Mercurial > repos > earlhaminst > ensembl_get_sequences

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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 14:49:24 +0000
parents 7af66c2b3831
children
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1 <tool id="get_sequences" name="Get sequences 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_sequences.py'
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13 --expand_3prime $expand_3prime
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14 --expand_5prime $expand_5prime
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15 -t $type_selector
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16 -i '$input'
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17 > '$output'
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18 ]]>
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19 </command>
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21 <inputs>
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22 <param name="input" type="data" format="txt" label="List of Ensembl IDs" />
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23 <param name="expand_3prime" type="integer" value="0" min="0" label="expand_3prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
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24 <param name="expand_5prime" type="integer" value="0" min="0" label="expand_5prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
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25 <param name="type_selector" type="select" label="Type" help="Type of sequence. Defaults to genomic where applicable, i.e. not translations. cDNA refers to the spliced transcript sequence with UTR; CDS refers to the spliced transcript sequence without UTR">
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26 <option value="genomic" selected="true">Genomic</option>
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27 <option value="cds">CDS</option>
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28 <option value="cdna">cDNA</option>
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29 <option value="protein">Protein</option>
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30 </param>
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31 </inputs>
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33 <outputs>
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34 <data name="output" format="fasta" label="$(tool.name) on ${on_string}" />
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35 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" ftype="txt" value="input.txt" />
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40 <param name="expand_3prime" value="0" />
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41 <param name="expand_5prime" value="0" />
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42 <param name="type_selector" value="genomic" />
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43 <output name="output" ftype="fasta">
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44 <assert_contents>
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45 <has_text text="ENSG00000157764" />
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46 <has_text text="ENSG00000248378" />
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47 </assert_contents>
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48 </output>
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49 </test>
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50 </tests>
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52 <help>
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53 <![CDATA[
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54 **What it does**
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56 Retrieves FASTA sequences from Ensembl using its REST API.
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57
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58 Uses the `"POST sequence/id"`_ API endpoint.
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59
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7af66c2b3831 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"
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60 .. _"POST sequence/id": https://rest.ensembl.org/documentation/info/sequence_id_post
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61 ]]>
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62 </help>
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63 <expand macro="citations" />
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64 </tool>