<?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <package name="rnashapes" version="2.1.6">
        <install version="1.0">
            <actions_group>
                <!-- Download the binaries for RNAshapes compatible with 32-bit OSX. -->
                <actions os="darwin" architecture="i386">
                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039523_10840/RNAshapes-2.1.6-osx.tar.gz</action>
                    <action type="move_file">
                        <source>RNAshapes</source>
                        <destination>$INSTALL_DIR/bin/</destination>
                    </action>
                </actions>
                <!-- Download the binaries for RNAshapes compatible with 32-bit Linux (i386). -->
                <actions os="linux" architecture="i386">
                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039480_10830/RNAshapes-2.1.6-i386-linux.tar.gz</action>
                    <action type="move_file">
                        <source>RNAshapes</source>
                        <destination>$INSTALL_DIR/bin/</destination>
                    </action>
                </actions>
                <!-- Download the binaries for RNAshapes compatible with 32-bit Linux (i686). -->
                <actions os="linux" architecture="i686">
                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039480_10830/RNAshapes-2.1.6-i386-linux.tar.gz</action>
                    <action type="move_file">
                        <source>RNAshapes</source>
                        <destination>$INSTALL_DIR/bin/</destination>
                    </action>
                </actions>
                <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
                <actions>
                    <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039313_10782/RNAshapes-2.1.6.tar.gz</action>
                    <action type="autoconf" />
                </actions>
                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
Downloads the precompiled 32bit Linux, or Mac OS X RNAshapes
binaries, which is faster than performing a local compliation,
avoids any issues with build dependencies, and is more reproducible between
installations as there is no variability from the compiler or library versions.

RNA shape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, 
but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms, 
and hence it can be applied during structure prediction rather than afterwards. 
This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule's folding space.

RNAshapes offers three powerful RNA analysis tools in one single software package:

- Computation of a small set of representative structures of different shapes, complete in a well-defined sense.
- Computation of accumulated shape probabilities.
- Comparative prediction of consensus structures, as an alternative to the over-expensive Sankoff Algorithm.


For more details, see:
http://bibiserv.techfak.uni-bielefeld.de/rnashapes/
        </readme>
    </package>
</tool_dependency>