--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/lib/help/pirate.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,93 @@
+// Help text for pirate within CPIPES.
+
+def pirateHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'pirate_run': [
+            clihelp: 'Run pirate tool. Default: ' +
+                (params.pirate_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'pirate_steps': [
+            clihelp: '% identity thresholds to use for pangenome construction. ' +
+                "Default: ${params.pirate_steps}",
+            cliflag: '-s',
+            clivalue: (params.pirate_steps ?: '')
+        ],
+        'pirate_features': [
+            clihelp: 'Choose features to use for pangenome construction. ' +
+                'Multiple may be entered, seperated by a comma' +
+                "Default: ${params.pirate_features}",
+            cliflag: '-f',
+            clivalue: (params.pirate_features ?: '')
+        ],
+        'pirate_nucl': [
+            clihelp: 'CDS are not translated to AA sequence. ' +
+                "Default: ${params.pirate_nucl}",
+            cliflag: '-n',
+            clivalue: (params.pirate_nucl ? ' ' : '')
+        ],
+        'pirate_pan_opt': [
+            clihelp: 'Additional arguments to pass to pangenome_contruction. ' +
+                "Default: ${params.pirate_pan_opt}",
+            cliflag: '--pan-opt',
+            clivalue: (params.pirate_pan_opt ?: '')
+        ],
+        'pirate_pan_off': [
+            clihelp: "Don't run pangenome tool. " +
+                "Default: ${params.pirate_pan_off}",
+            cliflag: '--pan-off',
+            clivalue: (params.pirate_pan_off ? ' ' : '')
+        ],
+        'pirate_min_len': [
+            clihelp: 'Minimum length for feature extraction. ' +
+                "Default: ${params.pirate_min_len}",
+            cliflag: '--min-len',
+            clivalue: (params.pirate_min_len ?: '')
+        ],
+        'pirate_para_off': [
+            clihelp: 'Switch off paralog identification. ' +
+                "Default: ${params.pirate_para_off}",
+            cliflag: '--para-off',
+            clivalue: (params.pirate_para_off ?: '')
+        ],
+        'pirate_para_args': [
+            clihelp: 'Options to pass to paralog splitting algorithm. ' +
+                "Default: ${params.pirate_para_args}",
+            cliflag: '--para-args',
+            clivalue: (params.pirate_para_args ?: '')
+        ],
+        'pirate_classify_off': [
+            clihelp: 'Do not classify paralogs, assumes this has been ' +
+                'run previously. ' +
+                "Default: ${params.pirate_classify_off}",
+            cliflag: '--classify-off',
+            clivalue: (params.pirate_classify_off ? ' ' : '')
+        ],
+        'pirate_align': [
+            clihelp: 'align all genes and produce core/pangenome alignments. ' +
+                "Default: ${params.pirate_align}",
+            cliflag: '--align',
+            clivalue: (params.pirate_align ? ' ' : '')
+        ],
+        'pirate_rplots': [
+            clihelp: 'Plot summaries using R. ' +
+                "Default: ${params.pirate_rplots}",
+            cliflag: '--rplots',
+            clivalue: (params.pirate_rplots ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file