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 @@
   <h1>Command Line: argument files</h1>
 
   <p>
-  <a href="clarguments.html">Command Line: summary</a>
-  <br/>
-  <a href="clarguments-intro.html">Command Line: introduction</a>
+  <a href="clarguments.html">Command Line: introduction</a>
   <br/>
   <a href="clarguments-basic.html">Command Line: basic usage</a>
   <br/>
   <a href="clarguments-advanced.html">Command Line: advanced usage</a>
   <br/>
-  Command Line: argument files
+  <a href="clarguments-argfiles.html">Command Line: argument files</a>
+  <br/>
+  <a href="clarguments-reference.html">Command Line: reference</a>
   </p>
 
   <hr/>
@@ -58,7 +58,7 @@
   <br/>
   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.
   <br/>
-  You can add comments to a line by starting the line with an octothorpe (hash, pound-sign '#').
+  You can add comments to a line by starting the line with an hash (octothorpe, pound-sign '#').
   <br/>
   e.g.
   <table border="1">
@@ -86,7 +86,7 @@
   </p>
 
   <p>
-  Because <code>--argfiles</code> takes a filename argument, and multiple <code>--argfiles</code> can be read on the command line, you can also use file globs to specify multiple <code>--argfile</code> 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 <code>&#8209;&#8209;argfiles</code> takes a filename argument, and multiple <code>&#8209;&#8209;argfiles</code> can be read on the command line, you can also use file globs to specify multiple <code>&#8209;&#8209;argfile</code> 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.
   <pre>
   jalview --argfile=*/argfile.txt --headless
   </pre>
@@ -117,21 +117,21 @@
   </p>
 
   <p>
-  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.
   </p>
 
 
   <h2><a name="onlyargumentfiles"></a>Only argument files</h2>
 
   <p>
-  When you use an <code>--argfile</code> argument, all other non-initialising arguments on the command line <em>will be ignored</em>.  Only the initialising arguments and any and all <code>--argfiles</code> arguments on the command line will be used.  You can also set initialising arguments in argument files.
+  When you use an <code>&#8209;&#8209;argfile</code> argument, all other non-initialising arguments on the command line <em>will be ignored</em>.  Only the initialising arguments and any and all <code>&#8209;&#8209;argfiles</code> arguments on the command line will be used.  You can also set initialising arguments in argument files.
   </p>
 
 
   <h2><a name="evenmoresubstitutions"></a>Even more substitutions</h2>
 
   <p>
-  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:
   <br/>
   <code>{argfilebasename}</code> - replaced with the base of the filename of the argument file (i.e. without directory path or file extension).
   <br/>
@@ -139,7 +139,7 @@
   </p>
 
   <p>
-  Another amusing substitution you can make in argument files is the <code>{n}</code> substitution, combined with an <code>-npp</code> 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 <code>{n}</code> substitution.  Combined with an <code>-npp</code> 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.
 
   <table border="1">
   <tr><td>File <code>alignment.argfile</code></td></tr>
@@ -153,7 +153,7 @@
   <pre>
   jalview --argfile alignment.argfile --argfile alignment.argfile --headless
   </pre>
-  would be processed like
+  would be processed the same as
   <pre>
   jalview --open=alignment-0.fa --wrap --output=alignment-0.stk --close --open=alignment-1.fa --wrap --output=alignment-1.stk --close --headless
   </pre>
@@ -161,7 +161,7 @@
 
 
   <hr/>
-  Return to <a href="clarguments.html">Command Line: summary</a>.
+  <a href="clarguments-reference.html">Command Line: reference</a>
 
 
 </body>