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comparison variant-associations.xml @ 2:88e1bd76b069 draft

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planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
author nathandunn
date Thu, 22 Jun 2017 15:28:43 -0400
parents 4f6fba8332ec
children
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1:8fdad43e4250 2:88e1bd76b069
1 <tool id="monarch-variant-associations" name="Variant Associations" version="0.1.0"> 1 <tool id="monarch-variant-associations" name="Variant Associations" version="0.1.0">
2 <requirements/> 2 <macros>
3 <stdio> 3 <import>macros.xml</import>
4 <exit_code range="1:" /> 4 </macros>
5 </stdio> 5 <expand macro="frontmatter" />
6 <command><![CDATA[ 6 <command><![CDATA[
7 curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/variant/$input/$association/?rows=$rows&fetch_objects=true' > $output 7 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/variant/$input/$association/?rows=$rows&fetch_objects=true' > $output
8 ]]></command> 8 ]]></command>
9 <inputs> 9 <inputs>
10 <param name="input" type="text" format="txt" multiple="false" label="Variant (e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783)" /> 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"> 11 <param name="association" type="select" multiple="false" display="radio" label="Type">
12 <option value="genes">Genes</option> 12 <option value="genes">Genes</option>
13 <option value="genotypes">Genotypes</option> 13 <option value="genotypes">Genotypes</option>
14 <option value="phenotypes">Phenotypes</option> 14 <option value="phenotypes">Phenotypes</option>
15 </param> 15 </param>
16 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/> 16 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
17 </inputs> 17 </inputs>
18 <outputs> 18 <expand macro="outputs" />
19 <data name="output" format="json" />
20 </outputs>
21 <tests> 19 <tests>
22 <test> 20 <test>
23 <param name="input" value="ZFIN:ZDB-ALT-010427-8"/> 21 <param name="input" value="ZFIN:ZDB-ALT-010427-8"/>
24 <param name="association" value="genes"/> 22 <param name="association" value="genes"/>
25 <output name="output" file="genes-for-variant.json"/> 23 <output name="output" file="genes-for-variant.json"/>
33 <param name="input" value="ClinVarVariant:65929"/> 31 <param name="input" value="ClinVarVariant:65929"/>
34 <param name="association" value="phenotypes"/> 32 <param name="association" value="phenotypes"/>
35 <output name="output" file="phenotypes-for-variant.json"/> 33 <output name="output" file="phenotypes-for-variant.json"/>
36 </test> 34 </test>
37 </tests> 35 </tests>
38 <help><![CDATA[ 36 <expand macro="citations" />
39 Pulls data from Monarch Initiative BioLink API web services as JSON.
40 https://api.monarchinitiative.org/api/
41 ]]></help>
42 <citations>
43 <citation type="doi">doi:10.5281/zenodo.56412</citation>
44 </citations>
45 </tool> 37 </tool>
46 38