view CADDSuite-1.6/galaxyconfigs/tools/DBExporter.xml @ 8:dbb480e39d95 draft

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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="1.6 (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>