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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: [Convert, combine and store]-->
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4 <tool id="MolCombine" name="MolCombine" version="1.1.0">
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5 <description>combine molecular files</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MolCombine</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>MolCombine
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13
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14 #if $param_i1:
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15 -i1 $param_i1
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16 #end if
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17 #if $param_i2:
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18 -i2 $param_i2
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19 #end if
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20 #if $param_mode:
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21 -mode
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22 #if " " in str($param_mode):
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23 "$param_mode"
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24 #else
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25 $param_mode
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26 #end if
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27 #end if
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28 #if $param_o:
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29 -o $param_o
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30 #end if
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31 #if $param_ignH:
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32 -ignH $param_ignH
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33 #end if
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34 #if $param_replace_prop:
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35 -replace_prop $param_replace_prop
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36 #end if
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37 #if $param_rm:
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38 -rm $param_rm
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39 #end if
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40 </command>
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41 <inputs>
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42 <param name="param_i1" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file A" help="(-i1) "/>
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43 <param name="param_i2" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file B" help="(-i2) "/>
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44 <param name="param_mode" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="'intersection', 'union' or 'b_not_a'" help="(-mode) ">
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45 <option value="intersection">intersection</option>
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46 <option value=" union"> union</option>
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47 <option value=" b_not_a"> b_not_a</option>
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48 </param>
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49 <param name="param_ignH" type="integer" min="0" max="1" optional="True" value="1" label="ignore hydrogens, i.e" help="(-ignH) match molecules to any protonation state"/>
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50 <param name="param_replace_prop" type="integer" min="0" max="1" optional="True" value="0" label="replace properties from file 1 w/ those from file 2" help="(-replace_prop) "/>
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51 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input files when finished" help="(-rm) "/>
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52 </inputs>
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53 <expand macro="advanced_options"/>
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54 <outputs>
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55 <data name="param_o" metadata_source="param_i1" format="input"/>
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56 </outputs>
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57 <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.
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58
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59 If you want to match molecules regardless of their protonation state, use option '-ignH'.
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60
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61 Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.
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62
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63 </help>
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64 </tool>
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