X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=c8a594a2ff8992bb066ca6cc9ee840103413ffb0;hb=6c00ad8c209574159bb6367963a1503cd95e4b23;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index e18e273..c8a594a 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -1,6 +1,6 @@ +
The Jalview Executable's Command Line + Arguments
+ See running Jalview from the command + line for more information.-nodisplay |
+ Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks) |
+
-props FILE |
+ Use the given Jalview properties file instead
+ of users default. |
+
-features FILE |
+
+
+ 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. | +
+ -tree FILE
+ |
+ 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
+ |
+ 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 or 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 |
+
+ -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
+ |
+
+
+ Create alignment file FILE in Fasta format.
+ |
+
-clustal FILE |
+ Create alignment file FILE in Clustal format. |
+
-msf FILE |
+
+ Create alignment file FILE in MSF format. |
+
-pileup FILE |
+ Create alignment file FILE in Pileup format. |
+
-pir FILE |
+
+ 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. |
+
-jalview FILE |
+
+ Create alignment file FILE in Jalview format. |
+
-png FILE |
+ Create PNG image FILE from alignment. |
+
-imgMap FILE |
+
+ Create HTML file FILE with image map of PNG
+ image. |
+
-eps FILE |
+ Create EPS file FILE from alignment. |
+