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diff PLIDflow/openbabel_SMI_plidflow.xml @ 6:795e11fac81b draft default tip

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Included new tools for standardization
author bitlab
date Wed, 22 Apr 2020 06:12:00 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/openbabel_SMI_plidflow.xml	Wed Apr 22 06:12:00 2020 -0400
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+<tool id="openbabelSMI_plidflow" name="PLIDflow: Open Babel SMI">
+  <description>Open Babel converts chemical structures from one file format to another. Use Open Babel to convert SMI files to SDF files</description>
+  <inputs>
+	  <param name="ligand_smi" type="data" format="smi" label="Drug SMI file" help="Open Babel is a chemical toolbox designed to speak the many languages of chemical data. To convert Line notation SMILES (Simplified Molecular Input Line Entry System) to coordinate data and bond matrix information in structure Data Format (SDF) format"/>
+	  <param name="stripsalts" type="select" label="Strip salts">
+		  <option value="" selected="true">Do not strip salts</option>
+		  <option value="-r">Strip salts</option>
+	  </param>
+  </inputs>
+  <command>(obabel -i smi $ligand_smi -o sdf -O $ligand_sdf --gen3D $stripsalts) &amp;>/dev/null </command>
+  <outputs>
+    <data name="ligand_sdf" format="sdf" label="Drug SDF file"/>
+  </outputs>
+</tool>