New tool addition: Alnchain#7911
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@as042 Could you please use VS Code Galaxy extension to format the wrapper appropriately? |
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It looks for the fasta.gz files which where used to produce the chrM_HGvMM.1aln input and it is not finding them. Specifically for the paths used in the FastGA command execution.
In you case: FastGA -1:test test-data/chrM_hg38.fa.gz test-data/chrM_mm39.fa.gz.
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@SaimMomin12 I did use the extension. Is something about it not formatted correctly because it didn't catch the errors? |
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Today I learned that planemo test can pass, but the pr check still fails for some reason. |
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@as042 make sure you run |
| cp 'output.1aln' '$output' | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input" type="data" format="txt" label="Input .1aln alignment file" |
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I do not think that txt is a good practice here. This would result into Error: Cannot count lines in dataset for the displayed job metadata.
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I changed it to binary. Should I register 1aln as its own data format in Galaxy?
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I changed it to binary. Should I register 1aln as its own data format in Galaxy?
Yes, if you intend to use .1aln format in other tools as well, it would be worthwhile to create a new datatype here: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/datatypes_conf.xml.sample
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I'm so confused. I barely changed anything since the CI passed last time, AND planemo test --biocontainers passes no problem. |
4 participants
FOR CONTRIBUTOR:
Adds ALNchain to the FastGA suite and adds thread control to FastGA.