Mercurial > repos > marpiech > norwich_tools_docking
diff rdock.xml @ 0:c7b5489be955 draft
planemo upload
| author | marpiech |
|---|---|
| date | Mon, 29 Aug 2016 07:57:38 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdock.xml Mon Aug 29 07:57:38 2016 -0400 @@ -0,0 +1,51 @@ +<tool id="rdock" name="rdock" version="1.0"> + <description>tail-to-head</description> + <command> + <![CDATA[ + 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; + cp -r $__tool_directory__/tools/rdock/data .; + mkdir data/ligands; + cp $inputsd data/ligands/ligand.sd; + LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbcavity -r new.prm -was > /tmp/rbcavity.log; + LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbdock -r new.prm -p dock.prm -n 100 -i $inputsd -o output_docking_out > /tmp/docking_out.log; + PERL5LIB=$__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; + PYTHONPATH=/usr/lib/python2.7/dist-packages/ $__tool_directory__/tools/rdock/bin/sdrmsd $inputsd sorted.sd > $output_rdock + ]]> + </command> + <inputs> + <param name="inputprm" format="prm" type="data" label="PRM file" /> + <param name="inputmol2" format="mol2" type="data" label="MOL2 file" /> + <param name="inputsd" format="sd" type="data" label="SD file" /> + </inputs> + <outputs> + <data name="output_rdock" format="data" /> + </outputs> + <tests> + <test> + <param name="inputprm" value="rdock/1sj0_rdock.prm" /> + <param name="inputmol2" value="rdock/1sj0_rdock.mol2" /> + <param name="inputsd" value="rdock/1sj0_ligand.sd" /> + <output name="output_rdock"> + <assert_contents> + <has_n_columns n="2" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputprm" value="rdock/1nem_rdock.prm" /> + <param name="inputmol2" value="rdock/1nem_rdock.mol2" /> + <param name="inputsd" value="rdock/1nem_lig.sd" /> + <output name="output_rdock"> + <assert_contents> + <has_n_columns n="2" /> + </assert_contents> + </output> + </test> + </tests> + <help> + rDock tool + </help> + <citations> + <citation type="doi">doi:10.1371/journal.pcbi.1003571</citation> + </citations> +</tool>