Mercurial > repos > marcel > caddsuite_mac10_6
view CADDSuite/galaxyconfigs/tools/MolFilter.xml @ 1:0dcf542923ab
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author | g2cmnty@test-web1.g2.bx.psu.edu |
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date | Tue, 28 Jun 2011 10:39:47 -0400 |
parents | 8ce0411aaeb3 |
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<!--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.--> <tool id="molfilter" name="MolFilter" version="0.9"> <description>filter molecule files</description> <command interpreter="bash"><![CDATA[../../MolFilter #if str( $i ) != '' and str( $i ) != 'None' : -i "$i" #end if #if str( $min_logP ) != '' and str( $min_logP ) != 'None' : -min_logP "$min_logP" #end if #if str( $max_logP ) != '' and str( $max_logP ) != 'None' : -max_logP "$max_logP" #end if #if str( $min_MW ) != '' and str( $min_MW ) != 'None' : -min_MW "$min_MW" #end if #if str( $max_MW ) != '' and str( $max_MW ) != 'None' : -max_MW "$max_MW" #end if #if str( $q ) != '' and str( $q ) != 'None' : -q "$q" #end if #if str( $min_sim ) != '' and str( $min_sim ) != 'None' : -min_sim "$min_sim" #end if #if str( $max_sim ) != '' and str( $max_sim ) != 'None' : -max_sim "$max_sim" #end if #if str( $smarts ) != '' and str( $smarts ) != 'None' : -smarts "$smarts" #end if #if str( $smarts_file ) != '' and str( $smarts_file ) != 'None' : -smarts_file "$smarts_file" #end if #if str( $o ) != '' and str( $o ) != 'None' : -o "$o" #end if -quiet | tail -n 5 ]]></command> <inputs> <param name="i" label="input molecule-file" optional="false" type="data" format="mol2/sdf/drf"/> <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="txt"/> <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/> <param name="min_logP" label="minimal logP value" optional="true" type="text" area="true" size="1x5" value=""/> <param name="max_logP" label="maximal logP value" optional="true" type="text" area="true" size="1x5" value=""/> <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> <param name="min_sim" label="minimal average similarity" optional="true" type="text" area="true" size="1x5" value=""/> <param name="max_sim" label="maximal similarity" optional="true" type="text" area="true" size="1x5" value=""/> <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/> </outputs> <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s). Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.</help> </tool>