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.
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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