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Fasta.gz implicitely converted to tabular instead of fasta with text inputs #18709

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Delphine-L opened this issue Aug 15, 2024 · 1 comment
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@Delphine-L
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Describe the bug
When trying to use a text processing tool on a fasta.gz, the tool converts it to tabular before running.

Galaxy Version and/or server at which you observed the bug
Galaxy Version: 24.1 main and eu

Browser and Operating System
Operating System: macOS
Browser: Chrome

To Reproduce
Steps to reproduce the behavior:

  1. Use history : https://usegalaxy.org/u/delphinel/h/compressed-fasta
  2. use any text processing tool (eg https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1)
  3. See that the dataset appears as Compressed Fasta (as tabular)
  4. After running the dataset is a fast converted to tabular

Expected behavior
For text inputs, the conversion should be from fasta.gz to fasta

Screenshots

Screenshot 2024-08-15 at 12 10 24 PM

@mvdbeek
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mvdbeek commented Aug 15, 2024

For now I'd add an explicit decompression step. The problem is that that is a valid conversion, just not the one you actually want.

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