Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.0.1/galaxyconfigs/tools/MolCombine.xml @ 9:2cff9609f2c7
Uploaded
author | marcel |
---|---|
date | Tue, 15 Nov 2011 10:40:26 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
8:9ab6da6cd36c | 9:2cff9609f2c7 |
---|---|
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> |