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.
+