annotate tool_dependencies.xml @ 3:f8a9a5eaca8a draft

Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)

<?xml version="1.0"?>
<tool_dependency>
    <package name="trimmomatic" version="0.32">
      <install version="1.0">
	<actions>
	  <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip</action>
	  <action type="move_file">
	    <source>trimmomatic-0.32.jar</source>
	    <destination>$INSTALL_DIR</destination>
	  </action>
          <action type="move_directory_files">
            <source_directory>adapters</source_directory>
            <destination_directory>$INSTALL_DIR/adapters</destination_directory>
          </action>
	  <action type="set_environment">
	    <environment_variable name="TRIMMOMATIC_DIR" action="set_to">$INSTALL_DIR</environment_variable>
	  </action>
	  <action type="set_environment">
	    <environment_variable name="TRIMMOMATIC_ADAPTERS_DIR" action="set_to">$INSTALL_DIR/adapters</environment_variable>
	  </action>
	</actions>
      </install>
      <readme>Trimmomatic requires the Java Runtime Environment
      </readme>
    </package>
</tool_dependency>