X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=049ddde326329792a1fe313b9e00276e042d727b;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=45dfab51ece7082389bdb766649bcc93b8705456;hpb=713c09ec2d6f35d74ba2c6ed114bb3a29f3f5cf5;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 45dfab5..049ddde 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -1,4 +1,22 @@ + Jalview Command Line Arguments @@ -9,34 +27,127 @@ - + - + - + + + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + @@ -55,6 +166,10 @@ + + + +
-nodisplay
Run Jalview without User Interface.
Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)
-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
Add precalculated annotations to the alignment. See Annotation - File description.
-fasta FILE
+
-annotations FILE/URL
+ 		Add precalculated annotations to the alignment. See Annotation File + description.
+
-tree FILE/URL
+ 		+
Load the given newick format tree file onto + the alignment
+
+
-questionnaire URL
+ 		+
Queries the given URL for information about + any Jalview user questionnaires
+
+
-noquestionnaire
+ 		+
Turn off questionnaire check
+
+
-nousagestats
+ 		+
Turn off google analytics usage tracking
+
+
-[no]sortbytree
+ 		+
Enable or disable automatic sorting of associated view when a new tree is displayed
+
+
-dasserver nickname=URL
+ 		+
Add and enable a DAS server with given + nickname (alphanumeric or underscores only) for retrieval of features + for all alignments
+ Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'
+ e.g. sequence:http://localdas.somewhere.org/das/source
+
+
-fetchfrom nickname
+ 		+
Query a DAS source called nickname for features for the alignments + and display them
+
+
-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
+
+
-vdoc VAMSAS DOCUMENT FILE/URL
+ 		+
Import the given vamsas document into a new session.
New in 2.5
+
+
-vsess VAMSAS SESSION URL
+ 		+
Join the given vamsas session
If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).New in 2.5
+
+
-fasta FILE
+
Create alignment file FILE in Fasta format.
+
Create alignment file FILE in Fasta format.
+
-clustal FILE
Create alignment file FILE in Clustal format.
Create alignment file FILE in PIR format.
-pfam FILE
Create alignment file FILE in PFAM format.
-blc FILE
Create alignment file FILE in BLC format.