X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=1cb1849f5fc520e6d979c5cc0405d36c5cb1c47c;hb=81edd609f9841a84d5799d221277d45413a177cf;hp=c8a594a2ff8992bb066ca6cc9ee840103413ffb0;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index c8a594a..1cb1849 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 @@ -55,7 +58,7 @@ -

-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
@@ -117,7 +120,7 @@ -
-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
@@ -125,7 +128,7 @@ -
-vdoc VAMSAS DOCUMENT FILE or URL
+
-vdoc VAMSAS DOCUMENT FILE/URL
Import the given vamsas document into a new session.
New in 2.5
@@ -139,14 +142,6 @@ -
-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 +194,10 @@
-eps FILE
Create EPS file FILE from alignment.
+ +
-svg FILE
+
Create Support Vector Graphics file FILE from alignment.
+