kkonganti@11: // Help text for sourmash sketch dna within CPIPES.
kkonganti@11: 
kkonganti@11: def sourmashsketchHelp(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:         'sourmashsketch_run': [
kkonganti@11:             clihelp: 'Run `sourmash sketch dna` tool. Default: ' +
kkonganti@11:                 (params.sourmashsketch_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'sourmashsketch_mode': [
kkonganti@11:             clihelp: "Select which type of signatures to be created: dna, protein, fromfile or translate. "
kkonganti@11:                 + "Default: ${params.sourmashsketch_mode}",
kkonganti@11:             cliflag: "${params.sourmashsketch_mode}",
kkonganti@11:             clivalue: ' '
kkonganti@11:         ],
kkonganti@11:         'sourmashsketch_p': [
kkonganti@11:             clihelp: 'Signature parameters to use. ' +
kkonganti@11:                 "Default: ${params.sourmashsketch_p}",
kkonganti@11:             cliflag: '-p',
kkonganti@11:             clivalue: (params.sourmashsketch_p ?: '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsketch_file': [
kkonganti@11:             clihelp: '<path>  A text file containing a list of sequence files to load. ' +
kkonganti@11:                 "Default: ${params.sourmashsketch_file}",
kkonganti@11:             cliflag: '--from-file',
kkonganti@11:             clivalue: (params.sourmashsketch_file ?: '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsketch_f': [
kkonganti@11:             clihelp: 'Recompute signatures even if the file exists. ' +
kkonganti@11:                 "Default: ${params.sourmashsketch_f}",
kkonganti@11:             cliflag: '-f',
kkonganti@11:             clivalue: (params.sourmashsketch_f ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsketch_merge': [
kkonganti@11:             clihelp: 'Merge all input files into one signature file with the specified name. ' +
kkonganti@11:                 "Default: ${params.sourmashsketch_merge}",
kkonganti@11:             cliflag: '--merge',
kkonganti@11:             clivalue: (params.sourmashsketch_merge ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsketch_singleton': [
kkonganti@11:             clihelp: 'Compute a signature for each sequence record individually. ' +
kkonganti@11:                 "Default: ${params.sourmashsketch_singleton}",
kkonganti@11:             cliflag: '--singleton',
kkonganti@11:             clivalue: (params.sourmashsketch_singleton ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsketch_name': [
kkonganti@11:             clihelp: 'Name the signature generated from each file after the first record in the file. ' +
kkonganti@11:                 "Default: ${params.sourmashsketch_name}",
kkonganti@11:             cliflag: '--name-from-first',
kkonganti@11:             clivalue: (params.sourmashsketch_name ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'sourmashsketch_randomize': [
kkonganti@11:             clihelp: 'Shuffle the list of input files randomly. ' +
kkonganti@11:                 "Default: ${params.sourmashsketch_randomize}",
kkonganti@11:             cliflag: '--randomize',
kkonganti@11:             clivalue: (params.sourmashsketch_randomize ? ' ' : '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }