--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/lib/help/prodigal.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,69 @@
+// Help text for prodigal within CPIPES.
+
+def prodigalHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'prodigal_run': [
+            clihelp: 'Run prodigal tool. Default: ' +
+                (params.prodigal_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'prodigal_c': [
+            clihelp: 'Closed ends. Do not allow genes to run off edges. ' +
+                "Default: ${params.prodigal_c}",
+            cliflag: '--c',
+            clivalue: (params.prodigal_c ? ' ' : '')
+        ],
+        'prodigal_f': [
+            clihelp: "Select output format (gbk, gff, or sco). " +
+                "Default: ${params.prodigal_f}",
+            cliflag: '-f',
+            clivalue: (params.prodigal_f ?: '')
+        ],
+        'prodigal_g': [
+            clihelp: "Specify translation table to use." +
+                "Default: ${params.prodigal_g}",
+            cliflag: '-g',
+            clivalue: (params.prodigal_g ?: '')
+        ],
+        'prodigal_m': [
+            clihelp: "Treat runs of N as masked sequence; don't build genes " +
+                'across them. ' +
+                "Default: ${params.prodigal_m}",
+            cliflag: '-m',
+            clivalue: (params.prodigal_m ? ' ' : '')
+        ],
+        'prodigal_n': [
+            clihelp: 'Bypass Shine-Dalgarno trainer and force a full motif scan. ' +
+                "Default: ${params.prodigal_n}",
+            cliflag: '-n',
+            clivalue: (params.prodigal_n ? ' ' : '')
+        ],
+        'prodigal_p': [
+            clihelp: "Select procedure (single or meta). " +
+                "Default: ${params.prodigal_p}",
+            cliflag: '-p',
+            clivalue: (params.prodigal_p ?: '')
+        ],
+        'prodigal_t': [
+            clihelp: 'Write a training file (if none exists) ending in suffix `.trnd`; ' +
+                'otherwise, read and use the specified training file. ' +
+                "Default: ${params.prodigal_t}",
+            cliflag: '-t',
+            clivalue: (params.prodigal_t ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file