view CADDSuite/galaxyconfigs/tools/DBImporter.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="dbimporter" name="DBImporter" version="0.9.6 (ob)">
    <description>import molecules into data base</description>
    <command interpreter="bash"><![CDATA[../../DBImporter 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $target ) != ''  and str( $target ) != 'None' :
   -target "$target"
#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( $vn ) != ''  and str( $vn ) != 'None' :
   -vn "$vn"
#end if
#if str( $vid ) != ''  and str( $vid ) != 'None' :
   -vid "$vid"
#end if
#if str( $vd ) != ''  and str( $vd ) != 'None' :
   -vd "$vd"
#end if
#if str( $vu ) != ''  and str( $vu ) != 'None' :
   -vu "$vu"
#end if
 | tail -n 5
        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
        <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/>
        <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="vn" optional="true" label="Optional: name of compound vendor" area="true" type="text" size="1x15"/>
        <param name="vid" optional="true" label="Optional: name of vendor's compound-ID tag in sd-file" area="true" type="text" size="1x15"/>
        <param name="vd" optional="true" label="Optional: vendor library date or version" area="true" type="text" size="1x15"/>
        <param name="vu" optional="true" label="Optional: url from wich vendor library was obtained" area="true" type="text" size="1x15"/>
        <data name="o" format="data"/>
    <help>This tool imports molecules into a database.
As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help>