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annotate CADDSuite-1.5/galaxyconfigs/tools/MolCombine.xml @ 15:ac342506cd4e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:08:49 -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="molcombine" name="MolCombine" version="1.5">
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4 <description>combine molecular files</description>
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5 <command interpreter="bash"><![CDATA[../../MolCombine
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6 #if str( $i1 ) != '' and str( $i1 ) != 'None' :
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7 -i1 "$i1"
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8 #end if
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9 #if str( $i2 ) != '' and str( $i2 ) != 'None' :
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10 -i2 "$i2"
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11 #end if
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12 #if str( $mode ) != '' and str( $mode ) != 'None' :
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13 -mode "$mode"
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14 #end if
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15 #if str( $o ) != '' and str( $o ) != 'None' :
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16 -o "$o"
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17 #end if
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18 #if str( $ignH ) != '' and str( $ignH ) != 'None' :
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19 -ignH
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20 #end if
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21 #if str( $replace_prop ) != '' and str( $replace_prop ) != 'None' :
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22 -replace_prop
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23 #end if
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24 #if str( $rm ) != '' and str( $rm ) != 'None' :
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25 -rm
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26 #end if
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27 | tail -n 5
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28 ]]></command>
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29 <inputs>
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30 <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/>
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31 <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/>
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32 <param name="mode" optional="false" label="'intersection', 'union' or 'b_not_a'" type="select">
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33 <option value="intersection">intersection</option>
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34 <option value="union">union</option>
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35 <option value="b_not_a">b_not_a</option>
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36 </param>
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37 <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/>
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38 <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/>
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39 <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/>
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40 </inputs>
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41 <outputs>
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42 <data name="o" format="mol2/sdf/drf" format_source="i1"/>
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43 </outputs>
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44 <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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46 If you want to match molecules regardless of their protonation state, use option '-ignH'.
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48 Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help>
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49 </tool>