--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.7.0/lib/help/amrfinderplus.nf	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,36 @@
+def amrfinderplusHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'amrfinderplus_run': [
+            clihelp: "Run AMRFinderPlus tool. Default: ${params.amrfinderplus_run}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'amrfinderplus_db': [
+            clihelp: 'Path to AMRFinderPlus database. Please note that ' +
+                ' the databases should be ready and formatted with blast for use. ' +
+                'Please read more at: ' +
+                'https://github.com/ncbi/amr/wiki/AMRFinderPlus-database ' +
+                "Default: ${params.amrfinderplus_db}",
+            cliflag: '--database',
+            clivalue: (params.amrfinderplus_db ?: '')
+        ],
+        'amrfinderplus_genes': [
+            clihelp: 'Add the plus genes to the report',
+            cliflag: '--plus',
+            clivalue: (params.amrfinderplus_genes ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file