JAL-629 JAL-4121 Added documentation to Help docs and Usage statement

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

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 20bcd10..b763a81 100644 (file)
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -32,6 +32,7 @@
   <ul>
   <li><a href="#introduction">Introduction</a></li>
   <li><a href="#syntax">Syntax</a></li>
+  <li><a href="#headlessmode">Headless mode</a></li>
   </ul>
 
   <h2><a name="introduction"></a>Introduction</h2>
@@ -105,9 +106,9 @@
         <br/>
         <code>--arg file1.fa otherfile.stk</code>
         <br/>
-        <code>--arg filename*.fa</code> <em>(expanded by shell)</em>
+        <code>--arg filename*.fa</code> <em>(filenames expanded by shell)</em>
         <br/>
-        <code>--arg=filename*.fa</code> <em>(expanded by Jalview)</em>
+        <code>--arg=filename*.fa</code> <em>(filenames expanded by Jalview)</em>
     </li>
     <li>
         For arguments that act as a switch, most can be negated by preceding the argument name with <code>no</code>.
@@ -149,9 +150,26 @@
   </p>
 
   <p>
-  This may sound complicated, but nearly everything can be done just with plain command line arguments, though in this case the ordering of the arguments is more important.
+  This may sound complicated, but nearly everything can be done just with plain command line arguments (see <a href="clarguments-basic.html">Command Line: basic usage</a>), though in this case the ordering of the arguments is more important.
   </p>
 
+
+  <h2><a name="headlessmode"></a>Headless mode</h2>
+
+  <p>
+  Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the <code>--headless</code> argument.  With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running.  Most likely you will want to output another file, either an alignment for image file.
+  </p>
+  <p>
+  <strong>If you specify an argument for an output file</strong> (one or more of <code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then it will be assumed that you wish to <strong>run in headless mode</strong>.
+  </p>
+  <p>
+  You can force Jalview to run in graphical mode using the <code>--gui</code> or <code>--noheadless</code> arguments.
+  </p>
+
+  <p>
+  </p>
+
+
   <hr/>
   Continue to <a href="clarguments-basic.html">Command Line: basic usage</a>.
   <br/>