--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/abricate.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,43 @@
+// Help text for abricate within CPIPES.
+
+def abricateHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'abricate_run': [
+            clihelp: 'Run ABRicate tool. Default: ' +
+                (params.abricate_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'abricate_minid': [
+            clihelp: 'Minimum DNA %identity. ' +
+                "Default: " + (params.abricate_minid ?: 80),
+            cliflag: '--minid',
+            clivalue: (params.abricate_minid ?: 80)
+        ], 
+        'abricate_mincov': [
+            clihelp: 'Minimum DNA %coverage. ' +
+                "Default: " + (params.abricate_mincov ?: 80),
+            cliflag: '--mincov',
+            clivalue: (params.abricate_mincov ?: 80)
+        ],
+        'abricate_datadir': [
+            clihelp: 'ABRicate databases folder. ' +
+                "Default: " + (params.abricate_datadir ?: 'undefined'),
+            cliflag: '--datadir',
+            clivalue: (params.abricate_datadir ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file