Hello everyone,
I hope this message is at the right place. I’m reaching out to share an issue I’ve encountered while working on adding tools to a Galaxy server. Your expertise and insights would be greatly appreciated in helping me find a solution.
In my endeavor to add wrap tools to a Galaxy server via XML files, I encountered a significant challenge. Despite diligently searching through the available documentation, I found the process far from straightforward. Rather than having a centralized resource containing all the necessary information, I had to gather bits and pieces from various sources scattered across the internet. While I did come across a substantial portion of documentation on Galaxy Tool XML File — Galaxy Project 24.1.dev0 documentation, it still lacked crucial details, leaving me feeling incomplete in my understanding.
For my initial tool, I focused on creating a data cleaning tool. This tool essentially generates an output labeled as follows: label="${molecule.element_identifier} [cleaner]", with ‘molecule’ defined within the XML as input <param name="molecule" type="data" format="mol2" />
My second tool is a mol2 analyzer, which generates an output labeled as follows: Analyze on ${molecule.element_identifier}, with ‘molecule’ defined within the XML as input <param name="molecule" type="data" format="mol2" />
While this second tool functions correctly when using an uploaded mol2 file, I encountered an issue when using a mol2 file that has been cleaned. Instead of the expected output label ‘Analyze on mymol.mol2 [cleaner]’, I got ‘Analyze on mymol.mol2 __cb__cleaner__ob__’.
In my search for a solution, I couldn’t locate an attribute with the appropriate name or a method to prevent the interpretation of square brackets [ ]. I also explored the possibility of computing the correct output label from a command or within the output definition but found no viable option. This raises the question: Is there a feasible way to achieve this desired outcome?
Best regards,
Olivier Demegeon
