+ <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.
+ <pre>
+ jalview --argfile=*/argfile.txt --headless
+ </pre>
+ </p>
+
+ <p>
+ You can even read argument files from within argument files, e.g.
+ <pre>
+ jalview --argfile=argfile*.txt --headless
+ </pre>
+ <table border="1">
+ <tr><td>File <code>argfile1.txt</code></td></tr>
+ <tr><td><pre>
+--open=file1.fa
+--argfile=myfavouriteformattingargfile.txt
+--argfile=mysecondfavouriteimageargfile.txt</pre></td></tr>
+ <tr><td>File <code>myfavouriteformattingargfile.txt</code></td></tr>
+ <tr><td><pre>
+--wrap
+--showannotations
+--annotations={dirname}/{basename}.annots</pre></td></tr>
+ <tr><td>File <code>mysecondfavouriteimageargfile.txt</code></td></tr>
+ <tr><td><pre>
+--image=images/{basename}.png
+--width=1920
+--height=1080</pre></td></tr>
+ </table>
+ </p>
+
+ <p>
+ 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>