X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=e571b124e04b2509c9f2602b10817fa31b16d8cc;hb=ed407473fa5bc185476cf2584f5551d1b4e1617c;hp=cf444a1265ff4fc1ed73c98595b21e2abb77f017;hpb=9a0f8bd63ac90b6afad56e321a7556be3cfabd49;p=jalview.git

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index cf444a1..e571b12 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -9,7 +9,7 @@
  <table width="100%" border="1" cellspacing="0" cellpadding="0">
  <tr > 
  <td width="27%"><div align="center">-nodisplay</div></td>
- <td width="73%"><div align="left">Run Jalview without User Interface.</div></td>
+ <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
  </tr>
 
  <tr> 
@@ -36,28 +36,6 @@
 	</tr>
 	<tr>
 		<td>
-		<div align="center"></div>
-		<td>
-		<div align="left"></div>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center">-nodisplay</div>
-		<td>
-		<div align="left">Run Jalview without User Interface</div>
-		</td>
-	</tr>
-	<!--  <tr>
-		<td>
-		<div align="center">-props FILE</div>
-		<td>
-		<div align="left">Use the given Jalview properties file instead
-		of users default</div>
-		</td>
-	</tr> -->
-	<tr>
-		<td>
 		<div align="center">-tree FILE</div>
 		<td>
 		<div align="left">Load the given newick format tree file onto
@@ -66,14 +44,6 @@
 	</tr>
 	<tr>
 		<td>
-		<div align="center">-features FILE</div>
-		<td>
-		<div align="left">Use the given file to mark features on the
-		alignment</div>
-		</td>
-	</tr>
-	<tr>
-		<td>
 		<div align="center">-questionnaire URL</div>
 		<td>
 		<div align="left">Queries the given URL for information about
@@ -87,6 +57,18 @@
 		<div align="left">Turn off questionnaire check</div>
 		</td>
 	</tr>
+	<tr><td>
+		<div align="center">-nousagestats</div>
+		<td>
+		<div align="left">Turn off google analytics usage tracking</div>
+		</td>
+	</tr>
+	<tr><td>
+	<div align="center">-[no]sortbytree</div>
+		<td>
+		<div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
+		</td>
+	</tr>
 	<tr>
 		<td>
 		<div align="center">-dasserver nickname=URL</div>
@@ -115,6 +97,28 @@
 		</td>
 	</tr>
 	<tr>
+	<td>
+		<div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
+		<td>
+		<div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
+		</td>
+	</tr>
+	<tr>
+		<td>
+		<div align="center">-vsess VAMSAS SESSION URL</div>
+		<td>
+		<div align="left">Join the given vamsas session<br>If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).<em>New in 2.5</em></div></div>
+		</td>
+	</tr>
+	<tr>
+		<td>
+		<div align="center">-groovy FILE</div>
+		<td>
+		<div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+		arguments have been processed</div>
+		</td>
+	</tr>
+	<tr>
 		<td>
 		<div align="center">-fasta FILE</div>
 		</td>