Hi and welcome, fcy!
You have done a good bit of reading, obviously, before asking here, but it looks like it is necessary to put a few things into perspective still.
It is true that Bowtie2 and BWA-MEM are excellent aligners, just like FreeBayes is an excellent variant caller - not just for C.elegans data, but in general. MiModD, on the other hand, is a complete suite of tools for identifying phenotype-causing mutations from genetic screens in model organisms. As part of its functionality, MiModD comes with samtools/bcftools, which it uses, among other things, for variant calling. For the alignment step, MiModD allows you to use any modern aligner, including bowtie2 or bwa-mem. For use on local machines (desktops and notebooks), MiModD offers the snap aligner as a built-in choice because this is the most performant solution on many typical single machines. On usegalaxy.org, the recommended aligner would, in fact, be Bowtie2 (see https://sourceforge.net/p/mimodd/wiki/MiModD%20on%20public%20Galaxy%20servers/).
Now what MiModD offers on top of variant calling is causative variant mapping, which is usually a key component of your analysis workflow if you have a mutant line of say worms obtained from a random mutagenesis screen. If you really want to go for the combination bowtie2/freebayes for producing a list of variants found in the mutant line, the resulting output is unlikely to be directly compatible with downstream MiModD tools (you could certainly make it compatible with a bit of command line effort, but then you said you were new to bioinformatics).
OTOH, if you go with the combination of bowtie2/bcftools (accesible via the MiModD tool suite) there is no problem at all. It is true that several papers demonstrate that freebayes is a bit better than bcftools mpileup/call in certain situations, but be assured the relatively small difference between these tools will almost certainly not affect you (unless I’m mistaken about your use case, and you are going to do some professional genome curation effort).
Finally, to answer your concrete question: the in-file metadata you are referring to is just an ID for your sequencing data and a sample name that the MiModD variant caller expects for each of your samples. You have to make sure the aligner adds this information to its BAM format output, or you would have to add it yourself later. The Galaxy wrapper for Bowtie2 has text boxes for entering these two pieces of info (and more) and that’s all.
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