Bedtools: BAM Filter fails with any rule combination, including those in tool help

[jennaj]

Tool version: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1

Earlier versions of the tool work fine. Is this an 18.05 problem or a tool problem?

Test history: https://usegalaxy.org/u/jen/h/test-history-filter-bam-datasets-on-a-variety-of-attributes-galaxy-version-241

Not tested at usegalaxy.eu (BamTools is not installed)

Error:

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/__init__.py", line 191, in prepare_job
    job_wrapper.prepare()
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/__init__.py", line 865, in prepare
    self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build
    raise e
TypeError: <galaxy.tools.wrappers.InputValueWrapper object at 0x7f2929ada2d0> is not JSON serializable

[jennaj]

Update: The selects for inputs with this tool is behaving strangely. What is chosen on the tool form is not always what is submitted to the tool (flips back to default selection before the user makes a choice).

If "rerun" is used, the selection seems to "stick" better. Sometimes takes a few attempts.

Found this during initial testing, not retested yet under the most recent update for pre-release 18.05 on main. Has been reported at Biostars today. Will test again to try to determine if a tool problem or Galaxy problem. Would this need a distinct ticket?

[jennaj]

Still a problem with (Galaxy Version 2.4.1). When corrected, please change the label back to retest.

[natefoo]

The object that it's trying to serialize is $rule_configuration.rules. I believe this can be fixed by changing it to:

        #set $config[ 'rule' ] = str($rule_configuration.rules)

It allows the tool to run locally for me, although I can't verify the results. @davebx does this change make sense to you?

[davebx]

@natefoo yeah, that looks reasonable. I do wonder why (or whether) it worked before, without casting to string.

[jennaj]

Is there a PR or issue ticket for the tool change already (that is what is needed, yes? not config on our side)? I can make one and link it back if that would help. Lmk

And I don't recall when I tested that function last .. and if I did, it was a long time ago in a Galaxy far far away, with a much earlier tool version.

[natefoo]

I created a PR at galaxyproject/tools-iuc#1922.

[natefoo]

The tool's been updated on Main and the job in the test history runs successfully for me now.