X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=b514e65bea65d96a5bf3e9fd107ef888f4308df9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=25e5fefcd4efb5f360a5e22175d0288567d17c16;hpb=e9f2b8c138a0050c5ab6b52014459b905cb621b1;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 25e5fef..b514e65 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -1,156 +1,252 @@ -Jalview Command Line Arguments - + +Jalview Command Line Arguments -

The Jalview Executable's Command Line - Arguments

- See running Jalview from the command - line for more information.
- - - - - +

+ 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)
+ + + + - - - - - - - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - + + + + + + + + - - - - - - -
-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.

+
-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. +

-
-
-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
-
-
-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
-
-
-fasta FILE
-
+
-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
+
+
-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 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 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 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 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.
+
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.
+ +