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:

      <when value="paired">
        <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">

The changes to run.mako seem a little hacked in to me (I am still getting a
handle on the mako format). I wasn'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.

The code is at https://bitbucket.org/aswarren/galaxy-cid 8cf8d25557b2
Hope this helps somebody.

Andrew Warren
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