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annotate CADDSuite-1.5/galaxyconfigs/tools/DBImporter.xml @ 15:ac342506cd4e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:08:49 -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="dbimporter" name="DBImporter" version="1.5 (ob)">
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4 <description>import molecules into data base</description>
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5 <command interpreter="bash"><![CDATA[../../DBImporter
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $o ) != '' and str( $o ) != 'None' :
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10 -o "$o"
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11 #end if
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12 #if str( $target ) != '' and str( $target ) != 'None' :
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13 -target "$target"
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14 #end if
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15 #if str( $d ) != '' and str( $d ) != 'None' :
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16 -d "$d"
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17 #end if
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18 #if str( $u ) != '' and str( $u ) != 'None' :
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19 -u "$u"
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20 #end if
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21 #if str( $h ) != '' and str( $h ) != 'None' :
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22 -h "$h"
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23 #end if
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24 #if str( $port ) != '' and str( $port ) != 'None' :
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25 -port "$port"
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26 #end if
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27 #if str( $p ) != '' and str( $p ) != 'None' :
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28 -p "$p"
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29 #end if
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30 #if str( $vn ) != '' and str( $vn ) != 'None' :
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31 -vn "$vn"
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32 #end if
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33 #if str( $vid ) != '' and str( $vid ) != 'None' :
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34 -vid "$vid"
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35 #end if
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36 #if str( $vd ) != '' and str( $vd ) != 'None' :
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37 -vd "$vd"
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38 #end if
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39 #if str( $vu ) != '' and str( $vu ) != 'None' :
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40 -vu "$vu"
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41 #end if
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42 #if str( $run_clustering ) != '' and str( $run_clustering ) != 'None' :
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43 -run_clustering
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44 #end if
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45 | tail -n 5
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46 ]]></command>
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47 <inputs>
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48 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
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49 <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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50 <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/>
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51 <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/>
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52 <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/>
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53 <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
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54 <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
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55 <param name="vn" optional="true" label="Optional: name of compound vendor" area="true" type="text" size="1x15"/>
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56 <param name="vid" optional="true" label="Optional: name of vendor's compound-ID tag in sd-file" area="true" type="text" size="1x15"/>
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57 <param name="vd" optional="true" label="Optional: vendor library date or version" area="true" type="text" size="1x15"/>
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58 <param name="vu" optional="true" label="Optional: url from wich vendor library was obtained" area="true" type="text" size="1x15"/>
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59 <param name="run_clustering" optional="true" label="cluster entire database after importing compounds" type="boolean" truevalue="true" falsevalue=""/>
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60 </inputs>
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61 <outputs>
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62 <data name="o" format="txt"/>
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63 </outputs>
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64 <help>This tool imports molecules into a database.
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65 As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help>
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66 </tool>