From: Ben Soares Date: Thu, 11 May 2023 19:39:10 +0000 (+0100) Subject: JAL-629 Move clarguments documentation to default. Completed clarguments summary... X-Git-Tag: Release_2_11_4_0~335 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5eca2a7ffd0c6b38898655d8b1c95310535cdfc8;p=jalview.git JAL-629 Move clarguments documentation to default. Completed clarguments summary. Most of clarguments basic --- diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 877c758..11f0541 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -29,7 +29,7 @@ - + diff --git a/help/help/html/features/clarguments-advanced.html b/help/help/html/features/clarguments-advanced.html new file mode 100644 index 0000000..e69de29 diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html new file mode 100644 index 0000000..8b64625 --- /dev/null +++ b/help/help/html/features/clarguments-basic.html @@ -0,0 +1,487 @@ + + +Jalview Command Line Arguments: basic usage + + +

Jalview Command Line Arguments: basic usage

+ +

+ Jalview Command Line Arguments: summary +
+ Jalview Command Line Arguments: introduction +
+ Jalview Command Line Arguments: basic usage +
+ Jalview Command Line Arguments: advanced usage +
+ Jalview Command Line Arguments: argfiles +

+ +
+ + + +

Opening alignments (--open, --append, --new)

+ +

+ To simply open one or more alignment files in different windows 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 window. +

+ +

+ 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 window 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
+
+

+ +

+ Note that whilst you can include a Jalview Project File (.jvp) as an --append value, the items in the file will always open in their original windows and not append to another. +

+ +

--new

+ +

+ To append different sets of alignment files in different windows, use --new to move on to a new alignment window: + 

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

+ +

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

+ + +

Alignment options (--colour, --wrap, --showannotations, --title)

+ +

--colour

+ +

+ You can specify a residue/base colouring for the alignment using the --colour option (note spelling -- Jalview is made in Scotland!): + 

+  jalview --open examples/uniref50.fa --colour gecos-flower
+
+ There are several colour schemes that you can use. See the page on Colour Schemes for details. + The names to use on the command line for colour schemes are: +

+

+ clustal, +
+ blosum62, +
+ pc-identity, +
+ zappo, +
+ taylor, +
+ gecos-flower, +
+ gecos-blossom, +
+ gecos-sunset, +
+ gecos-ocean, +
+ hydrophobic, +
+ helix-propensity, +
+ strand-propensity, +
+ turn-propensity, +
+ buried-index, +
+ nucleotide, +
+ nucleotide-ambiguity, +
+ purine-pyrimidine, +
+ rna-helices, +
+ t-coffee-scores, +
+ sequence-id +

+ +

--wrap

+

+ An alignment should open with your usual preferences stored in the .jalview_properties file. To open an alignment with the sequences (definitely) wrapped, following your --open (or first --append) argument use the argument --wrap: + 

+  jalview --open examples/uniref50.fa --wrap
+
+ To ensure an alignment is not wrapped use --nowrap: + 
+  jalview --open examples/uniref50.fa --nowrap
+
+

+ +

--showannotations / --noshowannotations

+ +

+ You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either --showannotations or --noshowannotations. If you don't specify then your saved preference will be used. + 

+  jalview --open examples/uniref50.fa --noshowannotations
+
+

+ +

--title

+ +

+ If you would like to give the alignment window a specific title you can do so with the --title option: + 

+  jalview --open examples/uniref50.fa --title "My example alignment"
+
+

+ + + + +

Adding 3D structures (--structure, --seqid, --structureviewer, --paematrix, --tempfac, --showssannotations)

+ +

+

+ +

--structure

+ +

+ You can add a 3D structure file to a sequence in the current alignment window with the --structure option: + 

+  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+
+ By default this attaches to the first sequence in the alignment but most likely you will want to attach it to a specific sequence. +

+ +

--seqid

+ +

+ The easiest way to specify a sequence ID for your structure is to follow the --structure argument with a --seqid argument with a value of a sequence ID in the alignment. This does of course require some knowledge of the sequences in the alignment files + that have been opened. +
+ Alternatively you can specify a sub-value with the --structure argument value. You do this by preceding the value with square brackets and seqid=SequenceId, + like this: + 

+  jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+
+ which is equivalent to + 
+  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid FER1_SPIOL
+
+

+ +

+ The sub-value seqid=FER1_SPIOL takes precedence over the following argument --seqid FER1_SPIOL if you accidentally specify both (in which case the argument will probably be completely unused). +

+ +

+ If you don't know the sequence IDs but do know the position of the sequence in the alignment, you can also specify an INDEX + in the sub-values to indicate which sequence in the alignment to attach the sequence to (although this is less precise). This is a zero-indexed value, so to specify the eighth sequence in the alignment use: + 

+  jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+
+ +

+ Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks. +

+ +

--structureviewer

+ +

+ You can specify which structure viewer (or none) to use to open the structure using either the --structureviewer argument or the structureviewer sub-value. Multiple sub-values can be specified together, separated by a comma ','. Possible values for the structureviewer are: +
+ none, +
+ jmol, +
+ chimera, +
+ chimerax, +
+ pymol. +

+

+ none and jmol will always be available, but to use the others you must have the appropriate software already set up on your computer and in Jalview. See the page Discovering and Viewing PDB and 3D-Beacons structures for more details. + 

+  jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+
+ or, if you prefer + 
+  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid FER1_SPIOL --structureviewer none
+
+

+ +

--paematrix

+ +

+ If you are opening a structure file that has a PAE matrix (provided as a JSON file), such as from an AlphaFold model or an nf-core pipeline, you can add the PAE matrix as an annotation by following the --structure argument with a --paematrix argument with the filename. You can also specify a paematrix=filename sub-value. + 

+  jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=pymol]examples/AlphaFold/AF-P00221-F1-model_v4.pdb --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json
+
+

+ +

--tempfac

+ +

+ Structure files may have a temperature factor associated with the structure component positions. If the temperature factor is a pLDDT confidence score, such as with an AlphaFold model, you can specify this by using a following argument of --tempfac with a value of plddt. This will enable standard pLDDT colouring of the temperature factor annotation. Valid values are: + default, + plddt. + More types of temperature factor may be added in future releases of Jalview. +
+ The value can also be specified as a sub-value: + 

+  jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+
+ which is equivalent to + 
+  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1+SPIOL
+   --structureviewer jmol
+
+ +

+ + + +

--showssannotations / --noshowssannotations

+ +

+ You can specify whether the currently opened alignment window should show secondary structure annotations or not with either --showssannotations or --noshowssannotations. If you don't specify then your saved preference will be used. + 

+  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --noshowssannotations
+
+ or you can use a sub-value modifier: + 
+  jalview --open examples/uniref50.fa --structure [noshowssannotations]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+
+

+ +

Outputting/converting alignment files and images (--output, --format, --image, --type, --textrenderer, --scale, --backups, --overwrite)

+ +

+ You can save an alignment as an alignment file, or exported as an image, in different formats. Jalview's alignment output formats are: + fasta, + pfam, + stockholm, + pir, + blc, + amsa, + json, + pileup, + msf, + clustal, + phylip, + jalview. +

+

+ Alignments can be exported as an image in formats EPS, SVG, HTML, BioJSON (vector formats) or PNG (bitmap format). +

+

+ In vector formats you can specify whether text should be rendered as text (which may have font changes, but will produce a smaller and more usable file) or as lineart (which will retain exact appearance of text, but will be less easy to edit or use to copy text). +

+

+ In bitmap formats (currently only PNG, but what else would you want?!) you can specify a scaling factor to improve the resolution of the output image. +

+ +

--output

+ +

+ To save the open alignment in a new alignment file use --output filename. The format for the file can be found from the extension of filename, or if you are using a non-standard extension you can use a following --format argument, or specify it as a sub-value modifier. +

+

+ Recognised formats and their recognised extensions are: +
+ fasta (fa, fasta, mfa, fastq), +
+ pfam (pfam), +
+ stockholm (sto, stk), +
+ pir (pir), +
+ blc (blc), +
+ amsa (amsa), +
+ json (json), +
+ pileup (pileup), +
+ msf (msf), +
+ clustal (aln), +
+ phylip (phy), +
+ jalview (jvp, jar). +

+ For example, to open a FASTA file, append another FASTA file and then save the concatenation as a Stockholm file, do + 

+  jalview --open alignment1.fa --append alignment2.fa --output bothalignments.stk
+
+ or + 
+  jalview --append alignment*.fa --output bigballofstring.txt --format stockholm
+
+ or + 
+  jalview --append alignment*.fa --output [format=stockholm]bigballofstring.txt
+
+

+ +

--format

+ +

+ To specify the format of the output file (if using an unrecognised file extension) use the --format argument to specify a value (see above). A sub-value modifier on the --output value can also be used. +

+ +

--image

+ +

+ 

+
+

+ +

--

+ +

+ 

+
+

+ +

--

+ +

+ 

+
+

+ +

--

+ +

+ 

+
+

+ + +

Filename substitutions and batch processing (--substitutions, --new, --close, --all)

+ +

--

+ +

+ 

+
+

+ +

--

+ +

+ 

+
+

+ +

--

+ +

+ 

+
+

+ +

--

+ +

+ 

+
+

+ +

--

+ +

+ 

+
+

+ + Continue to Jalview Command Line Arguments: advanced usage. + + + + + diff --git a/help/help/html/features/clarguments-intermediate.html b/help/help/html/features/clarguments-intermediate.html new file mode 100644 index 0000000..e69de29 diff --git a/help/help/html/features/clarguments-intro.html b/help/help/html/features/clarguments-intro.html new file mode 100644 index 0000000..cee0a04 --- /dev/null +++ b/help/help/html/features/clarguments-intro.html @@ -0,0 +1,85 @@ + + +Jalview Command Line Arguments: introduction + + +

Jalview Command Line Arguments: introduction

+ +

+ Jalview Command Line Arguments: summary +
+ Jalview Command Line Arguments: introduction +
+ Jalview Command Line Arguments: basic usage +
+ Jalview Command Line Arguments: advanced usage +
+ Jalview Command Line Arguments: argfiles +

+ +
+ +

+ 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. +
+ 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. +

+ + Continue to Jalview Command Line Arguments: basic usage. + + + + diff --git a/help/help/html/features/clarguments-ng-summary.html b/help/help/html/features/clarguments-ng-summary.html deleted file mode 100644 index c7b5be7..0000000 --- a/help/help/html/features/clarguments-ng-summary.html +++ /dev/null @@ -1,624 +0,0 @@ - - -Summary of Command Line Arguments (next generation) - - -

Summary of Command Line Arguments (next generation)

- -

- See Jalview Command Line Arguments (next generation) - for more explanation about using Jalview's command line arguments. -

- - - - - -

Initialising arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
argumentaction
‑‑help / -hDisplay a help statement
‑‑headlessRun Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.
‑‑jabaws URLSet a different URL to connect to a JABAWS server.
‑‑news / ‑‑nonewsShow (or don't show) the news feed.
‑‑splash / ‑‑nosplashShow (or don't show) the About Jalview splash screen.
‑‑questionnaire / ‑‑noquestionnaireShow (or don't show) the questionnaire if one is available.
‑‑usagestats / ‑‑nousagestatsSend (or don't send) initial launch usage stats. Note: usage stats are useful for future funding for Jalview!
‑‑webservicediscovery / ‑‑nowebservicediscoveryAttempt (or don't attempt) to connect to JABAWS web services.
‑‑props filenameUse file filename as the preferences file instead of the usual ~/.jalview_properties file.
‑‑debugStart Jalview in debug log level.
‑‑quietStop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.
‑‑initsubstitutions / ‑‑noinitsubstitutionsAssume that ‑‑substitutions are initially enabled (or initially disabled).
‑‑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. -
- The equals sign ("=") separator must be used with no spaces. -
- 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. -
- The equals sign ("=") separator must be used with no spaces. -
- See Memory usage settings for Jalview for more details. -
- - -

Opening an alignment

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
argumentactionsubval modifiers (optional)linked (optional)
‑‑open filename/URL ... - Opens one or more alignment files filename or URLs URL in new alignment windows. - - - colour=name, -
- title=string, -
- features=filename, -
- annotations=filename, -
- tree=filename, -
- showannotations, -
- showssannotations, -
- sortbytree, -
- wrap - - 		✓
‑‑append filename/URL ...Appends one or more alignment files filename or URLs URL to the open alignment window (or opens a new alignment if none already open). - - colour=name, -
- title=string, -
- features=filename, -
- annotations=filename, -
- tree=filename, -
- showannotations, -
- showssannotations, -
- sortbytree, -
- wrap - . - 		✓
‑‑title "string""Specifies the title for the open alignment window as string.✓
‑‑colour nameApplies the colour scheme name to the open alignment window. Valid values for name are: -
- clustal, -
- blosum62, -
- pc-identity, -
- zappo, -
- taylor, -
- gecos-flower, -
- gecos-blossom, -
- gecos-sunset, -
- gecos-ocean, -
- hydrophobic, -
- helix-propensity, -
- strand-propensity, -
- turn-propensity, -
- buried-index, -
- nucleotide, -
- nucleotide-ambiguity, -
- purine-pyrimidine, -
- rna-helices, -
- t-coffee-scores, -
- sequence-id. - 		✓
‑‑features filename/URLAdd a feature file filename or URL URL to the open alignment.✓
‑‑tree filename/URLAdd a tree file filename or URL URL to the open alignment.✓
‑‑sortbytree / ‑‑nosortbytreeEnforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.✓
‑‑annotations filename/URLAdd an annotations file filename or URL URL to the open alignment.✓
‑‑showannotations / ‑‑noshowannotationsEnforces showing (or not showing) alignment annotations.✓
‑‑wrap / ‑‑nowrapEnforces wrapped (or not wrapped) alignment formatting.✓
‑‑nostructureDo not open or process any 3D structure in the ‑‑open or ‑‑append files.✓
- - -

Adding a 3D structure

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
argumentactionsubval modifiers (optional)linked (optional)
‑‑structure filename/URLLoad a structure file filename or URL URL associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following ‑‑seqid argument, or the subval modifier seqid=ID can be used. A subval INDEX can also be used to specify the INDEX-th sequence in the open alignment. - - seqid=id or INDEX, -
- paefile=filename, -
- tempfac=name, -
- showssannotations, -
- notempfac, -
- structureviewer=name - 		✓
‑‑seqid IDSpecify the sequence name for the preceding ‑‑structure to be associated with.✓
‑‑paematrix filenameAdd a PAE json matrix file filename to the preceding ‑‑structure.✓
‑‑tempfac nameSet the type of temperature factor. Valid values for name are: -
- default, -
- plddt - 		✓
‑‑structureviewer nameSet the structure viewer to use to open the 3d structure file specified in previous ‑‑structure to name. Valid values of name are: -
- none, -
- jmol, -
- chimera - requires installation, might need configuring in Preferences, -
- chimerax - requires installation, might need configuring in Preferences, -
- pymol - requires installation, might need configuring in Preferences - 		✓
‑‑notempfacDo not show the temperature factor annotation for the preceding ‑‑structure✓
‑‑showssannotations / ‑‑noshowssannotationsDo not show secondary structure annotations for the preceding ‑‑structure✓
- - -

Outputting files

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
argumentactionsubval modifiers (optional)linked (optional)
‑‑image filenameOutput an image of the open alignment window. Format is specified by the subval modifier, a following ‑‑type argument or guessed from the file extension. Valid formats/extensions are: -
- svg, -
- png, -
- eps, -
- html, -
- biojs. - 		- type=name, - textrenderer=name - ✓
‑‑type nameSet the image format for the preceding ‑‑image to name. Valid values for name are: -
- svg, -
- png, -
- eps, -
- html, -
- biojs. - 		✓
‑‑textrenderer nameSets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Valid values for name are: -
- text, -
- lineart. - 		✓
‑‑output filenameExport the open alignment to file filename. The format name is specified by the subval modifier format=name, a following ‑‑format name argument or guessed from the file extension. Valid format names (and file extensions) are: -
- fasta (fa, fasta, mfa, fastq), -
- pfam (pfam), -
- stockholm (sto, stk), -
- pir (pir), -
- blc (blc), -
- amsa (amsa), -
- json (json), -
- pileup (pileup), -
- msf (msf), -
- clustal (aln), -
- phylip (phy), -
- jalview (jvp, jar). - 		format=name✓
‑‑format nameSets the format for the preceding ‑‑output file. Valid formats are: -
- fasta, -
- pfam, -
- stockholm, -
- pir, -
- blc, -
- amsa, -
- json, -
- pileup, -
- msf, -
- clustal, -
- phylip, -
- jalview. - 		✓
‑‑groovy filenameProcess a groovy script in the file for the open alignment.✓
‑‑backups / ‑‑nobackupsEnable (or disable) writing backup files when saving an ‑‑output file. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.✓
‑‑overwrite / ‑‑nooverwriteEnable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.✓
‑‑closeClose the current open alignment window. This occurs after other output arguments. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.✓
- - -

Controlling flow of arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
argumentactionsubval modifiers (optional)linked (optional)
‑‑newMove on to a new alignment window. This will ensure ‑‑append will start a new alignment window and other linked arguments will apply to the new alignment window.
‑‑substitutions / ‑‑nosubstitutionsThe following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are - {basename} - the filename-without-extension of the currently ‑‑opened file (or first ‑‑appended file), -
- {dirname}, - the directory (folder) name of the currently ‑‑opened file (or first ‑‑appended file), -
- {argfilebasename} - the filename-without-extension of the current ‑‑argfile, -
- {argfiledirname} - the directory (folder) name of the current ‑‑argfile, -
- {n} - the value of the index counter (starting at 0). -
- {++n} - increase and substitute the value of the index counter, -
- {} - the value of the current alignment window default index. -
‑‑argfile filename - Open one or more files filename and read, line-by-line, as arguments to Jalview. -
- Note that if you use one or more ‑‑argfile arguments then all other non-initialising arguments will be ignored. -
‑‑nppIncrease the index counter used in argument value substitutions.
‑‑allApply the following output arguments to all sets of linked arguments.
‑‑quitAfter all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.
diff --git a/help/help/html/features/clarguments-ng.html b/help/help/html/features/clarguments-ng.html deleted file mode 100644 index 799462b..0000000 --- a/help/help/html/features/clarguments-ng.html +++ /dev/null @@ -1,325 +0,0 @@ - - -Jalview Command Line Arguments (next generation) - - -

Jalview Command Line Arguments (next generation)

- -

- For a summary of Jalview command line arguments see Summary - of Command Line Arguments. -

- -

- 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. These 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, 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! -

- -

- Not everything that can be done with the old arguments is currently implemented in the new arguments but functionality of the new command line arguments will increase over releases. Significant new functionality, particularly allowing batch processing of files, is available in the new arguments. -

- -

- 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 - -

- - -

Typical Use Cases

- -

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

- -

- To simply open one or more alignment files in different windows 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 window. -

- -

- 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 window 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
-
-

- -

- Note that whilst you can include a Jalview Project File (.jvp) as an --append value, the items in the file will always open in their original windows and not append to another. -

- -
--new
- -

- To append different sets of alignment files in different windows, use --new to move on to a new alignment window: - 

-  jalview --append these/filename*.fa --new --append other/filename*.fa
-
-

- -

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

- - -

Alignment options (--colour, --wrap)

- -
--colour
- -

- You can specify a residue/base colouring for the alignment using the --colour option (note spelling -- Jalview is made in Scotland!): - 

-  jalview --open examples/uniref50.fa --colour gecos-flower
-
- There are several colour schemes that you can use. See the page on Colour Schemes for details. - The names to use on the command line for colour schemes are: -

-

- clustal, -
- blosum62, -
- pc-identity, -
- zappo, -
- taylor, -
- gecos-flower, -
- gecos-blossom, -
- gecos-sunset, -
- gecos-ocean, -
- hydrophobic, -
- helix-propensity, -
- strand-propensity, -
- turn-propensity, -
- buried-index, -
- nucleotide, -
- nucleotide-ambiguity, -
- purine-pyrimidine, -
- rna-helices, -
- t-coffee-scores, -
- sequence-id -

- -
--wrap
-

- An alignment should open with your usual preferences stored in the .jalview_properties file. To open an alignment with the sequences (definitely) wrapped, following your --open (or first --append) argument use the argument --wrap: - 

-  jalview --open examples/uniref50.fa --wrap
-
- To ensure an alignment is not wrapped use --nowrap: - 
-  jalview --open examples/uniref50.fa --nowrap
-
-

- -
--annotations
- -

- You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either --annotations or --noannotations. If you don't specify then your saved preference will be used. - 

-  jalview --open examples/uniref50.fa --noannotations
-
-

- -
--title
- -

- If you would like to give the alignment window a specific title you can do so with the --title option: - 

-  jalview --open examples/uniref50.fa --title "My example alignment"
-
-

- -
--structure
- -

- You can add a 3D structure file to a sequence in the current alignment window with the --structure option: - 

-  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
-
-

- - -

- seqid: - By default this attaches to the first sequence in the alignment but most likely you will want to attach it to another sequence. - To do this you can specify a sub-value with the sequence ID, by preceding the value with square brackets and seqid=SequenceId - like this: - 

-  jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
-
- - Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks. -

- -

- index: - You can alternatively specify the (zero-indexed) index of the sequence within the alignment, although this is less precise. So to attach the structure to the 8th sequence use: - 

-  jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
-
-

- -

- structureviewer: - You can specify which structure viewer (or not) to use to open the structure using the structureviewer sub-value. Multiple sub-values can be specified, separated by a comma ','. Possible values for the structureviewer sub-value are: -
- none, -
- jmol, -
- chimera, -
- chimerax, -
- pymol. -

-

- none and jmol will always be available, but to use the others you must have the appropriate software already set up on your computer and in Jalview. See the page Discovering and Viewing PDB and 3D-Beacons structures for more details. - 

-  jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
-
-

- - -

()

- -

-

- -
--
- -

- 

-
-

- - - - - - - - diff --git a/help/help/html/features/clarguments-old.html b/help/help/html/features/clarguments-old.html new file mode 100644 index 0000000..c0f4c42 --- /dev/null +++ b/help/help/html/features/clarguments-old.html @@ -0,0 +1,276 @@ + + +Jalview Command Line Arguments + +

+ The Jalview Executable's Command Line Arguments +

+ See + running Jalview from the command line + for more information. +
+
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/clarguments.html b/help/help/html/features/clarguments.html index c0f4c42..9a250da 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -1,15 +1,5 @@ -Jalview Command Line Arguments +Jalview Command Line Arguments: summary + +

Jalview Command Line Arguments: summary

+

- The Jalview Executable's Command Line Arguments + Jalview Command Line Arguments: summary +
+ Jalview Command Line Arguments: introduction +
+ Jalview Command Line Arguments: basic usage +
+ Jalview Command Line Arguments: advanced usage +
+ Jalview Command Line Arguments: argfiles

- See - running Jalview from the command line - for more information. -
-
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]
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +
+ + +

Initialising 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. -
-
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
argumentaction
‑‑help / -hDisplay a help statement
‑‑headlessRun Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.
‑‑jabaws URLSet a different URL to connect to a JABAWS server.
‑‑news / ‑‑nonewsShow (or don't show) the news feed.
‑‑splash / ‑‑nosplashShow (or don't show) the About Jalview splash screen.
‑‑questionnaire / ‑‑noquestionnaireShow (or don't show) the questionnaire if one is available.
‑‑usagestats / ‑‑nousagestatsSend (or don't send) initial launch usage stats. Note: usage stats are useful for future funding for Jalview!
‑‑webservicediscovery / ‑‑nowebservicediscoveryAttempt (or don't attempt) to connect to JABAWS web services.
‑‑props filenameUse file filename as the preferences file instead of the usual ~/.jalview_properties file.
‑‑debugStart Jalview in debug log level.
‑‑quietStop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.
‑‑initsubstitutions / ‑‑noinitsubstitutionsSet ‑‑substitutions to be initially enabled (or initially disabled).
‑‑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. +
+ The equals sign ("=") separator must be used with no spaces. +
+ 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. +
+ The equals sign ("=") separator must be used with no spaces. +
+ See Memory usage settings for Jalview for more details. +
+ + +

Opening an alignment

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
argumentactionsub-value modifiers (optional)linked (optional)
‑‑open filename/URL ... + Opens one or more alignment files filename or URLs URL in new alignment windows. + + + colour=name, +
+ title=string, +
+ features=filename, +
+ annotations=filename, +
+ tree=filename, +
+ showannotations, +
+ showssannotations, +
+ sortbytree, +
+ wrap + + 		✓
‑‑append filename/URL ...Appends one or more alignment files filename or URLs URL to the open alignment window (or opens a new alignment if none already open). + + colour=name, +
+ title=string, +
+ features=filename, +
+ annotations=filename, +
+ tree=filename, +
+ showannotations, +
+ showssannotations, +
+ sortbytree, +
+ wrap + + 		✓
‑‑title "string""Specifies the title for the open alignment window as string.✓
‑‑colour nameApplies the colour scheme name to the open alignment window. Valid values for name are: +
+ clustal, +
+ blosum62, +
+ pc-identity, +
+ zappo, +
+ taylor, +
+ gecos-flower, +
+ gecos-blossom, +
+ gecos-sunset, +
+ gecos-ocean, +
+ hydrophobic, +
+ helix-propensity, +
+ strand-propensity, +
+ turn-propensity, +
+ buried-index, +
+ nucleotide, +
+ nucleotide-ambiguity, +
+ purine-pyrimidine, +
+ rna-helices, +
+ t-coffee-scores, +
+ sequence-id. + 		✓
‑‑features filename/URLAdd a feature file filename or URL URL to the open alignment.✓
‑‑tree filename/URLAdd a tree file filename or URL URL to the open alignment.✓
‑‑sortbytree / ‑‑nosortbytreeEnforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.✓
‑‑annotations filename/URLAdd an annotations file filename or URL URL to the open alignment.✓
‑‑showannotations / ‑‑noshowannotationsEnforces showing (or not showing) alignment annotations.✓
‑‑wrap / ‑‑nowrapEnforces wrapped (or not wrapped) alignment formatting.✓
‑‑nostructureDo not open or process any 3D structure in the ‑‑open or ‑‑append files.✓
+ + +

Adding a 3D structure

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
argumentactionsub-value modifiers (optional)linked (optional)
‑‑structure filename/URLLoad a structure file filename or URL URL associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following ‑‑seqid argument, or the sub-value modifier seqid=ID can be used. A sub-value INDEX can also be used to specify the INDEX-th sequence in the open alignment. + + seqid=id or INDEX, +
+ paefile=filename, +
+ tempfac=name, +
+ showssannotations, + +
+ structureviewer=name + 		✓
‑‑seqid IDSpecify the sequence name for the preceding ‑‑structure to be associated with.✓
‑‑paematrix filenameAdd a PAE json matrix file filename to the preceding ‑‑structure.✓
‑‑tempfac nameSet the type of temperature factor. Valid values for name are: +
+ default, +
+ plddt + 		✓
‑‑structureviewer nameSet the structure viewer to use to open the 3d structure file specified in previous ‑‑structure to name. Valid values of name are: +
+ none, +
+ jmol, +
+ chimera - requires installation, might need configuring in Preferences, +
+ chimerax - requires installation, might need configuring in Preferences, +
+ pymol - requires installation, might need configuring in Preferences + 		✓
‑‑showssannotations / ‑‑noshowssannotationsDo not show secondary structure annotations for the preceding ‑‑structure✓
+ + +

Outputting files

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
argumentactionsub-value modifiers (optional)linked (optional)
‑‑output filenameExport the open alignment to file filename. The format name is specified by the sub-value modifier format=name, a following ‑‑format name argument or guessed from the file extension. Valid format names (and file extensions) are: +
+ fasta (fa, fasta, mfa, fastq), +
+ pfam (pfam), +
+ stockholm (sto, stk), +
+ pir (pir), +
+ blc (blc), +
+ amsa (amsa), +
+ json (json), +
+ pileup (pileup), +
+ msf (msf), +
+ clustal (aln), +
+ phylip (phy), +
+ jalview (jvp, jar). + 		format=name✓
‑‑format nameSets the format for the preceding ‑‑output file. Valid formats are: +
+ fasta, +
+ pfam, +
+ stockholm, +
+ pir, +
+ blc, +
+ amsa, +
+ json, +
+ pileup, +
+ msf, +
+ clustal, +
+ phylip, +
+ jalview. + 		✓
‑‑image filenameOutput an image of the open alignment window. Format is specified by the sub-value modifier, a following ‑‑type argument or guessed from the file extension. Valid formats/extensions are: +
+ svg, +
+ png, +
+ eps, +
+ html, +
+ biojs. + 		+ type=name, + textrenderer=name, + scale=number, + width=number, + height=number + ✓
‑‑type nameSet the image format for the preceding ‑‑image to name. Valid values for name are: +
+ svg, +
+ png, +
+ eps, +
+ html, +
+ biojs. + 		✓
‑‑textrenderer nameSets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Valid values for name are: +
+ text, +
+ lineart. + 		✓
‑‑scale numberSets a scaling for bitmap image format (PNG). Should be given as a floating point number. This can also be set as a sub-value modifier to the --image value. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).✓
‑‑width numberSets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the --image value. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).✓
‑‑height numberSets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the --image value. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image).✓
‑‑groovy filenameProcess a groovy script in the file for the open alignment.✓
‑‑backups / ‑‑nobackupsEnable (or disable) writing backup files when saving an ‑‑output file. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.✓
‑‑overwrite / ‑‑nooverwriteEnable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.✓
‑‑closeClose the current open alignment window. This occurs after other output arguments. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.✓
+ + +

Controlling flow of arguments

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
argumentaction
‑‑new + Move on to a new alignment window. This will ensure ‑‑append will start a new alignment window and other linked arguments will apply to the new alignment window. +
+ Note that --open already starts a new alignment window for each file it opens. +
‑‑substitutions / ‑‑nosubstitutionsThe following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are + {basename} - the filename-without-extension of the currently ‑‑opened file (or first ‑‑appended file), +
+ {dirname}, - the directory (folder) name of the currently ‑‑opened file (or first ‑‑appended file), +
+ {argfilebasename} - the filename-without-extension of the current ‑‑argfile, +
+ {argfiledirname} - the directory (folder) name of the current ‑‑argfile, +
+ {n} - the value of the index counter (starting at 0). +
+ {++n} - increase and substitute the value of the index counter, +
+ {} - the value of the current alignment window default index. +
‑‑argfile filename + Open one or more files filename and read, line-by-line, as arguments to Jalview. +
+ Values in an argfile should be given with an equals sign ("=") separator with no spaces. +
+ Note that if you use one or more ‑‑argfile arguments then all other non-initialising arguments will be ignored. +
‑‑nppIncrease the index counter used in argument value substitutions.
‑‑allApply the following output arguments to all sets of linked arguments.
‑‑quitAfter all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.
+ diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html index 7294dc0..b162740 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.html">range of arguments.

There are a few different ways to do this:

- Jalview's command line launch - script + Jalview's command line launch

Since version 2.11.2, the Jalview native application includes a launching shell script. This is the easiest way to launch an installed Jalview application from the command line.

To run the launch script, simply open a Terminal (or Command prompt on Windows), and type:

   jalview
@@ -168,7 +167,7 @@ included in the source distribution.

- Use '-help' to get more information on the command line arguments that Jalview accepts.