X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=2a040fe31f478a9c53c340d2a2c5e2c88c121745;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=9ca64a6d4258a9f0ec246e8e981edf7c2781d27f;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 9ca64a6..2a040fe 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 @@ -30,12 +33,12 @@ -
-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 @@ -50,12 +53,12 @@ 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 + (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 @@ -63,7 +66,7 @@ -
-tree FILE
+
-tree FILE/URL
Load the given newick format tree file onto the alignment
@@ -117,15 +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
@@ -139,14 +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
@@ -199,6 +201,10 @@
-eps FILE
Create EPS file FILE from alignment.
+ +
-svg FILE
+
Create Scalable Vector Graphics file FILE from alignment.
+