--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/mashscreen.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,49 @@
+// Help text for mash screen within CPIPES.
+
+def mashscreenHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'mashscreen_run': [
+            clihelp: 'Run `mash screen` tool. Default: ' +
+                (params.mashscreen_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'mashscreen_w': [
+            clihelp: 'Winner-takes-all strategy for identity estimates. After counting ' +
+                'hashes for each query, hashes that appear in multiple queries will ' +
+                'be removed from all except the one with the best identity (ties ' +
+                'broken by larger query), and other identities will be reduced. This ' +
+                'removes output redundancy, providing a rough compositional outline. ' +
+                " Default: ${params.mashscreen_w}",
+            cliflag: '-w',
+            clivalue: (params.mashscreen_w ? ' ' : '')
+        ], 
+        'mashscreen_i': [
+            clihelp: 'Minimum identity to report. Inclusive unless set to zero, in which ' +
+                'case only identities greater than zero (i.e. with at least one ' +
+                'shared hash) will be reported. Set to -1 to output everything. ' +
+                "(-1-1). Default: ${params.mashscreen_i}",
+            cliflag: '-i',
+            clivalue: (params.mashscreen_i ?: '')
+        ],
+        'mashscreen_v': [
+            clihelp: 'Maximum p-value to report (0-1). ' +
+                "Default: ${params.mashscreen_v}",
+            cliflag: '-v',
+            clivalue: (params.mashscreen_v ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file