X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=e06549431f860bd297bdc60940a8ecf2dadcc64a;hb=ac11d29a3ea51eb7ef40d73c2d953ca9567ec251;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
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--- a/help/html/features/clarguments.html
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@@ -1,18 +1,271 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ 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/URL |
+ Use the given Jalview properties
+ file instead of users default. |
+
-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/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
+ |
+
+ -nonews
+ |
+
+ Disable check for Jalview
+ news on startup (not recommended other than for classroom /
+ demo usage)
+
+ |
+
+ -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
+ |
+
+ -jabaws URL
+ |
+ Specify the URL of the preferred JABAWS
+ server
+ |
+
+ -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.
+ |
+
-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. |
+
-json FILE |
+ Create alignment file FILE in
+ JSON 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. |
+
-svg FILE |
+ Create Scalable Vector Graphics
+ file FILE from alignment. |
+
-biojsMSA FILE |
+ Write an HTML page to display
+ the alignment with the
+ BioJS MSAviewer MSA
+
+ |
+