Hi, I do not know for input but if you look at the json galaxy format (not the XML for a specific tool, the json format use to import/export a workflow, which describe how tools follow), you could rename a file with the "post_job_actions" tag. The path for this tag in JSON tree is { « steps »: { « Step number » : { Then, indicates the name you want for your file with "RenameDatasetAction(...)", where (...) is the name of the original file, define in the "output > name" tag ({ "steps": { "Step number" : { "tool": { "output" ). Good luck. -Regards, Remy 2012/1/1 Peter Cock <p.j.a.cock@googlemail.com>
On Sun, Jan 1, 2012 at 12:29 AM, Thon Deboer <thondeboer@me.com> wrote:
Thanks, but ${foo.name} did not work in the workflow to rename an output file. It takes ${foo.name} to be a user provided parameter.
${foo.name} will definitely work in tool definitions, but that means I have to change ALL the default tool names for all the tool in galaxy...Surely there must be a way to rename an output file to the original input file in the workflow step "Rename Dataset"?
Sorry - I thought you were still talking about tool XML files.
I'm not sure that there are any dynamic variables you can use in the workflow rename action to access properties of the tool that created the history item - but being able to use ${tool.param_name} or ${tool.input_file.name} or something like that could be quite powerful (where my made up syntax is $tool for the tool which created the history entry, and then dot and a tool parameter as named in the tool's XML). It would be possible even to expose those fields via the web interface, but for a first pass having an expert user type them in by hand would work.
Interesting idea... I wonder what the Galaxy team think?
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: