"Classify Sequences with MetaPhlAn2" worker output files URLs are not rolled

"Classify Sequences with MetaPhlAn2" has two parameters with output file URL: "Bowtie2 output file" and "Output file". If one sets any URL outside the workflow_output folder and launch the workflow with several input files, then only the first input file will be processed correctly. Other tool launches will fail with the following message:

Warning! Biom python library not detected!
Exporting to biom format will not work!
BowTie2 output file detected: /Users/atiunov/root/qwe/bowtieout.txt
Please use it as input or remove it if you want to re-perform the BowTie2 run.
Exiting...