galaxyproject / galaxyproject/tools-devteam
Enhance "Convert Characters" to include option to ignore chars in quotes
- Dominant language
- Python
- Stars
- 37
- Forks
- 94
- PR merge metrics
- No merged PRs in 30d
Description
Some common CSV formatted files have content in double quotes. This can include commas. Conversion to tabular format is then difficult.
Primary request to add in a option on the tool form to ignore characters bound by double quotes. This has limited but specific utility.
Another option is expand the tool to convert any of the characters to any of the other characters, instead of limiting this to just the list of chars to tabs (only). If this was done, multiple passes through the tool could eventually parse any cvs to tab. This enhancement of tool behavior is desirable outside of this particular request (fixing and converting other formats would be possible within Galaxy).
And yet another option is to wrap a tool like OpenCSV http://opencsv.sourceforge.net/ to convert csv to tabular specifically.
Example of current behavior:
original file:

after converting commas to tabs, this is the result (expected with current rules):
Contributor guide
Assessment
This issue has not been assessed yet.