Mercurial > repos > nathandunn > biolinkmonarchinitiative

comparison gene-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-genotype-associations" name="Genotype Associations" version="0.1.0"> 1 <tool id="monarch-gene-associations" name="Gene 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/gene/$input/$association/?rows=$rows&fetch_objects=true' > $output 7 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/gene/$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="Gene"/> 10 <param name="input" type="text" format="txt" multiple="false" label="Gene"/>
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="diseases">Diseases (e.g,. NCBIGene:4750, Orphanet:173505)</option> 12 <option value="diseases">Diseases (e.g,. NCBIGene:4750, Orphanet:173505)</option>
15 <option value="interactions">Interactions (e.g,. NCBIGene:4750, Orphanet:173505)</option> 15 <option value="interactions">Interactions (e.g,. NCBIGene:4750, Orphanet:173505)</option>
16 <option value="phenotypes">Phenotypes (e.g,. NCBIGene:4750, Orphanet:173505)</option> 16 <option value="phenotypes">Phenotypes (e.g,. NCBIGene:4750, Orphanet:173505)</option>
17 </param> 17 </param>
18 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/> 18 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
19 </inputs> 19 </inputs>
20 <outputs> 20 <expand macro="outputs" />
21 <data name="output" format="json"/>
22 </outputs>
23 <tests> 21 <tests>
24 <test> 22 <test>
25 <param name="input" value="NCBIGene:4750"/> 23 <param name="input" value="NCBIGene:4750"/>
26 <param name="association" value="diseases"/> 24 <param name="association" value="diseases"/>
27 <output name="output" file="diseases-for-gene.json"/> 25 <output name="output" file="diseases-for-gene.json"/>
45 <param name="input" value="NCBIGene:4750"/> 43 <param name="input" value="NCBIGene:4750"/>
46 <param name="association" value="phenotypes"/> 44 <param name="association" value="phenotypes"/>
47 <output name="output" file="phenotypes-for-gene.json"/> 45 <output name="output" file="phenotypes-for-gene.json"/>
48 </test> 46 </test>
49 </tests> 47 </tests>
50 <help><![CDATA[ 48 <expand macro="citations" />
51 Pulls data from Monarch Initiative BioLink API web services as JSON.
52 https://api.monarchinitiative.org/api/
53 ]]></help>
54 <citations>
55 <citation type="doi">doi:10.5281/zenodo.56412</citation>
56 </citations>
57 </tool> 49 </tool>