--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/lib/help/polypolish.nf	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,49 @@
+// Help text for `polypolish within CPIPES.
+
+def polypolishHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'polypolish_run': [
+            clihelp: 'Run polypolish tool. Default: ' +
+                (params.polypolish_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'polypolish_d': [
+            clihelp: 'A base must occur at least this many times in the pileup to be considered valid. ' +
+                "Default: ${params.polypolish_d}",
+            cliflag: '-d',
+            clivalue: (params.polypolish_d ?: '')
+        ],
+        'polypolish_i': [
+            clihelp: 'A base must make up less than this fraction of the read depth to be considered invalid. ' +
+                "Default: ${params.polypolish_i}",
+            cliflag: '-i',
+            clivalue: (params.polypolish_i ?: '')
+        ],
+        'polypolish_m': [
+            clihelp: 'Ignore alignments with more than this many mismatches and indels. ' +
+                "Default: ${params.polypolish_m}",
+            cliflag: '-m',
+            clivalue: (params.polypolish_m ?: '')
+        ],
+        'polypolish_v': [
+            clihelp: 'A base must make up at least this fraction of the read depth to be considered valid. ' +
+                "Default: ${params.polypolish_v}",
+            cliflag: '-v',
+            clivalue: (params.polypolish_v ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file