X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=27b4cb3caf9085d759b92ec4c3ff46abf904bf41;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=9bca34431f6cdb9a4caed932c9951f339bfffe64;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 9bca344..27b4cb3 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Jalview Command Line Arguments
@@ -30,22 +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
@@ -53,7 +66,7 @@
|
|
- -tree FILE
+ -tree FILE/URL
|
Load the given newick format tree file onto
the alignment
@@ -107,15 +120,22 @@
|
|
- -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 or URL
+ -vdoc VAMSAS DOCUMENT FILE/URL
|
Import the given vamsas document into a new session.
New in 2.5
|
@@ -129,14 +149,6 @@
|
- -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
|
@@ -189,6 +201,10 @@
-eps FILE |
Create EPS file FILE from alignment. |
+
+ -svg FILE |
+ Create Scalable Vector Graphics file FILE from alignment. |
+