I am a relatively new Galaxy user operating through GalaxyTrakr and I’ve pulled a bunch of our Salmonella isolate reads from SRA as collections and have done a number of analyses with them successfully within Galaxy.
However when I try and serotype them with sistr_cmd, it generates an output with all the appropriate information except for the corresponding SRR IDs. The only identifying information in the output I can see to differentiate isolates are the Galaxy History numbers corresponding to each contig assembly from Shovill (e.g., “Shovill on data 877 and data 876: Contigs”).
If I were only dealing with a couple isolates, I could go through my History and try and match everything up to the original IDs, but I am working with 400+. Does anyone know either how to get sistr_cmd to include identifying information or if there is anyway to download the History metadata so I could write a script to match History numbers with SRR IDs?
Thank you all!