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1 <tool id="rdock" name="rdock" version="1.0">
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2 <description>tail-to-head</description>
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3 <command>
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4 <![CDATA[
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5 cat $inputmol2 > inputmol2.mol2; cat $inputprm | sed "s|RECEPTOR_FILE.*|RECEPTOR_FILE inputmol2.mol2|g" | sed "s|REF_MOL.*|REF_MOL ligand.sd|g" > new.prm;
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6 cp -r $__tool_directory__/tools/rdock/data .;
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7 mkdir data/ligands;
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8 cp $inputsd data/ligands/ligand.sd;
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9 LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbcavity -r new.prm -was > /tmp/rbcavity.log;
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10 LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbdock -r new.prm -p dock.prm -n 100 -i $inputsd -o output_docking_out > /tmp/docking_out.log;
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11 PERL5LIB=$__tool_directory__/tools/rdock/lib/ LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/sdsort -n -f'SCORE' output_docking_out.sd > sorted.sd;
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12 PYTHONPATH=/usr/lib/python2.7/dist-packages/ $__tool_directory__/tools/rdock/bin/sdrmsd $inputsd sorted.sd > $output_rdock
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="inputprm" format="prm" type="data" label="PRM file" />
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17 <param name="inputmol2" format="mol2" type="data" label="MOL2 file" />
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18 <param name="inputsd" format="sd" type="data" label="SD file" />
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19 </inputs>
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20 <outputs>
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21 <data name="output_rdock" format="data" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="inputprm" value="rdock/1sj0_rdock.prm" />
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26 <param name="inputmol2" value="rdock/1sj0_rdock.mol2" />
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27 <param name="inputsd" value="rdock/1sj0_ligand.sd" />
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28 <output name="output_rdock">
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29 <assert_contents>
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30 <has_n_columns n="2" />
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31 </assert_contents>
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32 </output>
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33 </test>
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34 <test>
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35 <param name="inputprm" value="rdock/1nem_rdock.prm" />
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36 <param name="inputmol2" value="rdock/1nem_rdock.mol2" />
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37 <param name="inputsd" value="rdock/1nem_lig.sd" />
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38 <output name="output_rdock">
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39 <assert_contents>
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40 <has_n_columns n="2" />
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41 </assert_contents>
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42 </output>
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43 </test>
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44 </tests>
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45 <help>
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46 rDock tool
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47 </help>
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48 <citations>
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49 <citation type="doi">doi:10.1371/journal.pcbi.1003571</citation>
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50 </citations>
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51 </tool>
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