Mercurial > repos > marpiech > norwich_docking_tools

comparison rdock.xml @ 2:0faa03a92843 draft default tip

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author dzesikah
date Fri, 26 Aug 2016 10:19:49 -0400
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1:ad4bc82457e5 2:0faa03a92843
1 <tool id="rdock" name="rdock" version="1.0">
2 <description>tail-to-head</description>
3 <command>
4 <![CDATA[
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;
6 cp -r $__tool_directory__/tools/rdock/data .;
7 mkdir data/ligands;
8 cp $inputsd data/ligands/ligand.sd;
9 LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbcavity -r new.prm -was > /tmp/rbcavity.log;
10 LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbdock -r new.prm -p dock.prm -n 100 -i $inputsd -o output_docking_out > /tmp/docking_out.log;
11 PERL5LIB=$__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;
12 PYTHONPATH=/usr/lib/python2.7/dist-packages/ $__tool_directory__/tools/rdock/bin/sdrmsd $inputsd sorted.sd > $output_rdock
13 ]]>
14 </command>
15 <inputs>
16 <param name="inputprm" format="prm" type="data" label="PRM file" />
17 <param name="inputmol2" format="mol2" type="data" label="MOL2 file" />
18 <param name="inputsd" format="sd" type="data" label="SD file" />
19 </inputs>
20 <outputs>
21 <data name="output_rdock" format="data" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="inputprm" value="rdock/1sj0_rdock.prm" />
26 <param name="inputmol2" value="rdock/1sj0_rdock.mol2" />
27 <param name="inputsd" value="rdock/1sj0_ligand.sd" />
28 <output name="output_rdock">
29 <assert_contents>
30 <has_n_columns n="2" />
31 </assert_contents>
32 </output>
33 </test>
34 <test>
35 <param name="inputprm" value="rdock/1nem_rdock.prm" />
36 <param name="inputmol2" value="rdock/1nem_rdock.mol2" />
37 <param name="inputsd" value="rdock/1nem_lig.sd" />
38 <output name="output_rdock">
39 <assert_contents>
40 <has_n_columns n="2" />
41 </assert_contents>
42 </output>
43 </test>
44 </tests>
45 <help>
46 rDock tool
47 </help>
48 <citations>
49 <citation type="doi">doi:10.1371/journal.pcbi.1003571</citation>
50 </citations>
51 </tool>