annotate CADDSuite-1.5/galaxyconfigs/tools/PartialChargesCopy.xml @ 15:ac342506cd4e draft

CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:08:49 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
1
ac342506cd4e 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.-->
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
3 <tool id="partialchargescopy" name="PartialChargesCopy" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
4 <description>transfer part. charges between files</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../PartialChargesCopy
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
6 #if str( $i ) != '' and str( $i ) != 'None' :
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
7 -i "$i"
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
8 #end if
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
9 #if str( $chr ) != '' and str( $chr ) != 'None' :
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
10 -chr "$chr"
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
11 #end if
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
12 #if str( $o ) != '' and str( $o ) != 'None' :
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
13 -o "$o"
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
14 #end if
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
15 | tail -n 5
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
16 ]]></command>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
17 <inputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
18 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
19 <param name="chr" optional="false" label="file containing the same molecules as the input file, but with (different) partial charges" type="data" format="mol2"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
20 </inputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
21 <outputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
22 <data name="o" format="mol2" format_source="i"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
23 </outputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
24 <help>This tool copies partial charges from a given file to the conformations read from a different file.
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
25 This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.</help>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
26 </tool>