Mercurial > repos > bitlab > plidflow
comparison PLIDflow/autodocktools_rec_plidflow.xml @ 2:afd5b5ffc38f draft
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| author | bitlab |
|---|---|
| date | Tue, 14 Jan 2020 07:52:48 -0500 |
| parents | 6fcfa4756040 |
| children |
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| 1:eda62adfc858 | 2:afd5b5ffc38f |
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| 1 <tool id="autodocktools_receptor_plidflow" name="PLIDflow: AutoDock Receptor"> | |
| 2 <description>AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure</description> | |
| 3 <inputs> | |
| 4 <param name="receptor_pdb" type="data" format="pdb" label="Receptor PDB file" help="Preparing the receptor involves adding gasteiger charges and adding hydrogens. The formatted receptor is written in a 'pdbqt' file."/> | |
| 5 </inputs> | |
| 6 <command><![CDATA[ | |
| 7 | |
| 8 swpath=\$(which prepare_receptor4.py) ; | |
| 9 cp ${receptor_pdb} ${receptor_pdb}.pdb ; | |
| 10 pythonsh \$swpath -r ${receptor_pdb}.pdb -A hydrogens -o $receptor_pdbqt; | |
| 11 rm ${receptor_pdb}.pdb; | |
| 12 Rscript ${__tool_directory__}/scripts/pdbqtcorrector2step.R ${receptor_pdbqt} ${receptor_pdbqt_modified2} ${receptor_types}; | |
| 13 | |
| 14 ]]></command> | |
| 15 | |
| 16 <outputs> | |
| 17 <data name="receptor_pdbqt" format="pdbqt" label="Receptor PDBQT file"/> | |
| 18 <data name="receptor_pdbqt_modified" format="pdbqt" label="Receptor PDBQT file modified"/> | |
| 19 <data name="receptor_pdbqt_modified2" format="pdbqt" label="Receptor PDBQT file modified 2"/> | |
| 20 <data name="receptor_types" format="txt" label="Receptor types molecules"/> | |
| 21 </outputs> | |
| 22 </tool> |