Mercurial > repos > marcel > caddsuite_linux_x86_64

comparison CADDSuite/galaxyconfigs/tools/MolCombine.xml @ 8:9ab6da6cd36c

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author marcel
date Fri, 02 Sep 2011 08:48:21 -0400
parents 5b29b679ee6d
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7:5b29b679ee6d 8:9ab6da6cd36c
1 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.--> 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="molcombine" name="MolCombine" version="0.95"> 3 <tool id="molcombine" name="MolCombine" version="0.9.6">
4 <description>combine molecular files</description> 4 <description>combine molecular files</description>
5 <command interpreter="bash"><![CDATA[../../MolCombine 5 <command interpreter="bash"><![CDATA[../../MolCombine
6 #if str( $i1 ) != '' and str( $i1 ) != 'None' : 6 #if str( $i1 ) != '' and str( $i1 ) != 'None' :
7 -i1 "$i1" 7 -i1 "$i1"
8 #end if 8 #end if
19 -ignH 19 -ignH
20 #end if 20 #end if
21 #if str( $replace_prop ) != '' and str( $replace_prop ) != 'None' : 21 #if str( $replace_prop ) != '' and str( $replace_prop ) != 'None' :
22 -replace_prop 22 -replace_prop
23 #end if 23 #end if
24 #if str( $rm ) != '' and str( $rm ) != 'None' :
25 -rm
26 #end if
24 | tail -n 5 27 | tail -n 5
25 ]]></command> 28 ]]></command>
26 <inputs> 29 <inputs>
27 <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/> 30 <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/>
28 <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/> 31 <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/>
31 <option value="union">union</option> 34 <option value="union">union</option>
32 <option value="b_not_a">b_not_a</option> 35 <option value="b_not_a">b_not_a</option>
33 </param> 36 </param>
34 <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/> 37 <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/>
35 <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/> 38 <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/>
39 <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/>
36 </inputs> 40 </inputs>
37 <outputs> 41 <outputs>
38 <data name="o" format="mol2/sdf/drf" format_source="i1"/> 42 <data name="o" format="mol2/sdf/drf" format_source="i1"/>
39 </outputs> 43 </outputs>
40 <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. 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.