Mercurial > repos > marcel > caddsuite_linux_x86_64

comparison CADDSuite/galaxyconfigs/tools/DBExporter.xml @ 5:b7a89b15646f

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author marcel
date Tue, 12 Jul 2011 10:23:33 -0400
parents ff6df146c0d5
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4:02c8570cde57 5:b7a89b15646f
1 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.--> 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="0.94 (ob)"> 3 <tool id="dbexporter" name="DBExporter" version="0.95 (ob)">
4 <description>export molecules from data base</description> 4 <description>export molecules from data base</description>
5 <command interpreter="bash"><![CDATA[../../DBExporter 5 <command interpreter="bash"><![CDATA[../../DBExporter
6 #if str( $o ) != '' and str( $o ) != 'None' : 6 #if str( $o ) != '' and str( $o ) != 'None' :
7 -o "$o" 7 -o "$o"
8 #end if 8 #end if
67 -s 67 -s
68 #end if 68 #end if
69 | tail -n 5 69 | tail -n 5
70 ]]></command> 70 ]]></command>
71 <inputs> 71 <inputs>
72 <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="mol2/sdf/drf"/> 72 <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="mol2/sdf/drf"/>
73 <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/> 73 <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="data"/>
74 <param name="start_id" label="ID of the first conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/> 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" label="ID of the last conformation to be exported" optional="true" 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" label="minimal logP value" optional="true" type="text" min="-10.000000" max="10.000000" 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" label="maximal logP value" optional="true" 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" label="minimal molecular weight" optional="true" type="text" 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" label="maximal molecular weight" optional="true" 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" label="max. number of molecules to be exported" optional="true" 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" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/> 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" label="minimal average similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> 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" label="maximal similarity" optional="true" 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" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/> 84 <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
85 <param name="uck" label="UCK key" optional="true" 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" label="database name" optional="false" 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" label="database username" optional="false" 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" label="database host" optional="false" 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" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/> 89 <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
90 <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/> 90 <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
91 <param name="s" label="show summary of datasets in database" optional="true" type="boolean" truevalue="true" falsevalue=""/> 91 <param name="s" optional="true" label="show summary of datasets in database" type="boolean" truevalue="true" falsevalue=""/>
92 </inputs> 92 </inputs>
93 <outputs> 93 <outputs>
94 <data name="o" format="mol2/sdf/drf"/> 94 <data name="o" format="mol2/sdf/drf"/>
95 </outputs> 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> 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>