Mercurial > repos > marcel > caddsuite_mac10_6
view CADDSuite/galaxyconfigs/tools/DBExporter.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="dbexporter" name="DBExporter" version="0.94 (ob)"> <description>export molecules from data base</description> <command interpreter="bash"><![CDATA[../../DBExporter #if str( $o ) != '' and str( $o ) != 'None' : -o "$o" #end if #if str( $start_id ) != '' and str( $start_id ) != 'None' : -start_id "$start_id" #end if #if str( $end_id ) != '' and str( $end_id ) != 'None' : -end_id "$end_id" #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( $max_mols ) != '' and str( $max_mols ) != 'None' : -max_mols "$max_mols" #end if #if str( $target ) != '' and str( $target ) != 'None' : -target "$target" #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( $uck ) != '' and str( $uck ) != 'None' : -uck "$uck" #end if #if str( $d ) != '' and str( $d ) != 'None' : -d "$d" #end if #if str( $u ) != '' and str( $u ) != 'None' : -u "$u" #end if #if str( $h ) != '' and str( $h ) != 'None' : -h "$h" #end if #if str( $port ) != '' and str( $port ) != 'None' : -port "$port" #end if #if str( $p ) != '' and str( $p ) != 'None' : -p "$p" #end if #if str( $s ) != '' and str( $s ) != 'None' : -s #end if | tail -n 5 ]]></command> <inputs> <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="mol2/sdf/drf"/> <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/> <param name="start_id" label="ID of the first conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/> <param name="end_id" label="ID of the last conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/> <param name="min_logP" label="minimal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> <param name="max_logP" label="maximal logP value" optional="true" type="text" min="-10.000000" max="10.000000" 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="max_mols" label="max. number of molecules to be exported" optional="true" type="text" area="true" size="1x5" value=""/> <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/> <param name="min_sim" label="minimal average similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> <param name="max_sim" label="maximal similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/> <param name="uck" label="UCK key" optional="true" area="true" type="text" size="1x15"/> <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/> <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/> <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/> <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/> <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/> <param name="s" label="show summary of datasets in database" optional="true" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf"/> </outputs> <help>This tool exports compounds from a database to a molecular file. Compounds can be filtered according to (among others) SMARTS expressions, logP, molecular weight, or similarity to query molecule(s) and dataset name.</help> </tool>