Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.6/galaxyconfigs/tools/SpatialConstraintDefiner.xml @ 17:25a03362403c draft
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| author | marcel |
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| date | Sat, 15 Dec 2012 13:10:41 -0500 |
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| 16:1a24aef40d01 | 17:25a03362403c |
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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="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="1.6"> | |
| 4 <description>define spatial constraint</description> | |
| 5 <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner | |
| 6 #if str( $ini ) != '' and str( $ini ) != 'None' : | |
| 7 -ini "$ini" | |
| 8 #end if | |
| 9 #if str( $i ) != '' and str( $i ) != 'None' : | |
| 10 -i "$i" | |
| 11 #end if | |
| 12 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 13 -o "$o" | |
| 14 #end if | |
| 15 #if str( $type ) != '' and str( $type ) != 'None' : | |
| 16 -type "$type" | |
| 17 #end if | |
| 18 #if str( $n ) != '' and str( $n ) != 'None' : | |
| 19 -n "$n" | |
| 20 #end if | |
| 21 #if str( $p ) != '' and str( $p ) != 'None' : | |
| 22 -p "$p" | |
| 23 #end if | |
| 24 | tail -n 5 | |
| 25 ]]></command> | |
| 26 <inputs> | |
| 27 <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/> | |
| 28 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> | |
| 29 <param name="type" optional="false" label="'fraction' or 'number' of compound atoms" type="select"> | |
| 30 <option value="fraction">fraction</option> | |
| 31 <option value="number">number</option> | |
| 32 </param> | |
| 33 <param name="n" optional="false" label="desired number/fraction of atoms in spatial area" type="text" area="true" size="1x5" value=""/> | |
| 34 <param name="p" optional="true" label="Optional: penalty value" type="text" area="true" size="1x5" value="5e11"/> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data name="o" format="ini"/> | |
| 38 </outputs> | |
| 39 <help>This tool allows to define spatial constraints for docking or scoring. | |
| 40 | |
| 41 For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint. | |
| 42 Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this. | |
| 43 | |
| 44 Output of this tool is a ini-file that contains the desired spatial constraint.</help> | |
| 45 </tool> |