Mercurial > repos > marcel > caddsuite_linux_x86_64
view CADDSuite-1.5/galaxyconfigs/tools/DBExporter.xml @ 16:1a24aef40d01 draft
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author | marcel |
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date | Tue, 24 Jul 2012 11:10:07 -0400 |
parents | ac342506cd4e |
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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="1.5 (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( $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( $target ) != '' and str( $target ) != 'None' : -target "$target" #end if #if str( $vendors ) != '' and str( $vendors ) != 'None' : -vendors "$vendors" #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( $MW_dev ) != '' and str( $MW_dev ) != 'None' : -MW_dev "$MW_dev" #end if #if str( $max_mols_per_query ) != '' and str( $max_mols_per_query ) != 'None' : -max_mols_per_query "$max_mols_per_query" #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( $min_div ) != '' and str( $min_div ) != 'None' : -min_div "$min_div" #end if #if str( $max_mols ) != '' and str( $max_mols ) != 'None' : -max_mols "$max_mols" #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" optional="true" label="query molecules for similarity searching" type="data" format="mol2/sdf/drf"/> <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" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" min="-10.000000" max="10.000000" 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="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/> <param name="vendors" optional="true" label="Optional: use only compounds supplied by specified vendors" area="true" type="text" size="1x15"/> <param name="min_sim" optional="true" label="Optional: minimal similarity to a query molecule" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> <param name="max_sim" optional="true" label="Optional: maximal similarity to a query molecule" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> <param name="MW_dev" optional="true" label="Optional: maximal molecular weight deviation between hit and query" type="text" area="true" size="1x5" value=""/> <param name="max_mols_per_query" optional="true" label="Optional: max. number of mols for each query mol" type="text" area="true" size="1x5" value=""/> <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/> <param name="min_div" optional="true" label="Optional: min. pairwise diversity between hits" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> <param name="max_mols" optional="true" label="Optional: max. total number of molecules to be exported" type="text" area="true" size="1x5" value=""/> <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/> <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/> <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/> <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/> <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/> <param name="s" optional="true" label="show summary of datasets in database" 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>