X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-argfiles.html;h=ad27751160d826b1ebc02a2aee34cd9eea3901ba;hb=56ce5cb6fd0b54f831cf35859886cd69a7f522a3;hp=f4741eed7e748ce6105bbbffbcbf6080208ae536;hpb=79a798676859e1d82dbd947a0fd767bba9711c2d;p=jalview.git
diff --git a/help/help/html/features/clarguments-argfiles.html b/help/help/html/features/clarguments-argfiles.html
index f4741ee..ad27751 100644
--- a/help/help/html/features/clarguments-argfiles.html
+++ b/help/help/html/features/clarguments-argfiles.html
@@ -25,15 +25,15 @@
@@ -86,7 +86,7 @@
- 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.
+ 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
@@ -117,21 +117,21 @@
- If a "loop" of argument files is detected then Jalview will refuse to play (which is a Good Thing).
+ 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.
Only 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 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.
Even more substitutions
- When adding values that can use substitutions within argument files, there are two additional substitutions that are made:
+ 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).
@@ -139,7 +139,7 @@
- Another amusing 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, which gives the potential of having multiple argument files with the exact same content, or even re-using the same argument file multiple times. e.g.
+ 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 |
@@ -153,7 +153,7 @@
jalview --argfile alignment.argfile --argfile alignment.argfile --headless
- would be processed like
+ 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
@@ -161,7 +161,7 @@
- Return to Command Line: summary.
+ Command Line: reference