view CADDSuite/galaxyconfigs/tools/VendorFinder.xml @ 4:af446ca2d5c6

author marcel
date Fri, 02 Sep 2011 08:54:17 -0400
parents bb26168c5715
line wrap: on
line source

<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy ( This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
<tool id="vendorfinder" name="VendorFinder" version="0.9.6">
    <description>search vendors for compounds</description>
    <command interpreter="bash"><![CDATA[../../VendorFinder 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#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( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $opt ) != ''  and str( $opt ) != 'None' :
#end if
 | tail -n 5
        <param name="i" optional="false" label="input file containing compounds" type="data" format="mol2/sdf/drf"/>
        <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="opt" optional="true" label="optimize purchase, i.e. select cheapest sources and sort by vendor" type="boolean" truevalue="true" falsevalue=""/>
        <data name="o" format="txt"/>
    <help>This tool can be used to fetch information about vendors for each compound in the given input file from a data base.

Of course, vendors can only be found if they have been stored in the database that is to be used here. Use DBImporter with molecules files obtained from the compound vendors of your choice in order to create such a database.

Output of this tool is a text-file containing a list of vendor-name and vendor's compound-ID for each compound in the input file for which vendor-information was found in the database.</help>