From 82d84444cd1ee19ae45821d7a5f959d3cd6f93fa Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 27 Apr 2023 19:42:28 +0100 Subject: [PATCH] JAL-629 start of help text --- help/help/html/features/clarguments-ng.html | 426 +++++++++++++++++++++++++++ help/help/html/features/commandline.html | 2 +- 2 files changed, 427 insertions(+), 1 deletion(-) create mode 100644 help/help/html/features/clarguments-ng.html diff --git a/help/help/html/features/clarguments-ng.html b/help/help/html/features/clarguments-ng.html new file mode 100644 index 0000000..687853d --- /dev/null +++ b/help/help/html/features/clarguments-ng.html @@ -0,0 +1,426 @@ + + +Jalview Command Line Arguments (next generation) + + +

Jalview Command Line Arguments (version 2.11.3.0 and later)

+ +

+ From version 2.11.3.0 Jalview processes a new set of command line arguments + which allow more powerful and flexible combinations of arguments, though can + also be used for very 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. +

+ +

+ However, you cannot mix old and new style arguments, so if you use any + -singledash arguments, 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. +
+ Note! 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. +

+ + +

Processing command line arguments

+ +

+ Jalview no longer necessarily processes arguments sequentially, although + in typical use cases you may still want to think of it as doing so. +
+ For more advanced use please see + Advanced Command Line Arguments. +

+ + +

Typical Use Cases

+ +

Opening files (--open, --append, --newframe)

+ +

+ To simply open one or more alignment files in different frames just put the filenames as the first arguments: + 

+  jalview filename1 filename2 ...
+
+

+ +

+ You can use shell-expanded wildcards: + 

+  jalview this/filename* that/filename* other/filename*
+
+ and URLs: + 
+  jalview https://rest.uniprot.org/uniprotkb/P00221.fasta
+
+

+ +

+ (Using initial filenames is the same as using the --open argument, and further arguments can be used + after the initial filenames.) +

+ +
--open
+ +

+ Use the --open argument to open alignment files each in their own frame. +

+ +

+ The following are equivalent: + 

+  jalview --open filename1 filename2 ...
+
+  jalview --open filename*
+
+  jalview --open filename1 --open filename2 --open ...
+
+  jalview filename1 filename2 ...
+
+

+ +

+ Similarly you can open URLs: + 

+  jalview --open https://rest.uniprot.org/uniprotkb/P00221.fasta
+
+

+ +
--append
+ +

+ To append several alignment files together use: + 

+  jalview --open filename1.fa --append filename2.fa filename3.fa
+
+ or, if you haven't previously used --open then you can use --append to open one new frame and keep appending each set of alignments: + 
+  jalview --append these/filename*.fa --append more/filename*.fa
+
+  jalview --append https://rest.uniprot.org/uniprotkb/P00221.fasta https://www.uniprot.org/uniprotkb/A0A0K9QVB3/entry
+
+

+ +
--newframe
+ +

+ To append different sets of alignment files in different frames, use --newframe to move on to a new alignment frame: + 

+  jalview --append these/filename*.fa --newframe --append other/filename*.fa
+
+

+ +

+ --open is like using --newframe --append applied to every filename/URL given to --open +

+ + +

()

+ +

+

+ +
--
+ +

+ 

+
+

+ + + + + + + + + + + +

+ Jalview processes arguments on the command line sequentially. If + you would like to pass a 'JVL' file containing + memory settings or any other launch + parameters, then include it at the beginning of the command line to + ensure they are processed before any remaining arguments. +
+ Typical command line execution follows the following pattern: + 

+  jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
-nodisplay
Run Jalview without + User Interface. (automatically disables questionnaire, version + and usage stats checks)
-nowebservicediscovery
Do not query configured servers to + discover web services (Since 2.11.2.0)
-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.
-setprop PROPERTY=value
(JalviewJS ONLY) sets the given + property to the given value
-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. +
+
+ + diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html index 381478f..7294dc0 100644 --- a/help/help/html/features/commandline.html +++ b/help/help/html/features/commandline.html @@ -28,7 +28,7 @@

Jalview can be run from the command line, and provides a range of arguments. + href="clarguments-ng.html">range of arguments.

There are a few different ways to do this: