This does work, but it's an ugly workaround

workaround_tool_dependencies.xml

<?xml version="1.0"?>
<tool_dependency>
  <package name="libxml2" version="2.9.1">
    <repository name="package_libxml2_2_9_1" owner="jankanis" prior_installation_required="True"
                toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="98807f0505f0" />
  </package>

  <package name="libxslt" version="1.1.28">
    <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True"
                toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
  </package>

  <package name="zlib" version="1.2.8">
    <repository name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True"
                toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="63a4a902cda2" />
  </package>

  <package name="blast2html_venv" version="0.2">
    <install version="1.0">
      <actions>
        <action type="set_environment_for_install">
          <repository name="package_libxml2_2_9_1" owner="jankanis"
                      toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="98807f0505f0">
            <package name="libxml2" version="2.9.1" />
          </repository>
          <repository name="package_libxslt_1_1_28" owner="devteam"
                      toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
            <package name="libxslt" version="1.1.28" />
          </repository>
          <repository name="package_zlib_1_2_8" owner="iuc"
                      toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="63a4a902cda2">
            <package name="zlib" version="1.2.8" />
          </repository>
        </action>

	<action type="setup_virtualenv">
	  jinja2==2.7.3
	  six==1.7.2
	  argparse==1.2.1
	</action>

	<!-- install lxml manually, as the setup_virtualenv action does not include the environment
	     from set_environment_for_install but shell_command does -->
	<action type="shell_command">
	  $INSTALL_DIR/venv/bin/pip install lxml==3.3.5
	</action>
	
        <action type="set_environment">
          <!-- add libxml2/zlib library paths so the runtime can find the shared libraries -->
          <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
        </action>
      </actions>
    </install>
    <readme>A Python 2 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
  </package>

</tool_dependency>