X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;h=b763a8106fab8fde737b83d5855cfedacd95f7cc;hb=340ebd50b63087b4f8b2c4a26d94112dc51ada9c;hp=56bff895c3976f85f1e6eb2434925746bcb657df;hpb=c5dc8281494c9cf96f6736fc326653f782fa5dbd;p=jalview.git diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index 56bff89..b763a81 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -1,15 +1,5 @@ -
+ Command Line: introduction
+
+ Command Line: basic usage
+
+ Command Line: advanced usage
+
+ Command Line: argument files
+
+ Command Line: reference
+
+ From version 2.11.3.0 Jalview has a new set of command line arguments + which allow more powerful and flexible combinations of arguments, though can + also be used for simple use cases too. +
+ +
+ These new arguments are all accessed with a --doubledash
form of
+ command line argument (with the one exception where simply opening one or more
+ files can be performed without any arguments other than the filenames).
+
+ The old command line arguments can still be used (see
+ the old page on command line arguments) so
+ existing scripts utilising them should not break.
+
+ These are now deprecated and will be removed in a future version of Jalview.
+
- The Jalview Executable's Command Line Arguments
+ However, you cannot mix old and new style arguments, so if you use any
+ -singledash
arguments (with the exception of -help
or -h
), they will all be interpreted as
+ old style arguments with the new --doubledash
+ arguments being ignored. If you have a script
+ that uses the old arguments without any dashes, and uses the bare-word
+ open
then these will also be interpreted as old style arguments.
- jalview -open <Alignment File/URL> [additional import arguments] [export arguments] -- -
-nodisplay |
- Run Jalview without
- User Interface. (automatically disables questionnaire, version
- and usage stats checks) |
-
-open FILE/URL |
- Specify the alignment file to
- open or process by providing additional arguments. |
-
-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. - | -
- -no-annotation
- |
- Do not display annotation below the alignment. - | -
- -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
- |
-
- -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
- |
-
- -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
-
- |
-
-jvmmempc=PERCENT |
- Only available with standalone executable jar or jalview.bin.Launcher.
- Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
- This defaults to 90 if total physical memory can be detected.
- See Memory usage settings for Jalview for more details.
-
- |
-
-jvmmemmax=MAXMEMORY |
- Only available with standalone executable jar or jalview.bin.Launcher.
- Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
- gigabytes(g) or if you're lucky enough, terabytes(t).
- This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
- See Memory usage settings for Jalview for more details.
-
- |
-