X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=e06549431f860bd297bdc60940a8ecf2dadcc64a;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=277b1f6fa7dadfdcb2d6a4898d4463c32665b967;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 277b1f6..e065494 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -1,194 +1,271 @@ -
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
-
- | -[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
-
+ |
+ -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 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. |