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
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
e.g. from the bowtie wrapper:
<param name="pInput1" type="data"
format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ
help="Must have ASCII encoded quality scores" display="on_deck"/>
<param name="pInput2" type="data"
format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ
help="File format must match the Forward FASTQ file"
The changes to run.mako seem a little hacked in to me (I am still getting a
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
Hope this helps somebody.