Custom tool error: Weird input given to a parameter that requires a fastqc file -- Solution: debug with Planemo

Question: Custom tool error: Weird input given to a parameter that requires a fastqc file -- Solution: debug with Planemo

4 months ago by

luciaaheitor • 20

luciaaheitor • 20 wrote:

Greetings,

I added a script to my local galaxy and I got the following error:

    with open(filename, 'r') as file:

IOError: [Errno 2] No such file or directory: '34564740'

This error makes sense since what's expected is a fastq file. And that's exactly what I added as input: https://ibb.co/gaO1gK

Galaxy is giving as input not the fastq files (or the .dat files) but the first number introduced with a 0 and a 1 after it:

34564740
34564741

The parameter part of the xml file of the tool is the following:

<param type="data" name="fastq1" format="fastq" label="Read 1" />
<param type="data" name="fastq2" format="fastq" label="Read 2" />

All the other parameters work well and receive what's expected. Please let me know what I'm doing wrong!

planemo tool development galaxy input • 179 views

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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by luciaaheitor • 20

4 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please try using Planemo for tool development: http://planemo.readthedocs.io/

I don't see an obvious problem here but will try to recruit some more feedback or you can try the Galaxy Gitter channel to reach the developers directly: https://gitter.im/galaxyproject/Lobby. They will expect that you have already run the tool through Planemo for debugging purposes (now, and for publishing the tool later) and have encountered a problem.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you! The tool was initially written in Planemo and everything seems perfectly ok expect when I run the tool and give the parameters where it seems to "ignore" the fastqs. I'll try to reach the developers through Gitter then.

ADD REPLY • link written 4 months ago by luciaaheitor • 20

Gitter thread: https://gitter.im/galaxyproject/Lobby?at=5b60c535ac380e3f3a10ac1d

Glad they were able to help you to sort out the issues! Jen

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Yes, more than what I asked for was solved. Thank you for your help as well!

ADD REPLY • link written 4 months ago by luciaaheitor • 20

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