Hicup Mapper aligns paired reads independently to a reference genome and retains reads where both partners align.

hicup_mapper

Version	Tool Shed	Owner	Galaxy instances where the tool is available
0.8.3+galaxy0	toolshed.g2.bx.psu.edu	bgruening	usegalaxy.org
0.6.1.0	toolshed.g2.bx.psu.edu	bgruening	usegalaxy.no
0.5.10.0	toolshed.g2.bx.psu.edu	bgruening	usegalaxy.eu usegalaxy.no
0.1.0	toolshed.g2.bx.psu.edu	bgruening	usegalaxy.eu