X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;h=6df40b525556a8817b8c3acd7ab712114003f481;hb=95443a95c1282c050fe1f28a4ddcaf3f0f75dfb4;hp=60db0695f1d317bb1a164c1a8dff86b9f7ce9083;hpb=922ffe0c08b4ce25da2bf25f7dbdf0641d3fd46f;p=jalview.git diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index 60db069..6df40b5 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. +
+
- The Jalview Executable's Command Line Arguments
+ 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).
-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
- |
-
- -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
-
- |
-
+ 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.
+
+ 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.
+
+ Warning! If you use command line arguments without any dashes and
+ don't use the bare-word argument open
then all
+ your arguments will be interpreted as alignment files to be opened by the
+ new command line argument process!
+
+ To launch Jalview from the command line, see + running Jalview from the command line. +
+ + ++ The new command line argument parser can group certain labelled arguments together, or give them a default label based on their position in the list of arguments (in which case you won't ever need to know what the label is). All arguments are read before any alignment actions are performed. For basic usage without additional syntax, please see the Command Line: basic usage explanatory page. +
+ +jalview --argname[linkedId]=[subvalues]value --switch --noswitch --argname[linkedId] [subvalues]filename1 filename2 ...+ +
+ Different arguments can take one or more values, others take no value and act like a switch (some can be set on and off and others are only on, depending on the use).
+
+
‑‑arg value
+ ‑‑arg=value
+ ‑‑arg file1.fa otherfile.stk
+ ‑‑arg filename*.fa
(filenames expanded by shell)
+ ‑‑arg=filename*.fa
(filenames expanded by Jalview)
+ no
.
+ ‑‑switch
+ ‑‑noswitch
+ ‑‑image
output can be modified with a ‑‑scale=number
factor, or a ‑‑structure
can refer to a sequence with a ‑‑seqid=ID
). This additional information can be added in a number of different ways.
+ ‑‑image output.png --scale 2.5
+ ‑‑open=[nowrap,colour=gecos-blossom]uniref50.fa
+ no
to negate the value, as with the argument name.
+ ‑‑image[MYID]=output.png --other --args --scale[MYID]=2.5
+ ‑‑image=output.png --other --args --all --scale=2.5
+ ‑‑image=output.png --other --args --scale[*]=2.5
+ + This may sound complicated, but nearly everything can be done just with plain command line arguments (see Command Line: basic usage), though in this case the ordering of the arguments is more important. +
+ + +
+ Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the ‑‑headless
argument. With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running. Most likely you will want to output another file, either an alignment for image file.
+
+ If you specify an argument for an output file (one or more of ‑‑output
, ‑‑image
or ‑‑structureimage
) then it will be assumed that you wish to run in headless mode.
+
+ You can force Jalview to run in graphical mode using the ‑‑gui
argument.
+
+
+ + +