Mercurial > repos > bitlab > plidflow
comparison PLIDflow/drawSMI_plidflow.xml @ 6:795e11fac81b draft default tip
Included new tools for standardization
| author | bitlab |
|---|---|
| date | Wed, 22 Apr 2020 06:12:00 -0400 |
| parents | |
| children |
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| 5:97f12f7cc852 | 6:795e11fac81b |
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| 1 <tool id="drawSMI_plidflow" name="PLIDflow: Draw SMI"> | |
| 2 <description>Plot an SMI chain using the Rdkit package</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" >rdkit</requirement> | |
| 5 </requirements> | |
| 6 | |
| 7 <inputs> | |
| 8 <param name="smi" type="data" format="smi" label="Drug SMI file" help="Input an SMI file that will be plotted"/> | |
| 9 </inputs> | |
| 10 <command><![CDATA[ | |
| 11 | |
| 12 | |
| 13 cp $smi ${smi}.smi ; | |
| 14 | |
| 15 | |
| 16 ${__tool_directory__}/scripts/CONDA_RDKIT_ENV/bin/python ${__tool_directory__}/scripts/draw_mol.py ${smi}.smi ${smipng}.png ; | |
| 17 | |
| 18 mv ${smipng}.png $smipng ; | |
| 19 | |
| 20 rm ${smi}.smi ; | |
| 21 | |
| 22 | |
| 23 | |
| 24 ]]> </command> | |
| 25 | |
| 26 | |
| 27 <outputs> | |
| 28 <data name="smipng" format="png" label="PNG plot of the SMI file"/> | |
| 29 </outputs> | |
| 30 </tool> |