Hi all, I'm using the following XML: ... <inputs> <param type="data" format="txt" name="seqmeta" label="PAPS.seqmeta"/> <param type="data" format="txt" name="lib_info" label="Label Info"/> <repeat name="to_merge" title="Evaluation Inputs and Results"> <param type="select" name="pmm" label="Mismatch %" help="Maximum % of mismatch between the construct sequence and the comparison sequence."> <option value="10">10%</option> <option value="15">15%</option> <option value="20">20%</option> </param> <param type="text" name="max_length" label="Max Construct Length" value="25" /> <param format="fasta" name="fasta_in" type="data" label="FastA Output"/> <param format="txt" name="seq_stats" type="data" label="Sequence Stats"/> </repeat> </inputs> ... <configfiles> <configfile name="file_info"> #for $merge_set in enumerate( $to_merge ) #silent sys.stderr.write($merge_set.__str__() + "\n") #silent sys.stderr.write($merge_set.fasta_in.__str__()) #end for </configfile> </configfiles> ... And getting the resulting output: 127.0.0.1 - - [07/Apr/2010:15:31:50 -0500] "POST /admin/tool_reload HTTP/1.1" 200 - "http://localhost:8080/admin/reload_tool" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" 127.0.0.1 - - [07/Apr/2010:15:31:59 -0500] "POST /tool_runner/index HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,765 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6 galaxy.jobs DEBUG 2010-04-07 15:32:03,766 job 234 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,766 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-04-07 15:32:03,766 dispatching job 234 to local runner galaxy.jobs DEBUG 2010-04-07 15:32:05,423 job 234 dispatched (0, {'seq_stats': <galaxy.tools.DatasetFilenameWrapper object at 0x572b390>, '__index__': 0, 'max_length': <galaxy.tools.InputValueWrapper object at 0x572b8d0>, 'fasta_in': <galaxy.tools.DatasetFilenameWrapper object at 0x572b810>, 'pmm': <galaxy.tools.SelectToolParameterWrapper object at 0x572b290>}) 127.0.0.1 - - [07/Apr/2010:15:32:03 -0500] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" galaxy.jobs.runners.local ERROR 2010-04-07 15:32:07,356 failure running job 234 Traceback (most recent call last): File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/runners/local.py", line 55, in run_job job_wrapper.prepare() File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/__init__.py", line 386, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/tools/__init__.py", line 1364, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/jerdmann/Python/galaxy-central/eggs/Cheetah-2.2.2-py2.5-macosx-10.3-fat-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1270672326_31_15888.py", line 86, in respond NotFound: cannot find 'fasta_in' while searching for 'merge_set.fasta_in' So, I'm printing the merge_set dictionary and seeing a fasta_in key, but when I try to use fasta_in it can not be found. I'm assuming this is probably a syntax oversight on my part, but I'm not seeing it. -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123 jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann