comparison CADDSuite-1.0/galaxyconfigs/tools/DBImporter.xml @ 14:55c32b55c2c2

Uploaded Version 1.1
author marcel
date Thu, 12 Jan 2012 11:00:43 -0500
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13:cce3667779c2 14:55c32b55c2c2
1
2 <!--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.-->
3 <tool id="dbimporter" name="DBImporter" version="1.1 (ob)">
4 <description>import molecules into data base</description>
5 <command interpreter="bash"><![CDATA[../../DBImporter
6 #if str( $i ) != '' and str( $i ) != 'None' :
7 -i "$i"
8 #end if
9 #if str( $o ) != '' and str( $o ) != 'None' :
10 -o "$o"
11 #end if
12 #if str( $target ) != '' and str( $target ) != 'None' :
13 -target "$target"
14 #end if
15 #if str( $d ) != '' and str( $d ) != 'None' :
16 -d "$d"
17 #end if
18 #if str( $u ) != '' and str( $u ) != 'None' :
19 -u "$u"
20 #end if
21 #if str( $h ) != '' and str( $h ) != 'None' :
22 -h "$h"
23 #end if
24 #if str( $port ) != '' and str( $port ) != 'None' :
25 -port "$port"
26 #end if
27 #if str( $p ) != '' and str( $p ) != 'None' :
28 -p "$p"
29 #end if
30 #if str( $vn ) != '' and str( $vn ) != 'None' :
31 -vn "$vn"
32 #end if
33 #if str( $vid ) != '' and str( $vid ) != 'None' :
34 -vid "$vid"
35 #end if
36 #if str( $vd ) != '' and str( $vd ) != 'None' :
37 -vd "$vd"
38 #end if
39 #if str( $vu ) != '' and str( $vu ) != 'None' :
40 -vu "$vu"
41 #end if
42 | tail -n 5
43 ]]></command>
44 <inputs>
45 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
46 <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/>
47 <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/>
48 <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/>
49 <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/>
50 <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
51 <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
52 <param name="vn" optional="true" label="Optional: name of compound vendor" area="true" type="text" size="1x15"/>
53 <param name="vid" optional="true" label="Optional: name of vendor's compound-ID tag in sd-file" area="true" type="text" size="1x15"/>
54 <param name="vd" optional="true" label="Optional: vendor library date or version" area="true" type="text" size="1x15"/>
55 <param name="vu" optional="true" label="Optional: url from wich vendor library was obtained" area="true" type="text" size="1x15"/>
56 </inputs>
57 <outputs>
58 <data name="o" format="txt"/>
59 </outputs>
60 <help>This tool imports molecules into a database.
61 As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help>
62 </tool>