kkonganti@1: // Help text for salmon index within CPIPES.
kkonganti@1: 
kkonganti@1: def salmonidxHelp(params) {
kkonganti@1: 
kkonganti@1:     Map tool = [:]
kkonganti@1:     Map toolspecs = [:]
kkonganti@1:     tool.text = [:]
kkonganti@1:     tool.helpparams = [:]
kkonganti@1: 
kkonganti@1:     toolspecs = [
kkonganti@1:         'salmonidx_run': [
kkonganti@1:             clihelp: 'Run `salmon index` tool. Default: ' +
kkonganti@1:                 (params.salmonidx_run ?: false),
kkonganti@1:             cliflag: null,
kkonganti@1:             clivalue: null
kkonganti@1:         ],
kkonganti@1:         'salmonidx_k': [
kkonganti@1:             clihelp: 'The size of k-mers that should be used for the ' +
kkonganti@1:                 " quasi index. Default: ${params.salmonidx_k}",
kkonganti@1:             cliflag: '-k',
kkonganti@1:             clivalue: (params.salmonidx_k ?: '')
kkonganti@1:         ],
kkonganti@1:         'salmonidx_gencode': [
kkonganti@1:             clihelp: 'This flag will expect the input transcript FASTA ' +
kkonganti@1:                 'to be in GENCODE format, and will split the transcript ' +
kkonganti@1:                 'name at the first `|` character. These reduced names ' +
kkonganti@1:                 'will be used in the output and when looking for these ' +
kkonganti@1:                 'transcripts in a gene to transcript GTF.' +
kkonganti@1:                 " Default: ${params.salmonidx_gencode}",
kkonganti@1:             cliflag: '--gencode',
kkonganti@1:             clivalue: (params.salmonidx_gencode ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'salmonidx_features': [
kkonganti@1:             clihelp: 'This flag will expect the input reference to be in the ' +
kkonganti@1:                 'tsv file format, and will split the feature name at the first ' +
kkonganti@1:                 '`tab` character. These reduced names will be used in the output ' +
kkonganti@1:                 'and when looking for the sequence of the features. GTF.' +
kkonganti@1:                 " Default: ${params.salmonidx_features}",
kkonganti@1:             cliflag: '--features',
kkonganti@1:             clivalue: (params.salmonidx_features ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'salmonidx_keepDuplicates': [
kkonganti@1:             clihelp: 'This flag will disable the default indexing behavior of ' +
kkonganti@1:                 'discarding sequence-identical duplicate transcripts. If this ' +
kkonganti@1:                 'flag is passed then duplicate transcripts that appear in the ' +
kkonganti@1:                 'input will be retained and quantified separately.' +
kkonganti@1:                 " Default: ${params.salmonidx_keepDuplicates}",
kkonganti@1:             cliflag: '--keepDuplicates',
kkonganti@1:             clivalue: (params.salmonidx_keepDuplicates ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'salmonidx_keepFixedFasta': [
kkonganti@1:             clihelp: 'Retain the fixed fasta file (without short ' +
kkonganti@1:                 'transcripts and duplicates, clipped, etc.) generated ' +
kkonganti@1:                 "during indexing. Default: ${params.salmonidx_keepFixedFasta}",
kkonganti@1:             cliflag: '--keepFixedFasta',
kkonganti@1:             clivalue: (params.salmonidx_keepFixedFasta ?: '')
kkonganti@1:         ],
kkonganti@1:         'salmonidx_filterSize': [
kkonganti@1:             clihelp: 'The size of the Bloom filter that will be used ' +
kkonganti@1:                 'by TwoPaCo during indexing. The filter will be of ' +
kkonganti@1:                 'size 2^{filterSize}. A value of -1 means that the ' +
kkonganti@1:                 'filter size will be automatically set based on the ' +
kkonganti@1:                 'number of distinct k-mers in the input, as estimated by ' +
kkonganti@1:                 "nthll. Default: ${params.salmonidx_filterSize}",
kkonganti@1:             cliflag: '--filterSize',
kkonganti@1:             clivalue: (params.salmonidx_filterSize ?: '')
kkonganti@1:         ],
kkonganti@1:         'salmonidx_sparse': [
kkonganti@1:             clihelp: 'Build the index using a sparse sampling of k-mer ' +
kkonganti@1:                 'positions This will require less memory (especially ' +
kkonganti@1:                 'during quantification), but will take longer to construct' +
kkonganti@1:                 'and can slow down mapping / alignment.' +
kkonganti@1:                 " Default: ${params.salmonidx_sparse}",
kkonganti@1:             cliflag: '--sparse',
kkonganti@1:             clivalue: (params.salmonidx_sparse ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'salmonidx_n': [
kkonganti@1:             clihelp: 'Do not clip poly-A tails from the ends of target ' +
kkonganti@1:                 "sequences. Default: ${params.salmonidx_n}",
kkonganti@1:             cliflag: '-n',
kkonganti@1:             clivalue: (params.salmonidx_n ? ' ' : '')
kkonganti@1:         ]
kkonganti@1:     ]
kkonganti@1: 
kkonganti@1:     toolspecs.each {
kkonganti@1:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@1:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     return tool
kkonganti@1: }