X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=c8a594a2ff8992bb066ca6cc9ee840103413ffb0;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=25e5fefcd4efb5f360a5e22175d0288567d17c16;hpb=e9f2b8c138a0050c5ab6b52014459b905cb621b1;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 25e5fef..c8a594a 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -1,4 +1,21 @@
+
Jalview Command Line Arguments
@@ -24,7 +41,17 @@
See Features
File (Known as Groups file prior to 2.08) description.
-
+
+
+
+
+ |
+ -colour COLOURSCHEME
+ |
+ Set the colourscheme for the alignment. This can be any of
+ the built-in colourschemes, a name of a predefined colourscheme
+ (defined in the jalview properties file), or an 'inline' colourscheme
+ (see the applet's colour parameter for more information). |
|
@@ -36,13 +63,6 @@
|
|
-
- |
-
- |
-
-
- |
-tree FILE
|
Load the given newick format tree file onto
@@ -70,6 +90,12 @@
Turn off google analytics usage tracking
|
+ |
+ -[no]sortbytree
+ |
+ Enable or disable automatic sorting of associated view when a new tree is displayed
+ |
+
|
-dasserver nickname=URL
@@ -98,6 +124,28 @@
|
+ |
+ -vdoc VAMSAS DOCUMENT FILE or URL
+ |
+ Import the given vamsas document into a new session.
New in 2.5
+ |
+
+
+ |
+ -vsess VAMSAS SESSION URL
+ |
+ Join the given vamsas session
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!).New in 2.5
+ |
+
+
+ |
+ -groovy FILE
+ |
+ Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed
+ |
+
+
|
-fasta FILE
|