Mercurial > repos > earlhaminst > ensembl_get_feature_info

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
author earlhaminst
date Mon, 17 Feb 2025 14:49:19 +0000
parents d6bb417dc831
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1 <tool id="get_feature_info" name="Get features by Ensembl ID" version="1.0.0">
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2 <description>using REST API</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="3.13">python</requirement>
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8 <requirement type="package" version="2.32.3">requests</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 python '$__tool_directory__/get_feature_info.py'
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13 -e $expand
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14 -f $format_selector
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15 -i '$input'
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16 > '$output'
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17 ]]>
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18 </command>
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20 <inputs>
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21 <param name="input" type="data" format="txt" label="List of Ensembl IDs" help="Max 1000 IDs" />
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22 <param name="expand" type="boolean" truevalue="1" falsevalue="0" label="Expand the search to include any connected features" help="For example, if the object is a gene, its transcripts, translations and exons will be returned as well" />
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23 <param name="format_selector" type="select" label="Output format">
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24 <option value="full" selected="true">Full</option>
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25 <option value="condensed">Condensed</option>
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26 </param>
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27 </inputs>
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29 <outputs>
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30 <data name="output" format="json" label="$(tool.name) on ${on_string}" />
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31 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input" ftype="txt" value="input.txt" />
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36 <param name="expand" value="false" />
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37 <output name="output" ftype="json">
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38 <assert_contents>
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39 <has_text text="ENSG00000157764" />
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40 <has_text text="ENSG00000248378" />
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41 <has_text text="homo_sapiens" />
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42 <has_text text="protein_coding" />
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43 </assert_contents>
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44 </output>
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45 </test>
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46 </tests>
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47
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48 <help>
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49 <![CDATA[
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50 **What it does**
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52 Retrieve feature information in JSON format from Ensembl using its REST API.
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54 Uses the `"POST lookup/id"`_ API endpoint.
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56 .. _"POST lookup/id": https://rest.ensembl.org/documentation/info/lookup_post
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57 ]]>
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58 </help>
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59 <expand macro="citations" />
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60 </tool>