kkonganti@11: // Help text for gunc run within CPIPES.
kkonganti@11: 
kkonganti@11: def guncrunHelp(params) {
kkonganti@11: 
kkonganti@11:     Map tool = [:]
kkonganti@11:     Map toolspecs = [:]
kkonganti@11:     tool.text = [:]
kkonganti@11:     tool.helpparams = [:]
kkonganti@11: 
kkonganti@11:     toolspecs = [
kkonganti@11:         'guncrun_run': [
kkonganti@11:             clihelp: 'Run `gunc run` tool. Default: ' +
kkonganti@11:                 (params.guncrun_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'guncrun_in_is_fasta': [
kkonganti@11:             clihelp: 'Is input a file in FASTA format. ' +
kkonganti@11:                 "Default: ${params.guncrun_in_is_fasta}",
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'guncrun_in_is_fofn': [
kkonganti@11:             clihelp: 'Is input a file of file names. ' +
kkonganti@11:                 "Default: ${params.guncrun_in_is_fofn}",
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'guncrun_in_is_dir': [
kkonganti@11:             clihelp: 'Is input a directory of FASTA files. ' +
kkonganti@11:                 "Default: ${params.guncrun_in_is_dir}",
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'guncrun_file_suffix': [
kkonganti@11:             clihelp: "Suffix of files if input is a directory. " +
kkonganti@11:                 "Default: ${params.guncrun_file_suffix}",
kkonganti@11:             cliflag: '--file_suffix',
kkonganti@11:             clivalue: (params.guncrun_file_suffix ?: '')
kkonganti@11:         ],
kkonganti@11:         'guncrun_gene_calls': [
kkonganti@11:             clihelp: 'Input files are in FASTA faa format. ' +
kkonganti@11:                 "Default: ${params.guncrun_gene_calls}",
kkonganti@11:             cliflag: '--gene_calls',
kkonganti@11:             clivalue: (params.guncrun_gene_calls ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'guncrun_temp_dir': [
kkonganti@11:             clihelp: 'Path to directory to store temp files. ' +
kkonganti@11:                 "Default: ${params.guncrun_temp_dir}",
kkonganti@11:             cliflag: '--temp_dir',
kkonganti@11:             clivalue: (params.guncrun_temp_dir ?: '')
kkonganti@11:         ],
kkonganti@11:         'guncrun_sensitive': [
kkonganti@11:             clihelp: 'Run with high sensitivity. ' +
kkonganti@11:                 "Default: ${params.guncrun_sensitive}",
kkonganti@11:             cliflag: '--sensitive',
kkonganti@11:             clivalue: (params.guncrun_sensitive ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'guncrun_detailed_output': [
kkonganti@11:             clihelp: 'Output scores for every taxa level. ' +
kkonganti@11:                 "Default: ${params.guncrun_detailed_output}",
kkonganti@11:             cliflag: '--detailed_output',
kkonganti@11:             clivalue: (params.guncrun_detailed_output ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'guncrun_ctg_tax_output': [
kkonganti@11:             clihelp: 'Output assignments for each contig. ' +
kkonganti@11:                 "Default: ${params.guncrun_ctg_tax_output}",
kkonganti@11:             cliflag: '--contig_taxonomy_output',
kkonganti@11:             clivalue: (params.guncrun_ctg_tax_output ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'guncrun_use_species_lvl': [
kkonganti@11:             clihelp: 'Allow species level to be picked as maxCSS. ' +
kkonganti@11:                 "Default: ${params.guncrun_use_species_lvl}",
kkonganti@11:             cliflag: '--use_species_level',
kkonganti@11:             clivalue: (params.guncrun_use_species_lvl ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'guncrun_min_mapped_genes': [
kkonganti@11:             clihelp: 'Do not calculate GUNC score if number of mapped ' +
kkonganti@11:                 'genes is below this value. ' +
kkonganti@11:                 "Default: ${params.guncrun_min_mapped_genes}",
kkonganti@11:             cliflag: '--min_mapped_genes',
kkonganti@11:             clivalue: (params.guncrun_min_mapped_genes ?: '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }