kkonganti@11: // Help text for pirate within CPIPES.
kkonganti@11: 
kkonganti@11: def pirateHelp(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:         'pirate_run': [
kkonganti@11:             clihelp: 'Run pirate tool. Default: ' +
kkonganti@11:                 (params.pirate_run ?: false),
kkonganti@11:             cliflag: null,
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'pirate_steps': [
kkonganti@11:             clihelp: '% identity thresholds to use for pangenome construction. ' +
kkonganti@11:                 "Default: ${params.pirate_steps}",
kkonganti@11:             cliflag: '-s',
kkonganti@11:             clivalue: (params.pirate_steps ?: '')
kkonganti@11:         ],
kkonganti@11:         'pirate_features': [
kkonganti@11:             clihelp: 'Choose features to use for pangenome construction. ' +
kkonganti@11:                 'Multiple may be entered, seperated by a comma' +
kkonganti@11:                 "Default: ${params.pirate_features}",
kkonganti@11:             cliflag: '-f',
kkonganti@11:             clivalue: (params.pirate_features ?: '')
kkonganti@11:         ],
kkonganti@11:         'pirate_nucl': [
kkonganti@11:             clihelp: 'CDS are not translated to AA sequence. ' +
kkonganti@11:                 "Default: ${params.pirate_nucl}",
kkonganti@11:             cliflag: '-n',
kkonganti@11:             clivalue: (params.pirate_nucl ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'pirate_pan_opt': [
kkonganti@11:             clihelp: 'Additional arguments to pass to pangenome_contruction. ' +
kkonganti@11:                 "Default: ${params.pirate_pan_opt}",
kkonganti@11:             cliflag: '--pan-opt',
kkonganti@11:             clivalue: (params.pirate_pan_opt ?: '')
kkonganti@11:         ],
kkonganti@11:         'pirate_pan_off': [
kkonganti@11:             clihelp: "Don't run pangenome tool. " +
kkonganti@11:                 "Default: ${params.pirate_pan_off}",
kkonganti@11:             cliflag: '--pan-off',
kkonganti@11:             clivalue: (params.pirate_pan_off ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'pirate_min_len': [
kkonganti@11:             clihelp: 'Minimum length for feature extraction. ' +
kkonganti@11:                 "Default: ${params.pirate_min_len}",
kkonganti@11:             cliflag: '--min-len',
kkonganti@11:             clivalue: (params.pirate_min_len ?: '')
kkonganti@11:         ],
kkonganti@11:         'pirate_para_off': [
kkonganti@11:             clihelp: 'Switch off paralog identification. ' +
kkonganti@11:                 "Default: ${params.pirate_para_off}",
kkonganti@11:             cliflag: '--para-off',
kkonganti@11:             clivalue: (params.pirate_para_off ?: '')
kkonganti@11:         ],
kkonganti@11:         'pirate_para_args': [
kkonganti@11:             clihelp: 'Options to pass to paralog splitting algorithm. ' +
kkonganti@11:                 "Default: ${params.pirate_para_args}",
kkonganti@11:             cliflag: '--para-args',
kkonganti@11:             clivalue: (params.pirate_para_args ?: '')
kkonganti@11:         ],
kkonganti@11:         'pirate_classify_off': [
kkonganti@11:             clihelp: 'Do not classify paralogs, assumes this has been ' +
kkonganti@11:                 'run previously. ' +
kkonganti@11:                 "Default: ${params.pirate_classify_off}",
kkonganti@11:             cliflag: '--classify-off',
kkonganti@11:             clivalue: (params.pirate_classify_off ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'pirate_align': [
kkonganti@11:             clihelp: 'align all genes and produce core/pangenome alignments. ' +
kkonganti@11:                 "Default: ${params.pirate_align}",
kkonganti@11:             cliflag: '--align',
kkonganti@11:             clivalue: (params.pirate_align ? ' ' : '')
kkonganti@11:         ],
kkonganti@11:         'pirate_rplots': [
kkonganti@11:             clihelp: 'Plot summaries using R. ' +
kkonganti@11:                 "Default: ${params.pirate_rplots}",
kkonganti@11:             cliflag: '--rplots',
kkonganti@11:             clivalue: (params.pirate_rplots ? ' ' : '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }