Hi, We have begun dabbling with a local instance of Galaxy (amazingly impressive !!). I have 2 questions: 1. I have written a tool to implement Lucy (http://bioinformatics.oxfordjournals.org/cgi/content/short/17/12/1093). I can figure out how to handle output when the command line has a -o option to explicitly state the output file name. Or when the file output is always the same. I am trying to make a tool where the java executable is launched and makes an output file. The output file is named the same as the input file (input.txt) but has a new extension added to the end of it (.cal), i.e., inputfilename.txt.cal I can't for the life of me figure out the XML syntax to read this file back into galaxy as an output. Is the best strategy to write a wrapper in another language (perl, python, java), that will feed in $output, then read in the ".cal" output and spew out a file to satisfy $output for the XML ? 2. For testing, what is the best way to do the testing? I have written a few java based executable jars and the corresponding XML docs to go with them. I'd like to share with the world but I am not sure the best way to go testing. Thank you very much for your attention, Rob Reid Rob Reid, Ph.D. | Research Associate UNC Charlotte | Dept. of Bioinformatics and Genomics 9201 University City Blvd. | Charlotte, NC 28223 Phone: 704-250-5766 rreid2(a)uncc.edu | http://www.uncc.edu --------------------------------------------------------------------------- If you are not the intended recipient of this transmission or a person responsible for delivering it to the intended recipient, any disclosure, copying, distribution, or other use of any of the information in this transmission is strictly prohibited.