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comparison CADDSuite/galaxyconfigs/tools/LigCheck.xml @ 4:af446ca2d5c6

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author marcel
date Fri, 02 Sep 2011 08:54:17 -0400
parents bb26168c5715
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3:bb26168c5715 4:af446ca2d5c6
1 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.--> 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="ligcheck" name="LigCheck" version="0.95"> 3 <tool id="ligcheck" name="LigCheck" version="0.9.6">
4 <description>check molecules for errors</description> 4 <description>check molecules for errors</description>
5 <command interpreter="bash"><![CDATA[../../LigCheck 5 <command interpreter="bash"><![CDATA[../../LigCheck
6 #if str( $i ) != '' and str( $i ) != 'None' : 6 #if str( $i ) != '' and str( $i ) != 'None' :
7 -i "$i" 7 -i "$i"
8 #end if 8 #end if
16 -ri 16 -ri
17 #end if 17 #end if
18 #if str( $ut ) != '' and str( $ut ) != 'None' : 18 #if str( $ut ) != '' and str( $ut ) != 'None' :
19 -ut 19 -ut
20 #end if 20 #end if
21 #if str( $nc ) != '' and str( $nc ) != 'None' :
22 -nc
23 #end if
24 #if str( $rm ) != '' and str( $rm ) != 'None' :
25 -rm
26 #end if
21 | tail -n 5 27 | tail -n 5
22 ]]></command> 28 ]]></command>
23 <inputs> 29 <inputs>
24 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> 30 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
25 <param name="ef" optional="true" label="Optional: error fraction; print error if fraction of invalid mols is larger" type="text" area="true" size="1x5" value="0.5"/> 31 <param name="ef" optional="true" label="Optional: error fraction; print error if fraction of invalid mols is larger" type="text" area="true" size="1x5" value="0.5"/>
26 <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/> 32 <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/>
27 <param name="ut" optional="true" label="check for unique topologies (default: check only for unique conformation)" type="boolean" truevalue="true" falsevalue=""/> 33 <param name="ut" optional="true" label="check for unique topologies" type="boolean" truevalue="true" falsevalue=""/>
34 <param name="nc" optional="true" label="no not check for unique conformations" type="boolean" truevalue="true" falsevalue=""/>
35 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
28 </inputs> 36 </inputs>
29 <outputs> 37 <outputs>
30 <data name="o" format="mol2/sdf/drf" format_source="i"/> 38 <data name="o" format="mol2/sdf/drf" format_source="i"/>
31 </outputs> 39 </outputs>
32 <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). 40 <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).