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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 15:01:21 -0400
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5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool_dependency>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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3 <package name="rnashapes" version="2.1.6">
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4 <install version="1.0">
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5 <actions_group>
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6 <!-- Download the binaries for RNAshapes compatible with 32-bit OSX. -->
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7 <actions os="darwin" architecture="i386">
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8 <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039523_10840/RNAshapes-2.1.6-osx.tar.gz</action>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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9 <action type="move_file">
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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10 <source>RNAshapes</source>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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11 <destination>$INSTALL_DIR/bin/</destination>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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12 </action>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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13 </actions>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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14 <!-- Download the binaries for RNAshapes compatible with 32-bit Linux (i386). -->
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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15 <actions os="linux" architecture="i386">
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16 <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>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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17 <action type="move_file">
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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18 <source>RNAshapes</source>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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19 <destination>$INSTALL_DIR/bin/</destination>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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20 </action>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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21 </actions>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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22 <!-- Download the binaries for RNAshapes compatible with 32-bit Linux (i686). -->
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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23 <actions os="linux" architecture="i686">
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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24 <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>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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25 <action type="move_file">
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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26 <source>RNAshapes</source>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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27 <destination>$INSTALL_DIR/bin/</destination>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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28 </action>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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29 </actions>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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30 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
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31 <actions>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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32 <action type="download_by_url">http://bibiserv.techfak.uni-bielefeld.de/spool/download/bibiserv_1383039313_10782/RNAshapes-2.1.6.tar.gz</action>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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33 <action type="autoconf" />
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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34 </actions>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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35 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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36 <action type="set_environment">
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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37 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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38 </action>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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39 </actions_group>
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40 </install>
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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41 <readme>
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42 Downloads the precompiled 32bit Linux, or Mac OS X RNAshapes
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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43 binaries, which is faster than performing a local compliation,
5b8cbf3cd76c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rnashapes_2_1_6 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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44 avoids any issues with build dependencies, and is more reproducible between
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45 installations as there is no variability from the compiler or library versions.
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46
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47 RNA shape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features,
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48 but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms,
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49 and hence it can be applied during structure prediction rather than afterwards.
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50 This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule's folding space.
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51
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52 RNAshapes offers three powerful RNA analysis tools in one single software package:
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53
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54 - Computation of a small set of representative structures of different shapes, complete in a well-defined sense.
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55 - Computation of accumulated shape probabilities.
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56 - Comparative prediction of consensus structures, as an alternative to the over-expensive Sankoff Algorithm.
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57
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58
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59 For more details, see:
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60 http://bibiserv.techfak.uni-bielefeld.de/rnashapes/
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61 </readme>
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62 </package>
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63 </tool_dependency>
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64