galaxyproject / galaxyproject/tools-devteam

Enhance "Convert Characters" to include option to ignore chars in quotes

Open
#250 5 comments 0 reactions 1 assignee Claimed by @jennaj View on GitHub
enhancement
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:

screen shot 2015-10-16 at 12 51 56 pm

after converting commas to tabs, this is the result (expected with current rules):

screen shot 2015-10-16 at 12 52 14 pm

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