Question: Custom tool error: Weird input given to a parameter that requires a fastqc file -- Solution: debug with Planemo
0
gravatar for luciaaheitor
13 days ago by
luciaaheitor10
luciaaheitor10 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!

ADD COMMENTlink modified 13 days ago by Jennifer Hillman Jackson25k • written 13 days ago by luciaaheitor10
0
gravatar for Jennifer Hillman Jackson
13 days ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 13 days ago by Jennifer Hillman Jackson25k

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 REPLYlink written 13 days ago by luciaaheitor10

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

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

ADD REPLYlink written 13 days ago by Jennifer Hillman Jackson25k
1

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

ADD REPLYlink written 13 days ago by luciaaheitor10
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