Mercurial > repos > marcel > caddsuite_linux_x86_64

annotate CADDSuite/galaxyconfigs/tools/VendorFinder.xml @ 0:bac3c274238f

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Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 16:43:30 -0400
parents
children 867bf9f815a0
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bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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1
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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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="vendorfinder" name="VendorFinder" version="0.93">
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4 <description>search vendors for compounds</description>
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5 <command interpreter="bash"><![CDATA[../../VendorFinder
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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( $d ) != '' and str( $d ) != 'None' :
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10 -d "$d"
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11 #end if
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12 #if str( $u ) != '' and str( $u ) != 'None' :
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13 -u "$u"
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14 #end if
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15 #if str( $h ) != '' and str( $h ) != 'None' :
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16 -h "$h"
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17 #end if
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18 #if str( $port ) != '' and str( $port ) != 'None' :
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19 -port "$port"
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20 #end if
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21 #if str( $p ) != '' and str( $p ) != 'None' :
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22 -p "$p"
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23 #end if
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24 #if str( $o ) != '' and str( $o ) != 'None' :
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25 -o "$o"
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26 #end if
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27 #if str( $opt ) != '' and str( $opt ) != 'None' :
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28 -opt
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29 #end if
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30 | tail -n 5
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31 ]]></command>
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32 <inputs>
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33 <param name="i" label="input file containing compounds" optional="false" type="data" format="mol2/sdf/drf"/>
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34 <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
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35 <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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36 <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
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37 <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
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38 <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
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39 <param name="opt" label="optimize purchase, i.e. select cheapest sources and sort by vendor" optional="true" type="boolean" truevalue="true" falsevalue=""/>
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40 </inputs>
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41 <outputs>
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42 <data name="o" format="txt"/>
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43 </outputs>
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44 <help>This tool can be used to fetch information about vendors for each compound in the given input file from a data base.
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45
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46 Of course, vendors can only be found if they have been stored in the database that is to be used here. Use DBImporter with molecules files obtained from the compound vendors of your choice in order to create such a database.
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47
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48 Output of this tool is a text-file containing a list of vendor-name and vendor's compound-ID for each compound in the input file for which vendor-information was found in the database.</help>
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49 </tool>