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Question: Having issues uploading csv files as tables into galaxy
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gravatar for ewmartin
3.3 years ago by
ewmartin • 0
United States
ewmartin • 0 wrote:

I am trying to upload some data sets that are in csv format and I am having issues with galaxy formatting the inputted data as a table.  Can Galaxy read the csv into a table or do I need to do some file conversions? Thanks!
get data • 1.2k views
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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by ewmartin • 0
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gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Try replacing the commas with tabs using the tool "Convert delimiters to TAB".

If this still produces odd visual formatting, the contents of the uploaded dataset may be inconsistent for some reason. An inconsistent number of "columns" (in this case, commas) or the presence non-printing characters are common issues. Try to standardize the file or strip out these extra characters before loading to see if the problem resolves.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Jennifier,

I am having a similar issue with using csv files directly in Galaxy, without having to use an external application to convert them first. When I use the Convert delimiters to TAB tool, it splits the file on all commas, including those within double quoted strings which skewes some of the rows. Is there another way to convert csv to tab delimited? If not, is there a possibility you can develop the upload tool to convert csv to tabular, maintaining any commas within strings?

Many thanks

ADD REPLY • link written 3.1 years ago by joanna • 70

Hello - This functionality is expected with the current tool, but this is probably important enough to consider either modifying the current wrapper or creating a new one. I opened an enhancement request on Github here - please feel free to add comments! https://github.com/galaxyproject/tools-devteam/issues/250

Next time it might be best to post suggestions like this as a new question and reference prior related Q&A with a link.

Thanks, Jen, Galaxy team

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
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