JAL-629 STDOUT documentation. Opt.STDOUT narrower option. Fix for subvals and STDOU...

[jalview.git] / help / help / html / features / clarguments-basic.html

diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html
index 7a87602..70b42f1 100644 (file)
--- a/help/help/html/features/clarguments-basic.html
+++ b/help/help/html/features/clarguments-basic.html
@@ -393,6 +393,7 @@
   <code>phylip</code> (<code>phy</code>),
   <br/>
   <code>jalview</code> (<code>jvp, jar</code>).
+  </p>
   <p>
   For example, to open a FASTA file, append another FASTA file and then save the concatenation as a Stockholm file, do
   <pre>
@@ -412,6 +413,20 @@
   <em>Important!</em> If you use <code>--output</code> or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified <code>--headless</code>).  To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> or <code>--noheadless</code> argument (the order doesn't matter).
   </p>
 
+  <p>
+  If you would like to output an alignment file directly to standard output (often referred to as STDOUT), then use the filename <code>-</code> (a single hyphen).  In this case any messages that would normally appear on STDOUT will be diverted to STDERR to avoid invalidating the output file.
+  </p>
+  <p>
+  For example, to open a Stockholm file and pipe it to another command as a Block file, do
+  <pre>
+  jalview --open alignment1.stk --output - --format blc | another_command
+  </pre>
+  or equivalently
+  <pre>
+  jalview alignment1.stk --output=[format=blc]- | another_command
+  </pre>
+  </p>
+
   <h3><a name="format"></a><code>--format</code></h3>
 
   <p>