Add Pairtools sort #5910
Add Pairtools sort #5910
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Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Fixed errors, added more options and tests for the tool
Restructured the folder structure
Reduced the size of test-data
…'" wherever we can.
tools/pairtools/sort.xml
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| --nproc-out \${GALAXY_SLOTS:-4} | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="pairs_path" type="data" format="pairs" label="Input pairs file" help="Input .pairs/.pairsam file"/> |
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pairs is not a valid Galaxy format
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:(
in the parse xml we have this line and it worked...
<data name="output_parsed_pairs" format="pairs"
I can change it to text,tabular. Also pairsam?
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I just double checked, .pairs and .pairsam both are tabular format data as per https://pairtools.readthedocs.io/en/latest/formats.html#pairs
If we all agree, we can stick to "format=tabular"? If not, we are also happy to include .pairs and .pairsam format to Galaxy.
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Ok, I'll update all to tabular
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
tools/pairtools/sort.xml
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| <data name="output_sorted_pairs" format="pairs,pairsam" label="${tool.name} on ${on_string}: .pairsam"/> | ||
| </data> |
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It can only be one format.
| <data name="output_sorted_pairs" format="pairs,pairsam" label="${tool.name} on ${on_string}: .pairsam"/> | |
| </data> | |
| <data name="output_sorted_pairs" format="pairs,pairsam" label="${tool.name} on ${on_string}: .pairsam"/> |
This seems to be the format, correct? https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md
We should create a Galaxy datatype for it. @SaimMomin12 maybe we can talk about that tomorrow?
Co-authored-by: Björn Grüning <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
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Resolved: #5917 |
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Nice! Yes... both generating part of the files for the test dataset messed up the diff. I'm closing this PR now that #5917 is done |
FOR CONTRIBUTOR: