comparison CADDSuite-1.6/galaxyconfigs/tools/MolCombine.xml @ 8:dbb480e39d95 draft

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author marcel
date Sat, 15 Dec 2012 13:15:46 -0500
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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="1.6">
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="" checked="true"/>
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>