Hi Branden, The preferred batch execution method for the existing Galaxy framework is to iterate over the input dataset in a loop. The tool configuration wiki contains the details (jump to "<repeat> tag set"). http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Hopefully this helps! Jen Galaxy team On 10/21/10 8:36 AM, Branden Timm wrote:

Hi All, Is there any documentation on how to integrate tools that take a variable number of input files? We'd like to integrate a tool with the following command line syntax:

tool-name <n input files> <n column names> output1 output2

Thanks!

-- Branden Timm System Administrator Great Lakes Bioenergy Research Center btimm@glbrc.wisc.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

-- Jennifer Jackson http://usegalaxy.org