Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.5/galaxyconfigs/tools/Ligand3DGenerator.xml @ 7:bfab27640f5e draft
CADDSuite version 1.5
| author | Marcel Schumann <schumann.marcel@gmail.com> |
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| date | Tue, 24 Jul 2012 11:13:59 -0400 |
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| 6:decca54699e3 | 7:bfab27640f5e |
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| 1 | |
| 2 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> | |
| 3 <tool id="ligand3dgenerator" name="Ligand3DGenerator" version="1.5"> | |
| 4 <description>generate 3D coordinates for small molecules</description> | |
| 5 <command interpreter="bash"><![CDATA[../../Ligand3DGenerator | |
| 6 #if str( $i ) != '' and str( $i ) != 'None' : | |
| 7 -i "$i" | |
| 8 #end if | |
| 9 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 10 -o "$o" | |
| 11 #end if | |
| 12 #if str( $ph ) != '' and str( $ph ) != 'None' : | |
| 13 -ph "$ph" | |
| 14 #end if | |
| 15 #if str( $rm ) != '' and str( $rm ) != 'None' : | |
| 16 -rm | |
| 17 #end if | |
| 18 | tail -n 5 | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> | |
| 22 <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/> | |
| 23 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name="o" format="mol2/sdf/drf" format_source="i"/> | |
| 27 </outputs> | |
| 28 <help>This tool generates 3D conformations for small molecules and adds hydrogens to them. | |
| 29 As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary. | |
| 30 | |
| 31 Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other. | |
| 32 | |
| 33 Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz, mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.</help> | |
| 34 </tool> |