<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>
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<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>
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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.
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- 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 '#').
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e.g.
<table border="1">
</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="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:
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<code>{argfilebasename}</code> - replaced with the base of the filename of the argument file (i.e. without directory path or file extension).
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</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>
<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>
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- Return to <a href="clarguments.html">Command Line: summary</a>.
+ <a href="clarguments-reference.html">Command Line: reference</a>
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