|
7
|
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.-->
|
|
8
|
3 <tool id="molcombine" name="MolCombine" version="0.9.6">
|
|
7
|
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
|
|
8
|
24 #if str( $rm ) != '' and str( $rm ) != 'None' :
|
|
|
25 -rm
|
|
|
26 #end if
|
|
7
|
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=""/>
|
|
8
|
39 <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/>
|
|
7
|
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> |
