--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/lib/help/mlst.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,64 @@
+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_legacy': [
+            clihelp: "Use old legacy output with allele header row (requires --mlst_scheme). " +
+                "Default: ${params.mlst_legacy}",
+            cliflag: '--legacy',
+            clivalue: (params.mlst_legacy ? ' ' : '')
+        ],
+        'mlst_scheme': [
+            clihelp: "Don't autodetect, force this scheme on all inputs. " +
+                "Default: ${params.mlst_scheme}",
+            cliflag: '--scheme',
+            clivalue: (params.mlst_scheme ?: 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)
+        ],
+        'mlst_datadir': [
+            clihelp: 'PubMLST data directory. ' +
+                "Default: ${params.mlst_datadir}",
+            cliflag: '--datadir',
+            clivalue: (params.mlst_datadir ?: null)
+        ],
+        'mlst_blastdb': [
+            clihelp: 'BLAST database directory. ' +
+                "Default: ${params.mlst_blastdb}",
+            cliflag: '--blastdb',
+            clivalue: (params.mlst_blastdb ?: null)
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file