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1 <tool id="ensembl" name="ENSEMBL variant effect predictor">
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2 <description>to annotate variants using an ENSEMBL database</description>
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3 <command interpreter="perl">
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2
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4 variant_effect_predictor.pl -i=$input -o=$output -species=$species --sift b --polyphen b
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5 #if $database_options.database_options_selector == "advanced"
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6 --host=$database_options.host --user=$database_options.username --port=$database_options.portnum
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7 #if $database_options.password
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8 --password=$database_options.password
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9 #end if
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10 #else
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11 ## hardcoded default values - bad?
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12 --host=ensembldb.ensembl.org --user=anonymous --port=5306
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13 #end if
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14 </command>
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15 <inputs>
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16 <param format="vcf" name="input" type="data" label="Input variants file" help="This should be a variant file in vcf format."/> <!-- TODO: allow other variant format types? -->
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17 <param name="species" label="Name of the species being annotated" type="text" Default ="human" help="Species for your data. This can be the latin name e.g. 'human' or any Ensembl alias e.g. 'mouse'. Specifying the latin name can speed up initial database connection as the registry does not have to load all available database aliases on the server."/> <!-- TODO: files in galaxy have a reference genome specified. We should probaby try to use that instead. -->
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18 <conditional name="database_options">
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19 <param name="database_options_selector" type="select" label="Database Options">
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20 <option value="basic" selected="True">Use Default Database</option>
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21 <option value="advanced">Choose Database Manually</option>
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2
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22 </param>
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23 <when value="basic">
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24 <!-- no options -->
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25 </when>
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26 <when value="advanced">
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27 <param name="host" label="Database host address" type="text" default="ensembldb.ensembl.org" help="By default connects to ensembldb.ensembl.org"/> <!-- TODO: may want a drop-down list with the main EMBL database listed too and with an other field -->
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28 <param name="username" label="Username" Default="anonymous" type="text" help="Default='anonymous'"/>
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29 <param name="password" label="Password, if required" Default="" type="text" help="Most public ENSEMBL databases do not require a password for access"/>
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30 <param name="portnum" label="Database port" type="text" Default="5306" help="The default is 5306."/>
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31 </when>
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32 </conditional>
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33 </inputs>
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34 <outputs>
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35 <!-- TODO: Can we optionally make it vcf? -->
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36 <data format="tabular" name="output" label="${tool.name} on ${on_string}"/>
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37 </outputs>
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38
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39 <help>
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40 This tool connects to the ENSEMBL database using ENSEMBL's Variant Effect Predictor script and retrieves annotations for an input variants file.
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41 </help>
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42 </tool>
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43
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