Mercurial > repos > marcel > caddsuite_linux_x86_64
diff CADDSuite-1.5/galaxyconfigs/tools/MolFilter.xml @ 15:ac342506cd4e draft
CADDSuite version 1.5
author | Marcel Schumann <schumann.marcel@gmail.com> |
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date | Tue, 24 Jul 2012 11:08:49 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite-1.5/galaxyconfigs/tools/MolFilter.xml Tue Jul 24 11:08:49 2012 -0400 @@ -0,0 +1,68 @@ + +<!--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="1.5"> + <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( $min_div ) != '' and str( $min_div ) != 'None' : + -min_div "$min_div" +#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 +#if str( $rm ) != '' and str( $rm ) != 'None' : + -rm +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" optional="false" label="input molecule-file" type="data" format="mol2/sdf/drf"/> + <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="txt"/> + <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="txt"/> + <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" area="true" size="1x5" value=""/> + <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" area="true" size="1x5" value=""/> + <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/> + <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/> + <param name="min_sim" optional="true" label="Optional: minimal similarity to a query molecule" type="text" area="true" size="1x5" value=""/> + <param name="max_sim" optional="true" label="Optional: maximal similarity to a query molecule" type="text" area="true" size="1x5" value=""/> + <param name="min_div" optional="true" label="Optional: min. pairwise diversity between hits" type="text" area="true" size="1x5" value=""/> + <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/> + <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> + </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> \ No newline at end of file