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comparison variant-associations.xml @ 0:028a3ffc17b4 draft

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planemo upload commit b095175f34e78ceded24a6e1da99b328f50db86d
author nathandunn
date Fri, 23 Jun 2017 15:04:12 -0400
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-1:000000000000 0:028a3ffc17b4
1 <tool id="planteome-variant-associations" name="Variant Associations" version="0.1.0">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="frontmatter" />
6 <command><![CDATA[
7 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/bioentity/variant/$input/$association/?rows=$rows&fetch_objects=true' > $output
8 ]]></command>
9 <inputs>
10 <param name="input" type="text" format="txt" multiple="false" label="Variant (e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783)" />
11 <param name="association" type="select" multiple="false" display="radio" label="Type">
12 <option value="genes">Genes</option>
13 <option value="genotypes">Genotypes</option>
14 <option value="phenotypes">Phenotypes</option>
15 </param>
16 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
17 </inputs>
18 <expand macro="outputs" />
19 <tests>
20 <test>
21 <param name="input" value="ZFIN:ZDB-ALT-010427-8"/>
22 <param name="association" value="genes"/>
23 <output name="output" file="genes-for-variant.json"/>
24 </test>
25 <test>
26 <param name="input" value="ZFIN:ZDB-ALT-010427-8"/>
27 <param name="association" value="genotypes"/>
28 <output name="output" file="genotypes-for-variant.json"/>
29 </test>
30 <test>
31 <param name="input" value="ClinVarVariant:65929"/>
32 <param name="association" value="phenotypes"/>
33 <output name="output" file="phenotypes-for-variant.json"/>
34 </test>
35 </tests>
36 <expand macro="citations" />
37 </tool>
38