annotate tool_dependencies.xml @ 1:b654e5485eee draft

Updated tool dependency definition

<?xml version="1.0"?>
<tool_dependency>
    <package name="rnastructure" version="5.7">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://depot.galaxyproject.org/package/source/RNAstructure-5.7.tgz</action>
                <action type="shell_command">make</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/exe</environment_variable>
                    <environment_variable action="set_to" name="DATAPATH">$INSTALL_DIR/data_tables</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
<![CDATA[
RNAstructure is a complete package for RNA and DNA secondary structure 
prediction and analysis. It includes algorithms for   secondary structure 
prediction, including facility to predict base pairing probabilities. It 
also can be used to predict bimolecular structures and can predict the 
equilibrium binding affinity of an oligonucleotide to a structured RNA 
target. This is useful for siRNA design. It can also predict secondary 
structures common to two, unaligned sequences, which is much more accurate 
than single sequence secondary structure prediction. Finally, RNAstructure 
can take a number of different types of experiment mapping data to constrain 
or restrain structure prediction. These include chemical mapping, enzymatic 
mapping, NMR, and SHAPE data.
]]>
        </readme>
    </package>
</tool_dependency>