Mercurial > repos > earlhaminst > ensembl_get_feature_info

annotate get_feature_info.xml @ 2:840ea71e6318 draft

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author earlhaminst
date Wed, 21 Dec 2016 15:16:22 -0500
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840ea71e6318 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f
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1 <tool id="get_feature_info" name="Get features by Ensembl ID" version="0.1.2">
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2 <description>using REST API</description>
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3 <requirements>
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4 <requirement type="package" version="2.12.4">requests</requirement>
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5 <requirement type="package" version="1.10.0">six</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 python $__tool_directory__/get_feature_info.py
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10 -e $expand
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11 -f $format_selector
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12 -i "$input"
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13 -s $species_selector
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14 > "$output"
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15 ]]>
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16 </command>
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18 <inputs>
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19 <param name="input" type="data" format="txt" label="List of Ensembl IDs" help="Max 1000 IDs" />
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20 <param name="species_selector" type="select" label="Select species">
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21 <option value="ensembl" selected="true">Vertebrates</option>
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22 <option value="ensemblgenomes">Other species</option>
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23 </param>
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24 <param name="expand" type="boolean" truevalue="1" falsevalue="0" label="Expand the search to include any connected features" help="For example, if the object is a gene, its transcripts, translations and exons will be returned as well" />
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25 <param name="format_selector" type="select" label="Output format">
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26 <option value="full" selected="true">Full</option>
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27 <option value="condensed">Condensed</option>
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28 </param>
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29 </inputs>
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31 <outputs>
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32 <data name="output" format="json" label="$(tool.name) on ${on_string}" />
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33 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input" ftype="txt" value="input.txt" />
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38 <param name="expand" value="false" />
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39 <output name="outputFile" file="out.json" />
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40 </test>
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41 </tests>
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42
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43 <help>
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44 <![CDATA[
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45 **What it does**
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46
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47 Retrieve feature information in JSON format from Ensembl using its REST API.
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49 Uses the `"POST lookup/id"`_ API endpoint.
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51 .. _"POST lookup/id": http://rest.ensembl.org/documentation/info/lookup_post
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52 ]]>
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53 </help>
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54 <citations>
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55 </citations>
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56 </tool>