X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=ac44c46af8f6d6fab85eac11a4f59638ced9a7cd;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=277b1f6fa7dadfdcb2d6a4898d4463c32665b967;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 277b1f6..ac44c46 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -1,21 +1,22 @@
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
Jalview Command Line Arguments
@@ -30,22 +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
@@ -53,7 +64,7 @@
|
|
- -tree FILE
+ -tree FILE/URL
|
Load the given newick format tree file onto
the alignment
@@ -107,7 +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
@@ -115,7 +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
|
@@ -129,14 +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
|