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comparison get_sequences/get_sequences.xml @ 0:76b2c482f1e8 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
author earlhaminst
date Thu, 11 Aug 2016 14:29:50 -0400
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1 <tool id="get_sequences" name="Get sequences by Ensembl ID" version="0.1.1">
2 <description>using REST API</description>
3 <requirements>
4 <requirement type="package" version="2.7">requests</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8 python $__tool_directory__/get_sequences.py
9 -s $species_selector
10 --expand_3prime $expand_3prime
11 --expand_5prime $expand_5prime
12 -t $type_selector
13 -i "$input"
14 > "$output"
15 ]]>
16 </command>
17
18 <inputs>
19 <param name="input" type="data" format="txt" label="List of Ensembl IDs" />
20 <param name="species_selector" type="select" label="Select Species">
21 <option value="ensembl" selected="true">Vertebrates</option>
22 <option value="ensemblgenomes">Other species</option>
23 </param>
24 <param name="expand_3prime" type="integer" value="0" min="0" label="expand_3prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
25 <param name="expand_5prime" type="integer" value="0" min="0" label="expand_5prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
26 <param name="type_selector" type="select" label="Type" help="Type of sequence. Defaults to genomic where applicable, i.e. not translations. cDNA refers to the spliced transcript sequence with UTR; CDS refers to the spliced transcript sequence without UTR">
27 <option value="genomic" selected="true">Genomic</option>
28 <option value="cds">CDS</option>
29 <option value="cdna">cDNA</option>
30 <option value="protein">Protein</option>
31 </param>
32 </inputs>
33
34 <outputs>
35 <data name="output" format="fasta" label="$(tool.name) on ${on_string}" />
36 </outputs>
37
38 <tests>
39 <test>
40 <param name="input" ftype="txt" value="input.txt" />
41 <param name="expand_3prime" value="0" />
42 <param name="expand_5prime" value="0" />
43 <param name="type_selector" value="genomic" />
44 <output name="output" file="sequences.fasta" />
45 </test>
46 </tests>
47
48 <help>
49 <![CDATA[
50 **What it does**
51
52 Retrieves FASTA sequences from Ensembl using its REST API.
53
54 Uses the `"POST sequence/id"`_ API endpoint.
55
56 .. _"POST sequence/id": http://rest.ensembl.org/documentation/info/sequence_id_post
57 ]]>
58 </help>
59 <citations>
60 </citations>
61 </tool>