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workflow4metabolomics / tools-metabolomics

Galaxy tools for metabolomics maintained by Workflow4Metabolomics
https://workflow4metabolomics.org/
GNU General Public License v3.0
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Error when linking Isocor and Isoplot in a workflow #203

Closed llegregam closed 1 year ago

llegregam commented 3 years ago

I just finished getting the tool Isoplot online, and I tried linking it with Isocor in a workflow. The Isocor output file format is .tsv (tabular), but it seems that even though Isoplot accepts tabular and csv inputs, Galaxy will not let me link them together. Is this normal behaviour?

lecorguille commented 3 years ago

Strange! Can you point us the outputs within the xml wrappers (on GitHub), you want to link?

llegregam commented 3 years ago

Yes of course! The output of isocor that needs to be linked to isoplot can be found here: https://toolshed.g2.bx.psu.edu/repos/gmat/isocor/file/fa183805db31/isocor.xml And here is a snapshot of it: image The output is line 54 (output1, tabular format).

It is supposed to be linked to isoplot's data input (line 20): Capture

Thanks!

llegregam commented 2 years ago

Hello! Just wondering if there is any new info on the bug

lecorguille commented 2 years ago

Strange! Can you share an history on usegalaxy.fr with me?

llegregam commented 2 years ago

I can share a link to the workflow. As the tools cannot be linked through output/input I cannot launch any jobs in the history. Here is the workflow: https://workflow4metabolomics.usegalaxy.fr/workflow/editor?id=557b889a2f496bfb

lecorguille commented 2 years ago

I have just tested directly on the usegalaxy.fr instance. I didn't expect that but the issue comes from the space in format='csv, tabular' it should be format='csv,tabular'

llegregam commented 2 years ago

Okey then, that is surprising! So I need to release a new wrapper with the fix, right?

llegregam commented 2 years ago

Thank you! :)