Mercurial > repos > marcel > caddsuite_mac10_6
view CADDSuite-1.6/galaxyconfigs/tools/MolFilter.xml @ 8:dbb480e39d95 draft
Uploaded
author | marcel |
---|---|
date | Sat, 15 Dec 2012 13:15:46 -0500 |
parents | |
children |
line wrap: on
line source
<!--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="1.6"> <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 #if str( $pairs ) != '' and str( $pairs ) != 'None' : -pairs #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="pairs" optional="true" label="output result of sim. search as pairs of input-, query-molecule" type="boolean" truevalue="true" falsevalue=""/> <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>