--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/kraken2.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,72 @@
+// Help text for kraken2 within CPIPES.
+
+def kraken2Help(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'kraken2_db': [
+            clihelp: "Absolute path to kraken database. Default: ${params.kraken2_db}",
+            cliflag: '--db',
+            clivalue: null
+        ],
+        'kraken2_confidence': [
+            clihelp: 'Confidence score threshold which must be ' +
+                "between 0 and 1. Default: ${params.kraken2_confidence}",
+            cliflag: '--confidence',
+            clivalue: (params.kraken2_confidence ?: '')
+        ],
+        'kraken2_quick': [
+            clihelp: "Quick operation (use first hit or hits). Default: ${params.kraken2_quick}",
+            cliflag: '--quick',
+            clivalue: (params.kraken2_quick ? ' ' : '')
+        ],
+        'kraken2_use_mpa_style': [
+            clihelp: "Report output like Kraken 1's " +
+                "kraken-mpa-report. Default: ${params.kraken2_use_mpa_style}",
+            cliflag: '--use-mpa-style',
+            clivalue: (params.kraken2_use_mpa_style ? ' ' : '')
+        ],
+        'kraken2_minimum_base_quality': [
+            clihelp: 'Minimum base quality used in classification ' +
+                " which is only effective with FASTQ input. Default: ${params.kraken2_minimum_base_quality}",
+            cliflag: '--minimum-base-quality',
+            clivalue: (params.kraken2_minimum_base_quality ?: '')
+        ],
+        'kraken2_report_zero_counts': [
+            clihelp: 'Report counts for ALL taxa, even if counts are zero. ' +
+                "Default: ${params.kraken2_report_zero_counts}",
+            cliflag: '--report-zero-counts',
+            clivalue: (params.kraken2_report_zero_counts ? ' ' : '')
+        ],
+        'kraken2_report_minmizer_data': [
+            clihelp: 'Report minimizer and distinct minimizer count' +
+                ' information in addition to normal Kraken report. ' +
+                "Default: ${params.kraken2_report_minimizer_data}",
+            cliflag: '--report-minimizer-data',
+            clivalue: (params.kraken2_report_minimizer_data ? ' ' : '')
+        ],
+        'kraken2_use_names': [
+            clihelp: 'Print scientific names instead of just taxids. ' +
+                "Default: ${params.kraken2_use_names}",
+            cliflag: '--use-names',
+            clivalue: (params.kraken2_use_names ? ' ' : '')
+        ],
+        'kraken2_extract_bug': [
+            clihelp: 'Extract the reads or contigs beloging to this bug. ' +
+                "Default: ${params.kraken2_extract_bug}",
+            cliflag: null,
+            clivalue: null
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
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