wrappers for ppanggolin all and ppanggolin msa #6645
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tools/ppanggolin/.shed.yml
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| homepage_url: https://ppanggolin.readthedocs.io/en/latest/ | ||
| long_description: | | ||
| Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors. | ||
| remote_repository_url: https://github.com/labgem/PPanGGOLiN |
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I think this should point to the IUC repo. Use this one for homepage_url. The readthedocs URL might be cool to mention in the tool's help section.
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| remote_repository_url: https://github.com/labgem/PPanGGOLiN | |
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin |
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Thanks @bernt-matthias , I implemented your suggestions, does it look good to you ? I couldn't get the validator to work for checking the consistency of the input files format, I didn't find a way to loop through multiple datasets or dataset collection and didn't find an example of such a validator. I implemented this check in the section by raising an exception. Best, Thomas |
| #set extension_input_files = $file.ext | ||
| #else: | ||
| #if $file.ext != $extension_input_files: | ||
| #raise Exception("All the genome files must be of similar format, either all genbank files or all fasta files.") |
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Not sure if raising an exception is a good idea. Have you tried what happens in such a case?
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The exception appears in the history for each output files that have failed, see screenshot enclosed.
tools/ppanggolin/ppanggolin_all.xml
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| #raise Exception("All the genome files must be of similar format, either all genbank files or all fasta files.") | ||
| #end if | ||
| #end if | ||
| #set base_name = str($file.element_identifier).split('.')[0] |
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What happens if users have . in the identifiers. Maybe ".".join(str($file.element_identifier).split('.')[:-1])
FOR CONTRIBUTOR: