comparison PLIDflow/pubchemSMI_plidflow.xml @ 6:795e11fac81b draft default tip

Included new tools for standardization

6:795e11fac81b

<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>