Hello galaxy dev,
<div><br></div><div>I have done some work on enabling multiple input files for multiple tool parameters in a workflow. This could come in handy when running multiple paired end data files for RNA Seq through a pipeline (I know this has been discussed on a few different threads but I couldn&#39;t find any when writing this up).</div>

<div><br></div><div>The changes cause the workflow controller to step through the input data in synchronized fashion going down the list (of selected inputs). When running a workflow with multiple, multiple inputs the default ordering from the history can be problematic so I also did a little work on a new display/interaction method that I called &quot;on_deck.&quot; If you set the tool xml config to have parameter tag display=&quot;on_deck&quot; then it will enable this interaction method. </div>

<div>e.g. from the bowtie wrapper:</div><div><br></div><div><div>      &lt;when value=&quot;paired&quot;&gt;</div><div>        &lt;param name=&quot;pInput1&quot; type=&quot;data&quot; format=&quot;fastqsanger,fastqillumina,fastqsolexa&quot; label=&quot;Forward FASTQ file&quot; help=&quot;Must have ASCII encoded quality scores&quot; display=&quot;on_deck&quot;/&gt;</div>

<div>        &lt;param name=&quot;pInput2&quot; type=&quot;data&quot; format=&quot;fastqsanger,fastqillumina,fastqsolexa&quot; label=&quot;Reverse FASTQ file&quot; help=&quot;File format must match the Forward FASTQ file&quot; display=&quot;on_deck&quot;&gt;</div>

</div><div><br></div><div>The changes to run.mako seem a little hacked in to me (I am still getting a handle on the mako format). I wasn&#39;t sure where to stick the javascript that is in there. It only lets you go forward if the number of inputs, for all multiple toggled inputs, is equal.</div>

<div><br></div><div>The code is at <a href="https://bitbucket.org/aswarren/galaxy-cid">https://bitbucket.org/aswarren/galaxy-cid</a> 8cf8d25557b2</div><div>Hope this helps somebody.</div><div><br></div><div>Andrew Warren</div>