Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.0.1/galaxyconfigs/tools/MolCombine.xml @ 9:2cff9609f2c7
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| author | marcel |
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| date | Tue, 15 Nov 2011 10:40:26 -0500 |
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| 8:9ab6da6cd36c | 9:2cff9609f2c7 |
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| 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.--> | |
| 3 <tool id="molcombine" name="MolCombine" version="1.0.1"> | |
| 4 <description>combine molecular files</description> | |
| 5 <command interpreter="bash"><![CDATA[../../MolCombine | |
| 6 #if str( $i1 ) != '' and str( $i1 ) != 'None' : | |
| 7 -i1 "$i1" | |
| 8 #end if | |
| 9 #if str( $i2 ) != '' and str( $i2 ) != 'None' : | |
| 10 -i2 "$i2" | |
| 11 #end if | |
| 12 #if str( $mode ) != '' and str( $mode ) != 'None' : | |
| 13 -mode "$mode" | |
| 14 #end if | |
| 15 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 16 -o "$o" | |
| 17 #end if | |
| 18 #if str( $ignH ) != '' and str( $ignH ) != 'None' : | |
| 19 -ignH | |
| 20 #end if | |
| 21 #if str( $replace_prop ) != '' and str( $replace_prop ) != 'None' : | |
| 22 -replace_prop | |
| 23 #end if | |
| 24 #if str( $rm ) != '' and str( $rm ) != 'None' : | |
| 25 -rm | |
| 26 #end if | |
| 27 | tail -n 5 | |
| 28 ]]></command> | |
| 29 <inputs> | |
| 30 <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/> | |
| 31 <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/> | |
| 32 <param name="mode" optional="false" label="'intersection', 'union' or 'b_not_a'" type="select"> | |
| 33 <option value="intersection">intersection</option> | |
| 34 <option value="union">union</option> | |
| 35 <option value="b_not_a">b_not_a</option> | |
| 36 </param> | |
| 37 <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." 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=""/> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data name="o" format="mol2/sdf/drf" format_source="i1"/> | |
| 43 </outputs> | |
| 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. | |
| 45 | |
| 46 If you want to match molecules regardless of their protonation state, use option '-ignH'. | |
| 47 | |
| 48 Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help> | |
| 49 </tool> |