X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=fe5c8016aaa4e01373e1c6940821794a5793681d;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=e571b124e04b2509c9f2602b10817fa31b16d8cc;hpb=ed407473fa5bc185476cf2584f5551d1b4e1617c;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index e571b12..fe5c801 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -1,4 +1,22 @@
+
Jalview Command Line Arguments
@@ -13,22 +31,32 @@
- -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 +64,7 @@
|
|
- -tree FILE
+ -tree FILE/URL
|
Load the given newick format tree file onto
the alignment
@@ -90,7 +118,7 @@
|
|
- -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
@@ -98,7 +126,7 @@
|
|
- -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 +140,6 @@
|
- -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
|