Hello everyone, I have been struggling with a custom tool I have been trying to create for a bit now. The purpose of the tool is to pull files from the irods file system and drop them into galaxy's history. The tool can take a file path name either as text or from a drop down menu where the file paths are generated from a code file in the tool's config file. The tool works well for single files but there are two problems. 1) The tool can't detect the file format of the file it is putting in history and 2) The tool can only upload one file at a time. I thought of using the galaxy 'upload from computer' tool as a template but this tool must be workflow compatible even if it is to be used at the end of a workflow or whatnot.
What I have done to address the format detection problem: 1) Tried setting a variable in cheetah to just the file extension passed in from the tool's parameters. Problem: The format attribute of the data tag can't get at the value of the cheetah variable. 2) Tried setting the format value to 'auto'. Problem: Everything just gets set to 'data'.
What I have done to address the multiple file upload problem: 1) Tried to use a repeat for the text input of the file path, and a multiple selection box for the existing file path parameter and then just pass the arguments to my python script which creates a new file for each path name. Not quite sure what to do with the outputs tag.
*Right now my script doesn't do anything with the $output parameter
Any help on this would be much appreciated. I am a beginner to working with Galaxy but am determined to get this working.
Both problems have been solved using this forum post: https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-August/020361.html I just used the really specific file output names and that created multiple output files and assigned the correct file formats to the files.