X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;fp=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=9b527d6068c9a1554d67d091cfdb1094d729c35d;hb=2be644b535dd34da958a831f877cf63d87912b5b;hp=9bca34431f6cdb9a4caed932c9951f339bfffe64;hpb=2a6d70ec8fa41acdfed93b5a25f68dc3ca6e2375;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 9bca344..9b527d6 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -16,33 +16,55 @@
*
* 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) |
-
+ -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
+
+ |
+ 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
@@ -74,26 +96,30 @@
Turn off questionnaire check
|
|||||
+ | |||||
-nousagestats
|
Turn off google analytics usage tracking
|
||||
- -[no]sortbytree
+ | |||||
+ -[no]sortbytree
|
- Enable or disable automatic sorting of associated view when a new tree is displayed
+ 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:' + 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
+ 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
+ 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 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 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
+ Execute groovy script in FILE (where FILE may
+ be 'STDIN' to read from the standard input) after all other arguments
+ have been processed
|
||||
-clustal FILE |
- Create alignment file FILE in Clustal format. |
- ||||
-msf FILE |
+ |||||
+ -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.
+ |
+ ||||
+ -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. |
-