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annotate CADDSuite-1.5/galaxyconfigs/tools/DBExporter.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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1
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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.-->
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3 <tool id="dbexporter" name="DBExporter" version="1.5 (ob)">
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4 <description>export molecules from data base</description>
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5 <command interpreter="bash"><![CDATA[../../DBExporter
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6 #if str( $o ) != '' and str( $o ) != 'None' :
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7 -o "$o"
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8 #end if
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9 #if str( $min_logP ) != '' and str( $min_logP ) != 'None' :
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10 -min_logP "$min_logP"
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11 #end if
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12 #if str( $max_logP ) != '' and str( $max_logP ) != 'None' :
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13 -max_logP "$max_logP"
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14 #end if
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15 #if str( $min_MW ) != '' and str( $min_MW ) != 'None' :
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16 -min_MW "$min_MW"
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17 #end if
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18 #if str( $max_MW ) != '' and str( $max_MW ) != 'None' :
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19 -max_MW "$max_MW"
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20 #end if
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21 #if str( $target ) != '' and str( $target ) != 'None' :
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22 -target "$target"
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23 #end if
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24 #if str( $vendors ) != '' and str( $vendors ) != 'None' :
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25 -vendors "$vendors"
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26 #end if
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27 #if str( $q ) != '' and str( $q ) != 'None' :
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28 -q "$q"
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29 #end if
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30 #if str( $min_sim ) != '' and str( $min_sim ) != 'None' :
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31 -min_sim "$min_sim"
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32 #end if
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33 #if str( $max_sim ) != '' and str( $max_sim ) != 'None' :
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34 -max_sim "$max_sim"
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35 #end if
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36 #if str( $MW_dev ) != '' and str( $MW_dev ) != 'None' :
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37 -MW_dev "$MW_dev"
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38 #end if
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39 #if str( $max_mols_per_query ) != '' and str( $max_mols_per_query ) != 'None' :
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40 -max_mols_per_query "$max_mols_per_query"
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41 #end if
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42 #if str( $smarts ) != '' and str( $smarts ) != 'None' :
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43 -smarts "$smarts"
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44 #end if
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45 #if str( $smarts_file ) != '' and str( $smarts_file ) != 'None' :
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46 -smarts_file "$smarts_file"
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47 #end if
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48 #if str( $min_div ) != '' and str( $min_div ) != 'None' :
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49 -min_div "$min_div"
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50 #end if
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51 #if str( $max_mols ) != '' and str( $max_mols ) != 'None' :
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52 -max_mols "$max_mols"
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53 #end if
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54 #if str( $d ) != '' and str( $d ) != 'None' :
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55 -d "$d"
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56 #end if
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57 #if str( $u ) != '' and str( $u ) != 'None' :
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58 -u "$u"
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59 #end if
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60 #if str( $h ) != '' and str( $h ) != 'None' :
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61 -h "$h"
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62 #end if
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63 #if str( $port ) != '' and str( $port ) != 'None' :
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64 -port "$port"
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65 #end if
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66 #if str( $p ) != '' and str( $p ) != 'None' :
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67 -p "$p"
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68 #end if
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69 #if str( $s ) != '' and str( $s ) != 'None' :
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70 -s
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71 #end if
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72 | tail -n 5
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73 ]]></command>
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74 <inputs>
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75 <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="mol2/sdf/drf"/>
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76 <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="txt"/>
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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=""/>
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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=""/>
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79 <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/>
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80 <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/>
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81 <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/>
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82 <param name="vendors" optional="true" label="Optional: use only compounds supplied by specified vendors" area="true" type="text" size="1x15"/>
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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=""/>
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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=""/>
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85 <param name="MW_dev" optional="true" label="Optional: maximal molecular weight deviation between hit and query" type="text" area="true" size="1x5" value=""/>
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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=""/>
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87 <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
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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=""/>
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89 <param name="max_mols" optional="true" label="Optional: max. total number of molecules to be exported" type="text" area="true" size="1x5" value=""/>
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90 <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/>
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91 <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/>
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92 <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/>
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93 <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
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94 <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
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95 <param name="s" optional="true" label="show summary of datasets in database" type="boolean" truevalue="true" falsevalue=""/>
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96 </inputs>
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97 <outputs>
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98 <data name="o" format="mol2/sdf/drf"/>
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99 </outputs>
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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>
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101 </tool>