<?xml version="1.0"?>
<tool_dependency>
    <package name="shear" version="0.2.9">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://vk.cs.umn.edu/SHEAR/downloads/shear-v0.2.9-compiled.tar.gz</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="SHEAR_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
SHEAR: Sample Heterogeneity Estimation and Assembly by Reference

SHEAR is an assembly tool that accounts for heterogeneous variants by estimating their representative percentages and allowing for selective assembly of sample subpopulations. By utilizing structural variant detection algorithms, SHEAR also offers improved performance in the form of a stronger ability to handle difficult structural variant types and improved computational efficiency.

http://vk.cs.umn.edu/SHEAR/
        </readme>
    </package>
</tool_dependency>