X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=e06549431f860bd297bdc60940a8ecf2dadcc64a;hb=140b0d3f1d7a31d14cb02deb55214bbad44874be;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index e18e273..e065494 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -1,18 +1,271 @@ + * 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 + +

+ 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 +
+
+ +