Mercurial > repos > marcel > caddsuite_linux_x86_64
view CADDSuite-1.5/galaxyconfigs/tools/MolCombine.xml @ 16:1a24aef40d01 draft
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author | marcel |
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date | Tue, 24 Jul 2012 11:10:07 -0400 |
parents | ac342506cd4e |
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<!--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.--> <tool id="molcombine" name="MolCombine" version="1.5"> <description>combine molecular files</description> <command interpreter="bash"><![CDATA[../../MolCombine #if str( $i1 ) != '' and str( $i1 ) != 'None' : -i1 "$i1" #end if #if str( $i2 ) != '' and str( $i2 ) != 'None' : -i2 "$i2" #end if #if str( $mode ) != '' and str( $mode ) != 'None' : -mode "$mode" #end if #if str( $o ) != '' and str( $o ) != 'None' : -o "$o" #end if #if str( $ignH ) != '' and str( $ignH ) != 'None' : -ignH #end if #if str( $replace_prop ) != '' and str( $replace_prop ) != 'None' : -replace_prop #end if #if str( $rm ) != '' and str( $rm ) != 'None' : -rm #end if | tail -n 5 ]]></command> <inputs> <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/> <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/> <param name="mode" optional="false" label="'intersection', 'union' or 'b_not_a'" type="select"> <option value="intersection">intersection</option> <option value="union">union</option> <option value="b_not_a">b_not_a</option> </param> <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/> <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/> <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i1"/> </outputs> <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. If you want to match molecules regardless of their protonation state, use option '-ignH'. Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help> </tool>