1 | <!-- |
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2 | # ===================================================== |
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3 | # $Id: Molgenis.xml 151 2011-09-08 08:12:14Z pieter.neerincx@gmail.com $ |
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4 | # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/DataSources/Molgenis.xml $ |
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5 | # $LastChangedDate: 2011-09-08 10:12:14 +0200 (Thu, 08 Sep 2011) $ |
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6 | # $LastChangedRevision: 151 $ |
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7 | # $LastChangedBy: pieter.neerincx@gmail.com $ |
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8 | # ===================================================== |
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9 | --> |
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10 | <!-- |
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11 | Note: This is an example tool.xml file to add a Molgenis DB to your Galaxy. |
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12 | The only thing you'll need to change is the http://IPaddress:port/path/molgenis.do to where your Molgenis is hosted |
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13 | --> |
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14 | <tool name="Molgenis" id="Molgenis1" tool_type="data_source" version="1.0"> |
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15 | <description>test server</description> |
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16 | <!-- Removed interpreter="python" attribute from the command tag to prevent Galaxy from appending the tool's dir to the path |
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17 | before executing the command. Otherwise it won't respect $__app__.config.tool_path. --> |
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18 | <command>python $__app__.config.tool_path/data_source/data_source.py $output $__app__.config.output_size_limit</command> |
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19 | <inputs action="http://localhost:8082/molgenis_apps/molgenis.do" check_values="false" method="get" target="_top"> |
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20 | <display>go to Molgenis server $GALAXY_URL</display> |
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21 | <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=Molgenis1" /> |
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22 | </inputs> |
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23 | <request_param_translation> |
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24 | <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" /> |
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25 | <request_param galaxy_name="URL" remote_name="URL" missing="" /> |
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26 | <request_param galaxy_name="name" remote_name="name" missing="Imported from Molgenis" /> |
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27 | <request_param galaxy_name="data_type" remote_name="data_type" missing="tabular" /> |
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28 | <!-- If your Molgenis instance can provide additional meta-data for the data uploaded to Galaxy, |
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29 | you can specify these with the additional request params below. |
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30 | Note: dbkey = the database version and in the case of genomic data this is the genome assembly/annotation build number. |
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31 | For more details check the online docs @ the Galaxy Wiki. |
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32 | <request_param galaxy_name="dbkey" remote_name="" missing="" /> |
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33 | <request_param galaxy_name="table" remote_name="" missing="" /> |
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34 | <request_param galaxy_name="organism" remote_name="" missing="" /> |
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35 | <request_param galaxy_name="description" remote_name="" missing="" /> |
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36 | <request_param galaxy_name="info" remote_name="" missing="" /> |
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37 | --> |
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38 | </request_param_translation> |
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39 | <uihints minwidth="800"/> |
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40 | <outputs> |
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41 | <data name="output" format="tabular" /> |
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42 | </outputs> |
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43 | <options sanitize="False" refresh="True"/> |
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44 | </tool> |
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