|
6
|
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="dbexporter" name="DBExporter" version="1.1 (ob)">
|
|
|
4 <description>export molecules from data base</description>
|
|
|
5 <command interpreter="bash"><![CDATA[../../DBExporter
|
|
|
6 #if str( $o ) != '' and str( $o ) != 'None' :
|
|
|
7 -o "$o"
|
|
|
8 #end if
|
|
|
9 #if str( $start_id ) != '' and str( $start_id ) != 'None' :
|
|
|
10 -start_id "$start_id"
|
|
|
11 #end if
|
|
|
12 #if str( $end_id ) != '' and str( $end_id ) != 'None' :
|
|
|
13 -end_id "$end_id"
|
|
|
14 #end if
|
|
|
15 #if str( $min_logP ) != '' and str( $min_logP ) != 'None' :
|
|
|
16 -min_logP "$min_logP"
|
|
|
17 #end if
|
|
|
18 #if str( $max_logP ) != '' and str( $max_logP ) != 'None' :
|
|
|
19 -max_logP "$max_logP"
|
|
|
20 #end if
|
|
|
21 #if str( $min_MW ) != '' and str( $min_MW ) != 'None' :
|
|
|
22 -min_MW "$min_MW"
|
|
|
23 #end if
|
|
|
24 #if str( $max_MW ) != '' and str( $max_MW ) != 'None' :
|
|
|
25 -max_MW "$max_MW"
|
|
|
26 #end if
|
|
|
27 #if str( $max_mols ) != '' and str( $max_mols ) != 'None' :
|
|
|
28 -max_mols "$max_mols"
|
|
|
29 #end if
|
|
|
30 #if str( $target ) != '' and str( $target ) != 'None' :
|
|
|
31 -target "$target"
|
|
|
32 #end if
|
|
|
33 #if str( $q ) != '' and str( $q ) != 'None' :
|
|
|
34 -q "$q"
|
|
|
35 #end if
|
|
|
36 #if str( $min_sim ) != '' and str( $min_sim ) != 'None' :
|
|
|
37 -min_sim "$min_sim"
|
|
|
38 #end if
|
|
|
39 #if str( $max_sim ) != '' and str( $max_sim ) != 'None' :
|
|
|
40 -max_sim "$max_sim"
|
|
|
41 #end if
|
|
|
42 #if str( $smarts ) != '' and str( $smarts ) != 'None' :
|
|
|
43 -smarts "$smarts"
|
|
|
44 #end if
|
|
|
45 #if str( $smarts_file ) != '' and str( $smarts_file ) != 'None' :
|
|
|
46 -smarts_file "$smarts_file"
|
|
|
47 #end if
|
|
|
48 #if str( $uck ) != '' and str( $uck ) != 'None' :
|
|
|
49 -uck "$uck"
|
|
|
50 #end if
|
|
|
51 #if str( $d ) != '' and str( $d ) != 'None' :
|
|
|
52 -d "$d"
|
|
|
53 #end if
|
|
|
54 #if str( $u ) != '' and str( $u ) != 'None' :
|
|
|
55 -u "$u"
|
|
|
56 #end if
|
|
|
57 #if str( $h ) != '' and str( $h ) != 'None' :
|
|
|
58 -h "$h"
|
|
|
59 #end if
|
|
|
60 #if str( $port ) != '' and str( $port ) != 'None' :
|
|
|
61 -port "$port"
|
|
|
62 #end if
|
|
|
63 #if str( $p ) != '' and str( $p ) != 'None' :
|
|
|
64 -p "$p"
|
|
|
65 #end if
|
|
|
66 #if str( $s ) != '' and str( $s ) != 'None' :
|
|
|
67 -s
|
|
|
68 #end if
|
|
|
69 | tail -n 5
|
|
|
70 ]]></command>
|
|
|
71 <inputs>
|
|
|
72 <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="mol2/sdf/drf"/>
|
|
|
73 <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="txt"/>
|
|
|
74 <param name="start_id" optional="true" label="Optional: ID of the first conformation to be exported" type="text" area="true" size="1x5" value=""/>
|
|
|
75 <param name="end_id" optional="true" label="Optional: ID of the last conformation to be exported" type="text" area="true" size="1x5" value=""/>
|
|
|
76 <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
|
|
|
77 <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
|
|
|
78 <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/>
|
|
|
79 <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/>
|
|
|
80 <param name="max_mols" optional="true" label="Optional: max. number of molecules to be exported" type="text" area="true" size="1x5" value=""/>
|
|
|
81 <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/>
|
|
|
82 <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
|
|
|
83 <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
|
|
|
84 <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
|
|
|
85 <param name="uck" optional="true" label="Optional: UCK key" area="true" type="text" size="1x15"/>
|
|
|
86 <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/>
|
|
|
87 <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/>
|
|
|
88 <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/>
|
|
|
89 <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
|
|
|
90 <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
|
|
|
91 <param name="s" optional="true" label="show summary of datasets in database" type="boolean" truevalue="true" falsevalue=""/>
|
|
|
92 </inputs>
|
|
|
93 <outputs>
|
|
|
94 <data name="o" format="mol2/sdf/drf"/>
|
|
|
95 </outputs>
|
|
|
96 <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>
|
|
|
97 </tool> |
