add COMEBin utility script

[SantaMcCloud]

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)

[SantaMcCloud]

This tool doesnt work yet since the recipe isnt updated yet. I will restart the test when it was merged: bioconda/bioconda-recipes#59392

[SantaMcCloud]

I also dont know why the linting is failing since at there is no error when i run it locally with planemo. The only difference which i did see in the GitHub logs is this:

.. ERROR (ShedVersion): comebin: version 1.0.4+galaxy1 is less or equal than version of the latest installable revision 1.0.4+galaxy1
.. ERROR (ShedVersion): comebin_bam: version 1.0.4+galaxy0 is less or equal than version of the latest installable revision 1.0.4+galaxy1

Since i didnt change comebin this make no senee that this in an error and comebin_bam is new so there should be no version for it?

[SantaMcCloud]

Also there is an option to set RAM for this Tool. i know there is a galaxy variable to use but i didnt found anything to it how to use and there are not really good example in any wrapper uploaded in iuc. So can i only set it it in the command line or do i need specify a number such that it have this certain number of RAM?

[SantaMcCloud]

I also dont know why the linting is failing since at there is no error when i run it locally with planemo. The only difference which i did see in the GitHub logs is this:

.. ERROR (ShedVersion): comebin: version 1.0.4+galaxy1 is less or equal than version of the latest installable revision 1.0.4+galaxy1
.. ERROR (ShedVersion): comebin_bam: version 1.0.4+galaxy0 is less or equal than version of the latest installable revision 1.0.4+galaxy1

Since i didnt change comebin this make no senee that this in an error and comebin_bam is new so there should be no version for it?

okay now only the linting problem is there. I think it is the quoted error which keep it failing. Otherwise i couldnt found it in the logs why the linting is erroring

[SantaMcCloud]

@bgruening here is the problem as well which was in #7263

[SaimMomin12]

@SantaMcCloud Its green now! :)

[SantaMcCloud]

@SantaMcCloud Its green now! :)

oh okay nice then thank you :)

[bgruening]

The help is a bit sparse :)

[bgruening]

What is this bash script doing? Why is bowtie2 not good enough? This looks a bit suspicious to me :)

[SantaMcCloud]

I did change the help to answer this question.

This script was build using a modified version of the binning.sh of MetaWRAP and i assume the tool itself was build to fit to the these generated BAM files which means that other could work but i will not bet on this. Since BAM files are binary it is hard to see the difference but i could link you a history where 2 Comebin runs did run 1 with the BAM file generated by the the utitlity script and one with the Bowtie2 output: https://usegalaxy.eu/u/santinof/h/metagenome-assembled-genomes-mags-generation-imported-from-uploaded-file

[SaimMomin12]

@SantaMcCloud I still feel there is still room to update the help text. As of now, it lacks quite a lot of information. Maybe you could add what does the script does? Why is this script preferred over Bowtie2? What are inputs, expected outputs? That would be much helpful for the users.

[SantaMcCloud]

I added the help section a little bit. There si not a lot left what i could write there since this scritp use case is only the preprocessing for COMEBin. Bowtie2 doesnt work here and this script output doesnt work for other binnner. If this still is not enought since i can not write more detailed since i dont know metaWRAP i have to read a bit into it.

[SantaMcCloud]

@SaimMomin12 could you review it again? The test did error because of the CL all should be fine!

[SaimMomin12]

Some minor label corrections

[SantaMcCloud]

Thanks did commit them @SaimMomin12! :)