Mercurial > repos > earlhaminst > ensembl_get_sequences

annotate get_sequences.xml @ 2:4b7261f484bb draft

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author earlhaminst
date Wed, 21 Dec 2016 15:16:49 -0500
parents e5dd4bd78bbc
children bce784076824
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1 <tool id="get_sequences" name="Get sequences 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_sequences.py
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10 -s $species_selector
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11 --expand_3prime $expand_3prime
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12 --expand_5prime $expand_5prime
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13 -t $type_selector
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14 -i "$input"
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15 > "$output"
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16 ]]>
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17 </command>
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19 <inputs>
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20 <param name="input" type="data" format="txt" label="List of Ensembl IDs" />
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21 <param name="species_selector" type="select" label="Select Species">
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22 <option value="ensembl" selected="true">Vertebrates</option>
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23 <option value="ensemblgenomes">Other species</option>
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24 </param>
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25 <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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26 <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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27 <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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28 <option value="genomic" selected="true">Genomic</option>
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29 <option value="cds">CDS</option>
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30 <option value="cdna">cDNA</option>
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31 <option value="protein">Protein</option>
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32 </param>
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33 </inputs>
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34
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35 <outputs>
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36 <data name="output" format="fasta" label="$(tool.name) on ${on_string}" />
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37 </outputs>
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38
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39 <tests>
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40 <test>
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41 <param name="input" ftype="txt" value="input.txt" />
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42 <param name="expand_3prime" value="0" />
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43 <param name="expand_5prime" value="0" />
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44 <param name="type_selector" value="genomic" />
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45 <output name="output" file="sequences.fasta" />
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46 </test>
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47 </tests>
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48
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49 <help>
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50 <![CDATA[
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51 **What it does**
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52
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53 Retrieves FASTA sequences from Ensembl using its REST API.
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54
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55 Uses the `"POST sequence/id"`_ API endpoint.
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56
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57 .. _"POST sequence/id": http://rest.ensembl.org/documentation/info/sequence_id_post
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58 ]]>
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59 </help>
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60 <citations>
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61 </citations>
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62 </tool>