annotate CADDSuite-1.5/galaxyconfigs/tools/MolCombine.xml @ 7:bfab27640f5e draft

CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
1
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
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.-->
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
3 <tool id="molcombine" name="MolCombine" version="1.5">
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
4 <description>combine molecular files</description>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../MolCombine
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
6 #if str( $i1 ) != '' and str( $i1 ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
7 -i1 "$i1"
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
8 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
9 #if str( $i2 ) != '' and str( $i2 ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
10 -i2 "$i2"
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
11 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
12 #if str( $mode ) != '' and str( $mode ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
13 -mode "$mode"
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
14 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
15 #if str( $o ) != '' and str( $o ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
16 -o "$o"
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
17 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
18 #if str( $ignH ) != '' and str( $ignH ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
19 -ignH
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
20 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
21 #if str( $replace_prop ) != '' and str( $replace_prop ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
22 -replace_prop
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
23 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
24 #if str( $rm ) != '' and str( $rm ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
25 -rm
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
26 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
27 | tail -n 5
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
28 ]]></command>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
29 <inputs>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
30 <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
31 <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
32 <param name="mode" optional="false" label="'intersection', 'union' or 'b_not_a'" type="select">
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
33 <option value="intersection">intersection</option>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
34 <option value="union">union</option>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
35 <option value="b_not_a">b_not_a</option>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
36 </param>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
37 <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
38 <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
39 <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
40 </inputs>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
41 <outputs>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
42 <data name="o" format="mol2/sdf/drf" format_source="i1"/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
43 </outputs>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
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.
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
45
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
46 If you want to match molecules regardless of their protonation state, use option '-ignH'.
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
47
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
48 Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
49 </tool>