Question: Impossible to get the right columns from a CSV file when using type="data_colum"
0
gravatar for avillahoz
3 months ago by
avillahoz10
avillahoz10 wrote:

Hi,

I have the following source code for a better understanding of an issue during a tool development of mine:

  <inputs>
    <param name="galaxy_csv_file"
           type="data"
           format="tabular"
           label="Encoded Data" />
    <param name="galaxy_location_vector_column"
           type="data_column"
           data_ref="galaxy_csv_file"
           numerical="False"
           use_header_names="true"
           label="Column Containing Location"
           help="" />

I got the column headers pre-loaded to be chosen from the user, all fine until now.

As my team is using the CSV format to interchange data, I changed into

 <inputs>
    <param name="galaxy_csv_file"
           type="data"
           format="csv"
           label="Encoded Data" />
    <param name="galaxy_location_vector_column"
           type="data_column"
           data_ref="galaxy_csv_file"
           numerical="False"
           use_header_names="true"
           label="Column Containing Location"
           help="" />

It still captures all the row data as an entire column, not all the columns separated by commas, despite using standard CSV files and explicitly choosing the CSV format before uploading the CSV data. Even following the CSV dialect by default as csv.excel when saving as a .CSV file from Excel.

Any idea about why type="data_column" does not react to the CSV data?

Thanks,

Angel Villahoz-Baleta.

header galaxy datatype tabular csv • 140 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by avillahoz10
1
gravatar for avillahoz
3 months ago by
avillahoz10
avillahoz10 wrote:

It is the same bug described by https://github.com/galaxyproject/galaxy/issues/5026

ADD COMMENTlink written 3 months ago by avillahoz10

Correct, .csv files are still problematic. Output tabular format from Excel instead and use that within Galaxy for now. You can also ask the developers for an update on the fix. Directly on the ticket or at Gitter (reference the ticket in your question by link): https://gitter.im/galaxyproject/Lobby

ADD REPLYlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k
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