<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.2.1-atlas">
        <repository name="package_r_3_2_1_with_atlas" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="vegan" version="2.3-0">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository  name="package_r_3_2_1_with_atlas" owner="iuc" >
                        <package name="R" version="3.2.1-atlas" />
                    </repository>
                    <package>https://depot.galaxyproject.org/package/noarch/permute_0.8-4.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/lattice_0.20-31.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/vegan_2.3-0.tar.gz</package>
                </action>
            </actions>
        </install>
        <readme>
        Contains a tool dependency definition that downloads and installs version 2.3-0 of the vegan R library.
        
        Provides: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
        </readme>
    </package>
</tool_dependency>

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.2.1">
        <repository name="package_r_3_2_1" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="vegan" version="2.3-0">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository  name="package_r_3_2_1" owner="iuc" >
                        <package name="R" version="3.2.1" />
                    </repository>
                    <package>https://depot.galaxyproject.org/package/noarch/permute_0.8-4.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/lattice_0.20-31.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/vegan_2.3-0.tar.gz</package>
                </action>
            </actions>
        </install>
        <readme>
        Contains a tool dependency definition that downloads and installs version 2.3-0 of the vegan R library.
        
        Provides: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
        </readme>
    </package>
</tool_dependency>

Change package_r_vegan_2_3_0 to use package_r_3_2_1
Change package_r_vegan_2_3_0 to use package_r_3_2_1
