X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-argfiles.html;h=5c71d16ee8e707fff514f3e42f623ca764be79be;hb=847c502d6186eb62a30f37f608852e77c67c217f;hp=f4741eed7e748ce6105bbbffbcbf6080208ae536;hpb=1d1edb58c9ee8baec12686a512eb18d97b9bdba1;p=jalview.git
diff --git a/help/help/html/features/clarguments-argfiles.html b/help/help/html/features/clarguments-argfiles.html
index f4741ee..5c71d16 100644
--- a/help/help/html/features/clarguments-argfiles.html
+++ b/help/help/html/features/clarguments-argfiles.html
@@ -25,15 +25,15 @@
@@ -117,7 +117,7 @@
- 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.
@@ -131,7 +131,7 @@
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