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WorkflowConversion / CTDConverter

Series of python scripts to convert CTD files into other formats such as Galaxy, CWL
MIT License
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gather workflows for end-to-end testing #55

Open mr-c opened 3 years ago

mr-c commented 3 years ago

@timosachsenberg , Oliver said you might have some Galaxy workflows that used the output of CTDConverter?

timosachsenberg commented 3 years ago

Not sure. AFAIK, we generate our galaxy node wrappers using CTD and we have some galaxy workflows. Would this help?

bgruening commented 3 years ago

GTN has a few workflows included that worked last time we used them. However, those are training workflows.

mr-c commented 3 years ago

Not sure. AFAIK, we generate our galaxy node wrappers using CTD and we have some galaxy workflows. Would this help?

Yes, any workflow that uses CTD-derived tool descriptions would be useful!

bernt-matthias commented 3 years ago

Yep. All OpenMS tools for version > 2.5 are derived from CTD (99.9% automatically with a few [2] exceptions where patches are used). The workflows @timosachsenberg is working on should use the latest version of these tools.

mr-c commented 3 years ago

@timosachsenberg can you link me to your workflows? Is there (small) testing data?

mr-c commented 3 years ago

Metabolite_Adduct _Grouping

WF: https://usegalaxy.eu/u/annalefarova/w/metaboliteadduct-grouping History: https://usegalaxy.eu/u/annalefarova/h/metaboliteadductgrouping Data: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/

Proteomics_LFQ

WF: https://usegalaxy.eu/u/annalefarova/w/proteomicslfq Data: 1) https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Labelfree/datasets/ 2) https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Labelfree/databases/s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta