Mercurial > repos > earlhaminst > ensembl_get_feature_info

comparison get_feature_info.xml @ 1:396f0f54d115 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
author earlhaminst
date Mon, 12 Dec 2016 07:47:09 -0500
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0:874c067e4527 1:396f0f54d115
1 <tool id="get_feature_info" name="Get features 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_feature_info.py
9 -e $expand
10 -f $format_selector
11 -i "$input"
12 -s $species_selector
13 > "$output"
14 ]]>
15 </command>
16
17 <inputs>
18 <param name="input" type="data" format="txt" label="List of Ensembl IDs" help="Max 1000 IDs" />
19 <param name="species_selector" type="select" label="Select species">
20 <option value="ensembl" selected="true">Vertebrates</option>
21 <option value="ensemblgenomes">Other species</option>
22 </param>
23 <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" />
24 <param name="format_selector" type="select" label="Output format">
25 <option value="full" selected="true">Full</option>
26 <option value="condensed">Condensed</option>
27 </param>
28 </inputs>
29
30 <outputs>
31 <data name="output" format="json" label="$(tool.name) on ${on_string}" />
32 </outputs>
33
34 <tests>
35 <test>
36 <param name="input" ftype="txt" value="input.txt" />
37 <param name="expand" value="false" />
38 <output name="outputFile" file="out.json" />
39 </test>
40 </tests>
41
42 <help>
43 <![CDATA[
44 **What it does**
45
46 Retrieve feature information in JSON format from Ensembl using its REST API.
47
48 Uses the `"POST lookup/id"`_ API endpoint.
49
50 .. _"POST lookup/id": http://rest.ensembl.org/documentation/info/lookup_post
51 ]]>
52 </help>
53 <citations>
54 </citations>
55 </tool>