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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Docking]-->
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4 <tool id="SpatialConstraintDefiner" name="SpatialConstraintDefiner" version="1.1.0">
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5 <description>define spatial constraint</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SpatialConstraintDefiner</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>SpatialConstraintDefiner
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13
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14 #if $param_option:
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15 -option $param_option
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16 #end if
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17 #if $param_i:
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18 -i $param_i
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19 #end if
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20 #if $param_o:
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21 -o $param_o
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22 #end if
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23 #if $param_type:
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24 -type
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25 #if " " in str($param_type):
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26 "$param_type"
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27 #else
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28 $param_type
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29 #end if
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30 #end if
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31 #if $param_n:
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32 -n $param_n
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33 #end if
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34 #if $param_p:
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35 -p $param_p
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36 #end if
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37 </command>
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38 <inputs>
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39 <param name="param_option" type="data" format="ini" optional="True" value="0" label="input configuration file" help="(-option) "/>
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40 <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file" help="(-i) "/>
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41 <param name="param_type" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="'fraction' or 'number' of compound atoms" help="(-type) ">
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42 <option value="fraction">fraction</option>
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43 <option value=" number"> number</option>
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44 </param>
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45 <param name="param_n" type="float" value="0.0" label="desired number/fraction of atoms in spatial area" help="(-n) "/>
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46 <param name="param_p" type="float" value="0.0" label="penalty value" help="(-p) "/>
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47 </inputs>
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48 <expand macro="advanced_options"/>
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49 <outputs>
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50 <data name="param_o" format="ini"/>
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51 </outputs>
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52 <help>This tool allows to define spatial constraints for docking or scoring.
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53
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54 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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55 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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56
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57 Output of this tool is a ini-file that contains the desired spatial constraint.
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58
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59 </help>
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60 </tool>
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