autocycler suit #7247
autocycler suit #7247
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@bernt-matthias Can you review this autocycler suite and merge it when you can. Many thanks |
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@bernt-matthias Thank you for reviewing the tools . I am working on the improvements at the moment and will resubmit them when I am done. |
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@mthang please ping us when you think a new review is needed :) Thanks a lot this looks great! |
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@bgruening @bernt-matthias It took me a while to fix the wrapper and the test-data. Can you please review the wrappers again. Many thanks. |
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The shed.yml was for some reason broken, tests are now running. Lets see what happens :) Thanks a lot @mthang |
| <test> | ||
| <param name="in_gfa" value="consensus_assembly_unfiltered.gfa"/> | ||
| <param name="remove" value="743,782"/> | ||
| <output name="cleaned_gfa" file="clean.gfa" ftype="gfa1"> |
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Having file and assert_contents seems redundant.
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I removed the assert_contents and keep the file only. Should I remove all assert_contents if I use "file" in my test_unit?
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If an assertion captures the essence of the test I would even prefer the assertion over the file.
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I added the assertion back to the autocycler_clean.xml to ensure the test works. The planemo failed after I removed the file="clean.gfa" ftype="gfa1"
| </inputs> | ||
| <outputs> | ||
| <collection name="subsampled_reads" type="list" label="${tool.name} on ${on_string}: subsampled reads"> | ||
| <discover_datasets pattern="(?P<designation>.+)\.fastq" directory="out_dir" format="fastq" /> |
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infer format from input?
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Thank you for providing the changes ! I was puzzled what "infer format from input" means in Galaxy. I understand now. As you probably know, the autocycler subsample produces uncompressed fastq files instead of compressed fastq.gz. That's the reason I didnt update the test section. Anyway, thanks a lot!
if there is only one output
and split yaml output in separate output
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Hi @mthang I took some time to rewrite quite a bit to have a more Galaxy look-and-feel, i.e. mainly I removed the nested collectiond and split collections containing fasta and gfa. What do you think? |
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| <inputs> | ||
| <param argument="--reads" type="data" format="fastqsanger,fastqsanger.gz" label="Input long reads (FASTQ format)"/> | ||
| <param name="assembler" type="select" label="Tool"> | ||
| <option value="genome_size">genome_size</option> |
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I was thinking if we should only support the genome_size command?
We have tools for most assemblers, except for metamdbg, plassembler, lja, and myloasm.
This would also reduce the number of requirements.
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FOR CONTRIBUTOR:
This is a collection of tools for Autocycler - https://github.com/rrwick/Autocycler .