We have "Fetch taxonomic representation (Galaxy Version 1.1.0)" installed on our galaxy installation. A user tried to use it to get taxonomic information on gis in a tab delimited file, but it produces an empty file with no errors. So I created a test file containing the GI shown in the tool's example output to test it out. It also produced an empty output file.
I ended up downloading the ncbi taxonomy database and wrote a few perl one-liners to compile the user's results for him. Turns out, every GI in his file is in fact in the taxonomy database, along with lineage.
So why doesn't the galaxy tool produce this output?
Here's the example I tried in my test:
The GIs column was set to 2 and the name column to 1. The output file was empty.
I could not find that GI in the tax database I downloaded, but one of the GIs from the user's file that was there was
504863860. The example file for that I made is:
The expected output for that GI would be:
90002 504863860 root Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermacetogenium Thermacetogenium phaeum
However, the tool produces an empty file for that as well...