X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=2a040fe31f478a9c53c340d2a2c5e2c88c121745;hb=2273eba5668e5340354da60fed329c6c716cc439;hp=83465f9269ad42f0bb47a0525ad4f66fd082691d;hpb=fca960fd3008bd4a8742c10e6ae7259df2e1dd71;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 83465f9..2a040fe 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -1,4 +1,24 @@ +
-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. | -|
- - | - + | |
- -nodisplay
- |
- Run Jalview without User Interface
+ -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). | +
- -props FILE
- |
- Use the given Jalview properties file instead
- of users default
+ -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 +74,6 @@
| |
- -features FILE
- |
- Use the given file to mark features on the
- alignment
- |
- |
-questionnaire URL
|
Queries the given URL for information about
@@ -93,6 +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
@@ -114,12 +120,33 @@
| ||
- -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
|
|
+ -jabaws URL
+ |
+ Specify the URL of the preferred JABAWS server
+ |
+ |
+ -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
@@ -174,6 +201,10 @@
| -eps FILE |
Create EPS file FILE from alignment. |
-svg FILE |
+ Create Scalable Vector Graphics file FILE from alignment. |
+