X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=1cb1849f5fc520e6d979c5cc0405d36c5cb1c47c;hb=81edd609f9841a84d5799d221277d45413a177cf;hp=aebd7fef2dd403fd0cf018194f9f56514f928790;hpb=8dc3c506c4375c4a04fb2f1bd8deaae1c8f6aeff;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index aebd7fe..1cb1849 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -1,4 +1,24 @@
+
Jalview Command Line Arguments
@@ -13,22 +33,32 @@
- -props FILE |
+ -props FILE/URL |
Use the given Jalview properties file instead
of users default. |
- -features FILE |
+ -features FILE/URL |
Use the given file to add sequence features to an alignment.
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). |
|
- -annotations FILE
+ -annotations FILE/URL
|
Add precalculated annotations to the alignment. See Annotation File
@@ -36,7 +66,7 @@
|
|
- -tree FILE
+ -tree FILE/URL
|
Load the given newick format tree file onto
the alignment
@@ -63,6 +93,12 @@
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
@@ -84,13 +120,27 @@
|
|
- -groovy FILE
+ -groovy FILE/URL
|
Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
arguments have been processed
|
+ |
+ -vdoc VAMSAS DOCUMENT FILE/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
+ |
+
+
|
-fasta FILE
|
@@ -144,6 +194,10 @@
-eps FILE |
Create EPS file FILE from alignment. |
+
+ -svg FILE |
+ Create Support Vector Graphics file FILE from alignment. |
+