Galaxy: Filter by quality not working

[AngelicaLindlof]

I am using Filter by quality tool on FastQ data and it is giving the following error. Have tried two days in a row now, still the same issue.

/galaxy-repl/main/jobdir/028/593/28593634/tool_script.sh: line 41: -q: command not found

[bernt-matthias]

Hi @AngelicaLindlof. Thanks for the report. Could you open the issue over here: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter

• Please also include the information on the tool version.
• If possible the content of the tool_script.sh could be helpful.

I'm closing the issue here.

[mvdbeek]

That's generally useful advice @bernt-matthias. I've tracked this down due to other reports we received -- strings after tokens aren't expanded on 20.05. I'm working on it.

[AngelicaLindlof]

I'm not sure if this is what you request:

Galaxy Tool ID: | toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2+galaxy0
-- | --
Galaxy Tool Version: | 1.0.2+galaxy0

[mvdbeek]

Thanks, that's fine. All the necessary information will also be submitted to us if you click on the bug icon on the red dataset. I've reproduced this and will take care of it, you don't need to do anything else.

[AngelicaLindlof]

Unfortunately it never turned red, but became green.

From: Marius van den Beek <[email protected][e-mail]>
Reply-To: galaxyproject/galaxy <[email protected][e-mail]>
Date: Tuesday, 26 May 2020 at 11:56
To: galaxyproject/galaxy <[email protected][e-mail]>
Cc: Angelica Lindlöf [email protected][e-mail]>, Mention <[email protected][e-mail]>
Subject: Re: [galaxyproject/galaxy] Filter by quality not working (#9814)

Thanks, that's fine. All the necessary information will also be submitted to us if you click on the bug icon on the red dataset. I've reproduced this and will take care of it.

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