Mercurial > repos > bitlab > plidflow
diff PLIDflow/autodocktools_rec_plidflow.xml @ 6:795e11fac81b draft default tip
Included new tools for standardization
| author | bitlab |
|---|---|
| date | Wed, 22 Apr 2020 06:12:00 -0400 |
| parents | 6fcfa4756040 |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/autodocktools_rec_plidflow.xml Wed Apr 22 06:12:00 2020 -0400 @@ -0,0 +1,22 @@ +<tool id="autodocktools_receptor_plidflow" name="PLIDflow: AutoDock Receptor"> + <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> + <inputs> + <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."/> + </inputs> + <command><![CDATA[ + + swpath=\$(which prepare_receptor4.py) ; + cp ${receptor_pdb} ${receptor_pdb}.pdb ; + pythonsh \$swpath -r ${receptor_pdb}.pdb -A hydrogens -o $receptor_pdbqt; + rm ${receptor_pdb}.pdb; + Rscript ${__tool_directory__}/scripts/pdbqtcorrector2step.R ${receptor_pdbqt} ${receptor_pdbqt_modified2} ${receptor_types}; + + ]]></command> + + <outputs> + <data name="receptor_pdbqt" format="pdbqt" label="Receptor PDBQT file"/> + <data name="receptor_pdbqt_modified" format="pdbqt" label="Receptor PDBQT file modified"/> + <data name="receptor_pdbqt_modified2" format="pdbqt" label="Receptor PDBQT file modified 2"/> + <data name="receptor_types" format="txt" label="Receptor types molecules"/> + </outputs> +</tool>