kkonganti@17: // Help text for spades within CPIPES.
kkonganti@17: 
kkonganti@17: def spadesHelp(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:         'spades_run': [
kkonganti@17:             clihelp: 'Run SPAdes assembler. Default: ' +
kkonganti@17:                 (params.spades_run ?: false),
kkonganti@17:             cliflag: null,
kkonganti@17:             clivalue: null
kkonganti@17:         ],
kkonganti@17:         'spades_isolate': [
kkonganti@17:             clihelp: 'This flag is highly recommended for high-coverage isolate and ' +
kkonganti@17:                 "multi-cell data. Default: ${params.spades_isolate}",
kkonganti@17:             cliflag: '--isolate',
kkonganti@17:             clivalue: (params.spades_isolate ? ' ' : '')
kkonganti@17:         ], 
kkonganti@17:         'spades_sc': [
kkonganti@17:             clihelp: 'This flag is required for MDA (single-cell) data. ' +
kkonganti@17:                 "Default: ${params.spades_sc}",
kkonganti@17:             cliflag: '--sc',
kkonganti@17:             clivalue: (params.spades_sc ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_meta': [
kkonganti@17:             clihelp: 'This flag is required for metagenomic data. ' +
kkonganti@17:                 "Default: ${params.spades_meta}",
kkonganti@17:             cliflag: '--meta',
kkonganti@17:             clivalue: (params.spades_meta ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_bio': [
kkonganti@17:             clihelp: 'This flag is required for biosytheticSPAdes mode. ' +
kkonganti@17:                 "Default: ${params.spades_bio}",
kkonganti@17:             cliflag: '--bio',
kkonganti@17:             clivalue: (params.spades_bio ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_corona': [
kkonganti@17:             clihelp: 'This flag is required for coronaSPAdes mode. ' +
kkonganti@17:                 "Default: ${params.spades_corona}",
kkonganti@17:             cliflag: '--corona',
kkonganti@17:             clivalue: (params.spades_corona ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_rna': [
kkonganti@17:             clihelp: 'This flag is required for RNA-Seq data. ' +
kkonganti@17:                 "Default: ${params.spades_rna}",
kkonganti@17:             cliflag: '--rna',
kkonganti@17:             clivalue: (params.spades_rna ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_plasmid': [
kkonganti@17:             clihelp: 'Runs plasmidSPAdes pipeline for plasmid detection. ' +
kkonganti@17:                 "Default: ${params.spades_plasmid}",
kkonganti@17:             cliflag: '--plasmid',
kkonganti@17:             clivalue: (params.spades_plasmid ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_metaviral': [
kkonganti@17:             clihelp: 'Runs metaviralSPAdes pipeline for virus detection. ' +
kkonganti@17:                 "Default: ${params.spades_metaviral}",
kkonganti@17:             cliflag: '--metaviral',
kkonganti@17:             clivalue: (params.spades_metaviral ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_metaplasmid': [
kkonganti@17:             clihelp: 'Runs metaplasmidSPAdes pipeline for plasmid detection in ' +
kkonganti@17:                 "metagenomics datasets. Default: ${params.spades_metaplasmid}",
kkonganti@17:             cliflag: '--metaplasmid',
kkonganti@17:             clivalue: (params.spades_metaplasmid ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_rnaviral': [
kkonganti@17:             clihelp: 'This flag enables virus assembly module from RNA-Seq data. ' +
kkonganti@17:                 "Default: ${params.spades_rnaviral}",
kkonganti@17:             cliflag: '--rnaviral',
kkonganti@17:             clivalue: (params.spades_rnaviral ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_iontorrent': [
kkonganti@17:             clihelp: 'This flag is required for IonTorrent data. ' +
kkonganti@17:                 "Default: ${params.spades_iontorrent}",
kkonganti@17:             cliflag: '--iontorrent',
kkonganti@17:             clivalue: (params.spades_iontorrent ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_only_assembler': [
kkonganti@17:             clihelp: 'Runs only the SPAdes assembler module (without read error correction). ' +
kkonganti@17:                 "Default: ${params.spades_only_assembler}",
kkonganti@17:             cliflag: '--only-assembler',
kkonganti@17:             clivalue: (params.spades_only_assembler ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_careful': [
kkonganti@17:             clihelp: 'Tries to reduce the number of mismatches and short indels in the assembly. ' +
kkonganti@17:                 "Default: ${params.spades_careful}",
kkonganti@17:             cliflag: '--careful',
kkonganti@17:             clivalue: (params.spades_careful ? ' ' : '')
kkonganti@17:         ],
kkonganti@17:         'spades_cov_cutoff': [
kkonganti@17:             clihelp: 'Coverage cutoff value (a positive float number). ' +
kkonganti@17:                 "Default: ${params.spades_cov_cutoff}",
kkonganti@17:             cliflag: '--cov-cutoff',
kkonganti@17:             clivalue: (params.spades_cov_cutoff ?: '')
kkonganti@17:         ],
kkonganti@17:         'spades_k': [
kkonganti@17:             clihelp: 'List of k-mer sizes (must be odd and less than 128). ' +
kkonganti@17:                 "Default: ${params.spades_k}",
kkonganti@17:             cliflag: '-k',
kkonganti@17:             clivalue: (params.spades_k ?: '')
kkonganti@17:         ],
kkonganti@17:         'spades_hmm': [
kkonganti@17:             clihelp: 'Directory with custom hmms that replace the default ones (very rare). ' +
kkonganti@17:                 "Default: ${params.spades_hmm}",
kkonganti@17:             cliflag: '--custom-hmms',
kkonganti@17:             clivalue: (params.spades_hmm ?: '')
kkonganti@17:         ]
kkonganti@17:     ]
kkonganti@17: 
kkonganti@17:     toolspecs.each {
kkonganti@17:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     return tool
kkonganti@17: }