X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=16b0dc0f80ffcb0a1a7cf2688b5d9d3d066e8c18;hb=43d326c3a7616aedecfce6f7980b3831ec25243a;hp=e571b124e04b2509c9f2602b10817fa31b16d8cc;hpb=ed407473fa5bc185476cf2584f5551d1b4e1617c;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index e571b12..16b0dc0 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
@@ -90,15 +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
|
@@ -112,14 +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
|
@@ -153,6 +182,10 @@
-blc FILE |
Create alignment file FILE in BLC format. |
+
+ -json FILE |
+ Create alignment file FILE in JSON format. |
+
-jalview FILE |
@@ -172,6 +205,10 @@
-eps FILE |
Create EPS file FILE from alignment. |
+
+ -svg FILE |
+ Create Scalable Vector Graphics file FILE from alignment. |
+