Hello, Sorry if this is a double post, I tried to send a message earlier today and accidentally sent it incomplete. I am working on integrating SOAPaligner/soap2 into Galaxy. soap2 includes two executables, 2bwt-builder which takes a FASTA file and generates 13 index files, and soap which uses these index files for alignment. Here is my configuration for 2bwt-builder: <tool id="2bwt-builder" name="2bwt-Builder"> <description>build index files for soap</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> The tool runs in Galaxy, but when it finishes it puts 13 empty data files in my history. I can see in database/files/.../ that the output of 2bwt-builder is correct and the indexes are non-empty files. I'm guessing that tabular may be the wrong format for these output files, but I'm not really sure what other datatype they would be. Perhaps I need to define my own. Where am I going wrong? Cheers -- Branden Timm System Administrator Great Lakes Bioenergy Research Center University of Wisconsin btimm(a)glbrc.wisc.edu