Hi Mark, Use a workflow to make this simpler. Put as many steps that are redundant into the workflow then add an "Input" dataset to the beginning (this is the important part). In the workflow editor, the "input" dataset is located in tool list (left column), near the bottom. Then, when bringing up the workflow to run it, there will be a little multi-paged icon next the input dataset's label. See the png here: After choosing inputs, down the page where you click to execute the workflow there is checkbox option to send the results to a new history. This can come in handy sometimes when running on multiple dataset inputs, since it will sort the output into distinct histories for you. Not always wanted, but good to know about. Hopefully this helps, Jen Galaxy team Look for more here in the upcoming week: https://wiki.galaxyproject.org/Learn/AdvancedWorkflow On 2/26/14 3:30 PM, mark.rose@syngenta.com wrote:

Hello

Is there a approved way to configure or otherwise use galaxy to process multiple files with a tool or workflow? Using FASTQ Groomer on dozens of files individually is excruciating.

Thanks

Mark

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