Great -- it seems support for batch processing of many files was recently added. See "Workflows & Multiple datasets" at http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 . Many thanks to the Galaxy developers, and in this case Martijn Vermaat, who I think wrote this feature. Now, to return to my second question - is there a Reduce for this Map? -Andrew On 24-Jul-11 09:19, Andrew Straw wrote:

Hi,

(Warning: Galaxy newbie here.)

I'd like to run a series of galaxy tools repeatedly on multiple input files. In other words, I have input data files [data1, data2, ..., dataN] and I want to apply [step1, step2] to each of these files to produce [output1, output2, ..., outputN]. I know that I can automate the application of the multiple steps to a single input file as a workflow, but is there any way to automate running a workflow multiple times on multiple inputs through the Galaxy web interface? (I see the scripts in scripts/api, but I'm looking for something entirely driven by the web user interface.)

For a second question, is there a recommended way of combining then merging the results (e.g. from multiple workflows) into a single file?

The use case for this is that we're doing experiments on lots of individual flies from several genotypes and we want to analyze data from our individual fly experiments but then pool results across flies from the same genotype and compare with other genotypes. I imagine this is pretty similar to what a lot of people are doing, but somehow I'm not getting how this might be done with Galaxy.

Thanks, Andrew

-- Andrew D. Straw, Ph.D. Research Institute of Molecular Pathology Vienna, Austria http://www.imp.ac.at/research/andrew-straw/