomp_seronamecol': [
kkonganti@17:             clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
kkonganti@17:                 'name is "serovar". ' +
kkonganti@17:                 " Default: ${params.wcomp_seronamecol}",
kkonganti@17:             cliflag: '--seronamecol',
kkonganti@17:             clivalue: (params.wcomp_seronamecol ?: '')
kkonganti@17:         ],
kkonganti@17:         'wcomp_acc_col': [
kkonganti@17:             clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
kkonganti@17:                 'name is "acc". ' +
kkonganti@17:                 " Default: ${params.wcomp_seronamecol}",
kkonganti@17:             cliflag: '--acc_col',
kkonganti@17:             clivalue: (params.wcomp_acc_col ?: '')
kkonganti@17:         ],
kkonganti@17:         'wcomp_target_acc_col': [
kkonganti@17:             clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
kkonganti@17:                 'name is "target_acc". ' +
kkonganti@17:                 " Default: ${params.wcomp_seronamecol}",
kkonganti@17:             cliflag: '--target_acc_col',
kkonganti@17:             clivalue: (params.wcomp_target_acc_col ?: '')
kkonganti@17:         ],
kkonganti@17:         'wcomp_complete_sero': [
kkonganti@17:             clihelp: 'Skip indexing serotypes when the serotype name in the column ' +
kkonganti@17:                 'number 49 (non 0-based) of PDG metadata file consists a "-". For example, if ' +
kkonganti@17:                 'an accession has a serotype= string as such in column ' +
kkonganti@17:                 'number 49 (non 0-based): ' +
kkonganti@17:                 '"serotype=- 13:z4,z23:-" ' +
kkonganti@17:                 'then, the indexing of that accession is skipped.' +
kkonganti@17:                 " Default: ${params.wcomp_complete_sero}",
kkonganti@17:             cliflag: '--complete_serotype_name',
kkonganti@17:             clivalue: (params.wcomp_complete_sero ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'wcomp_not_null_serovar': [
kkonganti@17:             clihelp: 'Only index the computed_serotype column ' +
kkonganti@17:                 'i.e. column number 49 (non 0-based), if the serovar column' +
kkonganti@17:                 ' is not NULL. ' +
kkonganti@17:                 " Default: ${params.wcomp_not_null_serovar}",
kkonganti@17:             cliflag: '--not_null_serotype_name',
kkonganti@17:             clivalue: (params.wcomp_not_null_serovar ?: '')
kkonganti@17:         ],
kkonganti@17:         'wcomp_i': [
kkonganti@17:             clihelp: 'Force include this serovar. Ignores ' +
kkonganti@17:                 '--wcomp_complete_sero for only this serovar. ' +
kkonganti@17:                 'Mention multiple serovars separated by a ! (Exclamation mark). ' +
kkonganti@17:                 'Ex: --wcomp_complete_sero I 4,[5],12:i:-!Agona' +
kkonganti@17:                 " Default: ${params.wcomp_i}",
kkonganti@17:             cliflag: '-i',
kkonganti@17:             clivalue: (params.wcomp_i ? params.wcomp_i.split(/\!/).join(' -i ').trim().replace(/^\-i\s+/, '') : '')
kkonganti@17:         ],
kkonganti@17:         'wcomp_num': [
kkonganti@17:             clihelp: 'Number of genome accessions to be collected per serotype.' +
kkonganti@17:                 " Default: ${params.wcomp_num}",
kkonganti@17:             cliflag: '-num',
kkonganti@17:             clivalue: (params.wcomp_num ?: '')
kkonganti@17:         ],
kkonganti@17:         'wcomp_min_contig_size': [
kkonganti@17:             clihelp: 'Minimum contig size to consider a genome for indexing.' +
kkonganti@17:                 " Default: ${params.wcomp_min_contig_size}",
kkonganti@17:             cliflag: '--min_contig_size',
kkonganti@17:             clivalue: (params.wcomp_min_contig_size ?: '')
kkonganti@17:         ]
kkonganti@17:     ]
kkonganti@17: 
kkonganti@17:     toolspecs.each {
kkonganti@17:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     return tool
kkonganti@17: }