On Wednesday, February 19, 2014, Peter Cock &lt;<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>&gt; wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On Wed, Feb 19, 2014 at 2:16 PM, John Chilton &lt;<a href="javascript:;" onclick="_e(event, &#39;cvml&#39;, &#39;jmchilton@bx.psu.edu&#39;)">jmchilton@bx.psu.edu</a>&gt; wrote:<br>
&gt; Hey Peter,<br>
&gt;<br>
&gt; Have you seen this solution?<br>
&gt;<br>
&gt; <a href="https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run" target="_blank">https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run</a><br>

&gt;<br>
&gt; It always seems to get mentioned when this topic is brought up. It has<br>
&gt; serious limitations in terms or workflow running, but it can probably<br>
&gt; be made to work for individual tool executions.<br>
<br>
Hmm. Any real life examples of this in use? I guess looking for<br>
the magic string $__new_file_path__ in the &lt;command&gt; tag<br>
is the only way to identify this?<br>
<br></blockquote><div><br></div><div>Hi Peter,</div><div><br></div><div>I used the current functionality here:</div><div><div><a href="http://toolshed.g2.bx.psu.edu/view/cjav/split_by_barcode">http://toolshed.g2.bx.psu.edu/view/cjav/split_by_barcode</a></div>
</div><div><br></div><div>The code for the underlining tool is available here:</div><div><a href="https://github.com/cjav/ngs-tools">https://github.com/cjav/ngs-tools</a></div><div><br></div><div>Hope it helps,</div><div>
Carlos </div>