Workflow execution of "Join two Datasets" tool

Question: Workflow execution of "Join two Datasets" tool

19 months ago by

I'm trying to use a workflow that includes one step where I take two datasets with similar columns and perform a "Join two Datasets" operation. I've done this manually, and it works perfectly whenever I do it. However, when I run a workflow to do this automatically, it always returns an error -- "Error parsing command line".

This isn't a critical issue, as I can still do my work without this functionality, but it would be nice if this worked.

tool workflow join • 429 views

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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by jamieson.pierce • 10

Hello, This function was working at http://usegalaxy.org last time I checked. However, we are in the process of updating the source code on the server. I'll test and see if can reproduce the problem. Feedback soon! Thanks for reporting the issue so clearly, Jen, Galaxy team

ADD REPLY • link modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool is working as expected at Galaxy Main http://usegalaxy.org. This is true whether run within a history directly or within a workflow. I also tested a related join tool and that also worked as expected.

Start troubleshooting by checking the tool setting versus the input data contents. Why there are different results could also be because the direct run tool options differ from the workflow tool options. The test I ran was very simple and can be reviewed here:

Example workflow: https://usegalaxy.org/u/jen/w/test-join-tools-in-a-workflow
Example history with sample inputs and workflow-produced outputs: https://usegalaxy.org/u/jen/h/join-tool-testing

Should you be running a local Galaxy, make sure that it is current with the latest Galaxy release and with the most current tool version(s). Note that the tool "Join two Datasets" comes with Galaxy pre-installed. The related tool tested "Join two files" is installed from the tool shed.

If you need more help, please let us know. Jen, Galaxy team

ADD COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k

Hey thanks for your help with this Jen, I was able to troubleshoot it using your examples. You're doing a really excellent and thankless job with all this support. Thank you

ADD REPLY • link written 19 months ago by jamieson.pierce • 10

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