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comparison CADDSuite-1.6/galaxyconfigs/tools/DBExporter.xml @ 10:eda78e0f5df6 draft default tip

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author marcel
date Sun, 30 Nov 2014 03:46:08 -0500
parents 488032d372e1
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9:488032d372e1 10:eda78e0f5df6
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="1.6 (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( $min_logP ) != '' and str( $min_logP ) != 'None' :
10 -min_logP "$min_logP"
11 #end if
12 #if str( $max_logP ) != '' and str( $max_logP ) != 'None' :
13 -max_logP "$max_logP"
14 #end if
15 #if str( $min_MW ) != '' and str( $min_MW ) != 'None' :
16 -min_MW "$min_MW"
17 #end if
18 #if str( $max_MW ) != '' and str( $max_MW ) != 'None' :
19 -max_MW "$max_MW"
20 #end if
21 #if str( $target ) != '' and str( $target ) != 'None' :
22 -target "$target"
23 #end if
24 #if str( $vendors ) != '' and str( $vendors ) != 'None' :
25 -vendors "$vendors"
26 #end if
27 #if str( $q ) != '' and str( $q ) != 'None' :
28 -q "$q"
29 #end if
30 #if str( $min_sim ) != '' and str( $min_sim ) != 'None' :
31 -min_sim "$min_sim"
32 #end if
33 #if str( $max_sim ) != '' and str( $max_sim ) != 'None' :
34 -max_sim "$max_sim"
35 #end if
36 #if str( $MW_dev ) != '' and str( $MW_dev ) != 'None' :
37 -MW_dev "$MW_dev"
38 #end if
39 #if str( $max_mols_per_query ) != '' and str( $max_mols_per_query ) != 'None' :
40 -max_mols_per_query "$max_mols_per_query"
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( $min_div ) != '' and str( $min_div ) != 'None' :
49 -min_div "$min_div"
50 #end if
51 #if str( $max_mols ) != '' and str( $max_mols ) != 'None' :
52 -max_mols "$max_mols"
53 #end if
54 #if str( $d ) != '' and str( $d ) != 'None' :
55 -d "$d"
56 #end if
57 #if str( $u ) != '' and str( $u ) != 'None' :
58 -u "$u"
59 #end if
60 #if str( $h ) != '' and str( $h ) != 'None' :
61 -h "$h"
62 #end if
63 #if str( $port ) != '' and str( $port ) != 'None' :
64 -port "$port"
65 #end if
66 #if str( $p ) != '' and str( $p ) != 'None' :
67 -p "$p"
68 #end if
69 #if str( $s ) != '' and str( $s ) != 'None' :
70 -s
71 #end if
72 | tail -n 5
73 ]]></command>
74 <inputs>
75 <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="mol2/sdf/drf"/>
76 <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="txt"/>
77 <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
78 <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
79 <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/>
80 <param name="max_MW" optional="true" label="Optional: maximal molecular weight" 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="vendors" optional="true" label="Optional: use only compounds supplied by specified vendors" area="true" type="text" size="1x15"/>
83 <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=""/>
84 <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=""/>
85 <param name="MW_dev" optional="true" label="Optional: maximal molecular weight deviation between hit and query" type="text" area="true" size="1x5" value=""/>
86 <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=""/>
87 <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
88 <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=""/>
89 <param name="max_mols" optional="true" label="Optional: max. total number of molecules to be exported" type="text" area="true" size="1x5" value=""/>
90 <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/>
91 <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/>
92 <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/>
93 <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
94 <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
95 <param name="s" optional="true" label="show summary of datasets in database" type="boolean" truevalue="true" falsevalue=""/>
96 </inputs>
97 <outputs>
98 <data name="o" format="mol2/sdf/drf"/>
99 </outputs>
100 <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>
101 </tool>