New tool Addition: Chopper a tool for fast processing (filtering, trimming, ..) of long reads

[lsterck]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

Hi,
this is a pull request to add the Chopper tool to the iuc toolshed.
I'm happy to amend any review comments.

best regards,
lieven

[SaimMomin12]

Thanks @lsterck for the addition, some review comments inline.

[lsterck]

right, I think I know what the problem is ... on it.

[lsterck]

OK,
I'm stuck now ....
I thought it was (and it still is apparently) the comparison of the gzipped output files, but that still seems to fail once in a while. The only thing I can imagine is that the stream that gzip receives is not deterministic and thus the gzip version is different (though content is the same but likely different order of reads in the output)

I've ran the local planemo test a couple of times and after the edit I pushed before it seems to consistently pass (which was indeed not the case before) but not here apparently.

What am I missing? Any ideas how to resolve this?

[lsterck]

I could remove the gzip test but I would prefer to keep it if in any way possible (just to also check the gzip option)

[SaimMomin12]

I could remove the gzip test but I would prefer to keep it if in any way possible (just to also check the gzip option)

Maybe you can have try using asserts as per here:

tools-iuc/tools/pbtk/bam2fastx.xml

Line 46 in eca92f6

<output name="output_fastq_gz" decompress="true">