Hello galaxy dev,
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't find any when writing this up).
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 "on_deck." If you set the tool xml config to have parameter tag display="on_deck" then it will enable this interaction method.
e.g. from the bowtie wrapper:
<param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores" display="on_deck"/>
<param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file" display="on_deck">
Hope this helps somebody.