annotate PLIDflow/openbabel_SMI_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 |
|
| rev |
line source |
|
6
|
1 <tool id="openbabelSMI_plidflow" name="PLIDflow: Open Babel SMI">
|
|
|
2 <description>Open Babel converts chemical structures from one file format to another. Use Open Babel to convert SMI files to SDF files</description>
|
|
|
3 <inputs>
|
|
|
4 <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"/>
|
|
|
5 <param name="stripsalts" type="select" label="Strip salts">
|
|
|
6 <option value="" selected="true">Do not strip salts</option>
|
|
|
7 <option value="-r">Strip salts</option>
|
|
|
8 </param>
|
|
|
9 </inputs>
|
|
|
10 <command>(obabel -i smi $ligand_smi -o sdf -O $ligand_sdf --gen3D $stripsalts) &>/dev/null </command>
|
|
|
11 <outputs>
|
|
|
12 <data name="ligand_sdf" format="sdf" label="Drug SDF file"/>
|
|
|
13 </outputs>
|
|
|
14 </tool>
|
