Hi all,
I've noticed from a couple of examples that when defining the command line string in an tool's XML wrapper (i.e. cheetah template), you can use $input_param_name.extension (or apparently $input_param_name.ext) to get the file format (metadata) for an input parameter called input_param_name (while of course you use $input_param_name to get the filename for this param).
This doesn't seem to be documented on the tool conf wiki: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
Most of the examples I found looking at the tool XML use the longer form (.extension), although interestingly in a recent commit Dan used just .ext in the fastx_clipper.xml file to special case Sanger FASTQ. Is that a valid alternative too? https://bitbucket.org/galaxy/galaxy-central/changeset/93d7007bd859
I'm curious about the naming here - did Galaxy once use the format name as the actual file extension? Now at least all data files seem to have .dat as the extension (which I'm sure presents a small problem for some command line tools which make file format inferences from the filename extension, requiring hacks in their Galaxy wrappers).
Peter