17 months ago by
All BWA tools at http://usegalaxy.org do not offer an option to output fastq datasets of unmapped reads directly. Instead, use tools to filter the mapped BAM result dataset to only include unmapped reads then convert SAM/BAM to fastq. There are a few tools to do the filtering and multiple filtering criteria can be set - including filters to capture low-quality mapping results.
One SAM/BAM filtering tool is in the Picard group along with a tool to convert SAM to FASTQ (it also accepts BAM input). SamTools and BAMtools also have BAM/SAM filtering tools. When using these tools be sure to sort the BAM/SAM dataset first, as a distinct step: https://galaxyproject.org/support/sort-your-inputs/
Some of the newer wrappers for mapping tools do include this option, including RNASTAR.
RNASTAR is pending indexes, so use a custom genome for now: https://galaxyproject.org/learn/custom-genomes/
The same fastq data generally not appropriate for both BWA and RNASTAR but this may be why you want to capture the unmapped reads in your search for contamination.
Hope this helps! Jen, Galaxy team