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diff PLIDflow/pubchemSMI_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/pubchemSMI_plidflow.xml	Wed Apr 22 06:12:00 2020 -0400
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+<tool id="pubchemSMI_plidflow" name="PLIDflow: PubChem SMI">
+  <description>Standardize a SMILE chain using the PubChem service</description>
+  <inputs>
+	  <param name="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"/>
+  </inputs>
+  <command><![CDATA[
+
+	  source ${__tool_directory__}/scripts/ADT_VENV/bin/activate ; 
+	 
+	  chain=\$(cat $smi);
+	  python ${__tool_directory__}/scripts/scrapPubChem.py \$chain > $standard_smi
+ 
+	  ]]> </command>
+
+
+  <outputs>
+    <data name="standard_smi" format="smi" label="Standardized SMI file"/>
+  </outputs>
+</tool>