Mercurial > repos > bitlab > plidflow

annotate PLIDflow/drawSMI_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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1 <tool id="drawSMI_plidflow" name="PLIDflow: Draw SMI">
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2 <description>Plot an SMI chain using the Rdkit package</description>
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3 <requirements>
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4 <requirement type="package" >rdkit</requirement>
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5 </requirements>
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6
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7 <inputs>
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8 <param name="smi" type="data" format="smi" label="Drug SMI file" help="Input an SMI file that will be plotted"/>
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9 </inputs>
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10 <command><![CDATA[
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12
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13 cp $smi ${smi}.smi ;
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16 ${__tool_directory__}/scripts/CONDA_RDKIT_ENV/bin/python ${__tool_directory__}/scripts/draw_mol.py ${smi}.smi ${smipng}.png ;
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17
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18 mv ${smipng}.png $smipng ;
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20 rm ${smi}.smi ;
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24 ]]> </command>
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25
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27 <outputs>
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28 <data name="smipng" format="png" label="PNG plot of the SMI file"/>
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29 </outputs>
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30 </tool>