kkonganti@11: // Help text for centrifuge within CPIPES.
kkonganti@11: 
kkonganti@11: def centrifugeHelp(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:         'centrifuge_x': [
kkonganti@11:             clihelp: "Absolute path to centrifuge database. Default: ${params.centrifuge_x}",
kkonganti@11:             cliflag: '-x',
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'centrifuge_save_unaligned': [
kkonganti@11:             clihelp: 'Save SINGLE-END reads that did not align. For PAIRED-END' +
kkonganti@11:                 " reads, save read pairs that did not align concordantly. Default: ${params.centrifuge_save_unaligned}",
kkonganti@11:             cliflag: null, // Handled in modules logic.
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'centrifuge_save_aligned': [
kkonganti@11:             clihelp: 'Save SINGLE-END reads that aligned. For PAIRED-END' +
kkonganti@11:                 " reads, save read pairs that aligned concordantly. Default: ${params.centrifuge_save_aligned}",
kkonganti@11:             cliflag: null, // Handled in modules logic.
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'centrifuge_out_fmt_sam': [
kkonganti@11:             clihelp: "Centrifuge output should be in SAM. Default: ${params.centrifuge_save_aligned}",
kkonganti@11:             cliflag: null, // Handled in modules logic.
kkonganti@11:             clivalue: null
kkonganti@11:         ],
kkonganti@11:         'centrifuge_extract_bug': [
kkonganti@11:             clihelp: "Extract this bug from centrifuge results." +
kkonganti@11:                 " Default: ${params.centrifuge_extract_bug}",
kkonganti@11:             cliflag: null, // Handled in modules logic.
kkonganti@11:             clivalue: null,
kkonganti@11:         ],
kkonganti@11:         'centrifuge_ignore_quals': [
kkonganti@11:             clihelp: 'Treat all quality values as 30 on Phred scale. ' +
kkonganti@11:                 "Default: ${params.centrifuge_ignore_quals}",
kkonganti@11:             cliflag: '--ignore-quals',
kkonganti@11:             clivalue: (params.centrifuge_ignore_quals ? ' ' : '')
kkonganti@11:         ]
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     toolspecs.each {
kkonganti@11:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return tool
kkonganti@11: }
kkonganti@11: