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annotate CADDSuite-1.5/galaxyconfigs/tools/SpatialConstraintDefiner.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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1
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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.-->
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3 <tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="1.5">
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4 <description>define spatial constraint</description>
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5 <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner
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6 #if str( $ini ) != '' and str( $ini ) != 'None' :
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7 -ini "$ini"
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8 #end if
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9 #if str( $i ) != '' and str( $i ) != 'None' :
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10 -i "$i"
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11 #end if
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12 #if str( $o ) != '' and str( $o ) != 'None' :
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13 -o "$o"
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14 #end if
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15 #if str( $type ) != '' and str( $type ) != 'None' :
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16 -type "$type"
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17 #end if
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18 #if str( $n ) != '' and str( $n ) != 'None' :
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19 -n "$n"
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20 #end if
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21 #if str( $p ) != '' and str( $p ) != 'None' :
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22 -p "$p"
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23 #end if
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24 | tail -n 5
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25 ]]></command>
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26 <inputs>
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27 <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
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28 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
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29 <param name="type" optional="false" label="'fraction' or 'number' of compound atoms" type="select">
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30 <option value="fraction">fraction</option>
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31 <option value="number">number</option>
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32 </param>
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33 <param name="n" optional="false" label="desired number/fraction of atoms in spatial area" type="text" area="true" size="1x5" value=""/>
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34 <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="1e13"/>
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35 </inputs>
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36 <outputs>
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37 <data name="o" format="ini"/>
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38 </outputs>
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39 <help>This tool allows to define spatial constraints for docking or scoring.
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40
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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.
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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.
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43
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44 Output of this tool is a ini-file that contains the desired spatial constraint.</help>
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45 </tool>