+ Command Line: introduction
+
+ Command Line: basic usage
+
+ Command Line: advanced usage
+
+ Command Line: argument files
+
+ Command Line: reference
+
+ If you want to save a set of arguments to reuse, you can save them in a text file, say argfile.txt, and read them into Jalview with
+
+ jalview --argfile=argfile.txt ++ + +
+ The argument file has one argument and value per line, still using the double-dash ('--') before the argument name, and separating the argument and value with an equals sign ('=').
+
+ Because the argument file is read by the application and not read by the shell, you do not need to escape any values -- all spaces will be read as part of the value until the end of the line.
+
+ You can add comments to a line by starting the line with an hash (octothorpe, pound-sign '#').
+
+ e.g.
+
+ File argfile.txt
+ |
+
+ +--nonews +--nosplash +--open=[nowrap,colour=gecos-flower,showannotations]examples/plantfdx.fa +--features=examples/plantfdx.features +--annotations=examples/plantfdx.annotations +--image=images/alignment.png +--scale=2.5 +#--scale=10 +# let's see what's happening +#--headless+ |
+
+ Because ‑‑argfiles takes a filename argument, and multiple ‑‑argfiles can be read on the command line, you can also use file globs to specify multiple ‑‑argfile values. If you produce an argument file for each set of alignment files that you wish to associate then you can act on all of them with, e.g.
+
+ jalview --argfile=*/argfile.txt --headless ++ + +
+ You can even read argument files from within argument files, e.g. +
+ jalview --argfile=argfile*.txt --headless ++
File argfile1.txt |
+--open=file1.fa +--argfile=myfavouriteformattingargfile.txt +--argfile=mysecondfavouriteimageargfile.txt |
File myfavouriteformattingargfile.txt |
+--wrap
+--showannotations
+--annotations={dirname}/{basename}.annots |
File mysecondfavouriteimageargfile.txt |
+--image=images/{basename}.png
+--width=1920
+--height=1080 |
+ If an argument file that has already been read is found in a firther argument file, then Jalview will exit with a warning. This is to avoid loops of argument files. +
+ + +
+ When you use an ‑‑argfile argument, all other non-initialising arguments on the command line will be ignored. Only the initialising arguments and any and all ‑‑argfiles arguments on the command line will be used. You can also set initialising arguments in argument files.
+
+ When adding values that can use substitutions within argument files, there are two additional substitutions that can be made:
+
+ {argfilebasename} - replaced with the base of the filename of the argument file (i.e. without directory path or file extension).
+
+ {argfiledirname} - replaced with the path to the filename of the argument file.
+
+ Another substitution you can make in argument files is the {n} substitution. Combined with an -npp increment at the start (or end) of the argument file gives the potential to reuse an argument files in the same command but referring to different files, e.g.
+
+
File alignment.argfile |
+--open={argfilebasename}-{n}.fa
+--wrap
+--output={basename}.stk
+--close
+--npp |
+ jalview --argfile alignment.argfile --argfile alignment.argfile --headless ++ would be processed the same as +
+ jalview --open=alignment-0.fa --wrap --output=alignment-0.stk --close --open=alignment-1.fa --wrap --output=alignment-1.stk --close --headless ++ + + +