--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/lib/help/mlst.nf	Fri May 29 13:27:47 2026 +0000
@@ -0,0 +1,40 @@
+def mlstHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'mlst_run': [
+            clihelp: "Run MLST tool. Default: ${params.mlst_run}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'mlst_minid': [
+            clihelp: "DNA %identity of full allelle to consider 'similar' [~]. " +
+                "Default: ${params.mlst_minid}",
+            cliflag: '--minid',
+            clivalue: (params.mlst_minid ?: 95)
+        ],
+        'mlst_mincov': [
+            clihelp: 'DNA %cov to report partial allele at all [?].' +
+                "Default: ${params.mlst_mincov}",
+            cliflag: '--mincov',
+            clivalue: (params.mlst_mincov ?: 10)
+        ],
+        'mlst_minscore': [
+            clihelp: 'Minumum score out of 100 to match a scheme.' +
+                "Default: ${params.mlst_minscore}",
+            cliflag: '--minscore',
+            clivalue: (params.mlst_minscore ?: 50)
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file