X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=fe5c8016aaa4e01373e1c6940821794a5793681d;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=cf444a1265ff4fc1ed73c98595b21e2abb77f017;hpb=9a0f8bd63ac90b6afad56e321a7556be3cfabd49;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index cf444a1..fe5c801 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -1,4 +1,22 @@ + Jalview Command Line Arguments @@ -9,56 +27,44 @@ - + - + - + - - - - - + + + - - - - + + + + + + + + + +
-nodisplay
Run Jalview without User Interface.
Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)
-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.

-
-
-annotations FILE
+ 		Add precalculated annotations to the alignment. See Annotation File - 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).
-
-nodisplay
- 		-
Run Jalview without User Interface
+
-annotations FILE/URL
Add precalculated annotations to the alignment. See Annotation File + description.
-
-tree FILE
+
-tree FILE/URL
Load the given newick format tree file onto the alignment
@@ -66,14 +72,6 @@
-
-features FILE
- 		-
Use the given file to mark features on the - alignment
-
-questionnaire URL
Queries the given URL for information about @@ -87,6 +85,18 @@
Turn off questionnaire check
+
-nousagestats
+ 		+
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
@@ -108,13 +118,27 @@
-
-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