JAL-3830 JAL-4160 Remove --noheadless as --gui does this. Simplifies wrapper scripts

[jalview.git] / help / help / html / features / clarguments-basic.html

diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html
index 626fb8c..e2f984f 100644 (file)
--- a/help/help/html/features/clarguments-basic.html
+++ b/help/help/html/features/clarguments-basic.html
@@ -408,6 +408,10 @@
   </pre>
   </p>
 
+  <p>
+  <em>Important!</em> If you use <code>--output</code> or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified <code>--headless</code>).  To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> argument (the order doesn't matter).
+  </p>
+
   <h3><a name="format"></a><code>--format</code></h3>
 
   <p>