Mercurial > repos > nathandunn > biolinkmonarchinitiative

comparison get-object.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
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1:8fdad43e4250 2:88e1bd76b069
1 <tool id="monarch-get-object" name="Get Object" version="0.1.0"> 1 <tool id="monarch-get-object" name="Get Object" 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/$type$input$associations?rows=$rows&fetch_objects=true' > $output 7 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/$type$input$associations?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="Object ID" /> 10 <param name="input" type="text" format="txt" multiple="false" label="Object ID" />
11 <param name="type" type="select" multiple="false" display="radio" label="Type"> 11 <param name="type" type="select" multiple="false" display="radio" label="Type">
12 <option value="">Any</option> 12 <option value="">Any</option>
17 <option value="/associations/">True</option> 17 <option value="/associations/">True</option>
18 <option value="" checked="true">False</option> 18 <option value="" checked="true">False</option>
19 </param> 19 </param>
20 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/> 20 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
21 </inputs> 21 </inputs>
22 <outputs> 22 <expand macro="outputs" />
23 <data name="output" format="json" />
24 </outputs>
25 <tests> 23 <tests>
26 <test> 24 <test>
27 <param name="input" value="OMIM:605543"/> 25 <param name="input" value="OMIM:605543"/>
28 <param name="type" value=""/> 26 <param name="type" value=""/>
29 <output name="output" file="bioentity-object-for-disease.json"/> 27 <output name="output" file="bioentity-object-for-disease.json"/>
43 <param name="input" value="ZFIN:ZDB-FISH-150901-6607"/> 41 <param name="input" value="ZFIN:ZDB-FISH-150901-6607"/>
44 <param name="association" value="genotype/"/> 42 <param name="association" value="genotype/"/>
45 <output name="output" file="bioentity-object-for-genotype.json"/> 43 <output name="output" file="bioentity-object-for-genotype.json"/>
46 </test> 44 </test>
47 </tests> 45 </tests>
48 <help><![CDATA[ 46 <expand macro="citations" />
49 Pulls data from Monarch Initiative BioLink API web services as JSON.
50 https://api.monarchinitiative.org/api/
51 ]]></help>
52 <citations>
53 <citation type="doi">doi:10.5281/zenodo.56412</citation>
54 </citations>
55 </tool> 47 </tool>
56 48