Hi all, There are two copies of the wiggle_to_simple tool in the main repository, and this duplication appears to have happened back in 2009. $ grep wiggle_to_simple tool_conf.xml.sample <tool file="filters/wiggle_to_simple.xml" /> <tool file="stats/wiggle_to_simple.xml" /> $ diff tools/filters/wiggle_to_simple.py tools/stats/wiggle_to_simple.py (no changes) $ diff -w tools/filters/wiggle_to_simple.xml tools/stats/wiggle_to_simple.xml 15,18d14 < <test> < <param name="input" value="3.wig" /> < <output name="out_file1" file="3_wig.bed"/> < </test> The tools/filters/wiggle_to_simple.xml version has Windows newlines, and 2 tests. The tools/stats/wiggle_to_simple.xml version has Unix newlines, but only 1 test. I would therefore suggest merging the two (Unix newlines, both tests). Peter