Hello, I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a test integration case. soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder takes a FASTA files and generates a set of 13 different index files, which soap needs in order to do it's alignment. I have started by just creating the tool XML configuration for 2bwt-builder. The configuration follows: <tool id="2bwt-builder" name="2bwt-Builder"> <description>build index files for the SOAPaligner/soap2</description> <command>2bwt-builder $input</command> <inputs> <param type="data" format="fasta" name="input" label="Source file"/> </inputs> <outputs> <data format="tabular" name=".amb Index File"/> <data format="tabular" name=".ann Index File"/> <data format="tabular" name=".bwt Index File"/> <data format="tabular" name=".fmv Index File"/> <data format="tabular" name=".hot Index File"/> <data format="tabular" name=".lkt Index File"/> <data format="tabular" name=".pac Index File"/> <data format="tabular" name=".rev.bwt Index File"/> <data format="tabular" name=".rev.fmv Index File"/> <data format="tabular" name=".rev.lkt Index File"/> <data format="tabular" name=".rev.pac Index File"/> <data format="tabular" name=".sa Index File"/> <data format="tabular" name=".sai Index File"/> </outputs> </tool> I've used the tabular data type for the output files, which I'm not sure is correct. When the script runs, it generates 13 output files in my history, but they are all empty according to galaxy. When I look at galaxy_dist/database/files/.../, the output files have been generated correctly and are non-empty. Where am I going wrong? Thank you in advance for any advice. -- Branden Timm System Administrator Great Lakes Bioenergy Research Center University of Wisconsin btimm@glbrc.wisc.edu