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comparison genotype-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-genotype-associations" name="Genotype 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/genotype/$input/$association/?rows=$rows&fetch_objects=true' > $output 7 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/genotype/$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="Genotype (e.g. ZFIN:ZDB-FISH-150901-4286)" /> 10 <param name="input" type="text" format="txt" multiple="false" label="Genotype (e.g. dbSNPIndividual:12141)" />
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 </option> 12 <option value="diseases">Diseases </option>
13 <option value="genes">Genes</option> 13 <option value="genes">Genes</option>
14 <option value="genotypes">Genotypes</option> 14 <option value="genotypes">Genotypes</option>
15 <option value="phenotypes">Phenotypes</option> 15 <option value="phenotypes">Phenotypes</option>
16 </param> 16 </param>
17 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/> 17 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
18 </inputs> 18 </inputs>
19 <outputs> 19 <expand macro="outputs" />
20 <data name="output" format="json" />
21 </outputs>
22 <tests> 20 <tests>
23 <test> 21 <test>
24 <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/> 22 <param name="input" value="dbSNPIndividual:12141"/>
25 <param name="association" value="diseases"/> 23 <param name="association" value="diseases"/>
26 <output name="output" file="diseases-for-genotype.json"/> 24 <output name="output" file="diseases-for-genotype.json"/>
27 </test> 25 </test>
28 <test> 26 <test>
29 <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/> 27 <param name="input" value="dbSNPIndividual:12141"/>
30 <param name="association" value="genes"/> 28 <param name="association" value="genes"/>
31 <output name="output" file="genes-for-genotype.json"/> 29 <output name="output" file="genes-for-genotype.json"/>
32 </test> 30 </test>
33 <test> 31 <test>
34 <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/> 32 <param name="input" value="dbSNPIndividual:12141"/>
35 <param name="association" value="genotypes"/> 33 <param name="association" value="genotypes"/>
36 <output name="output" file="genotypes-for-genotype.json"/> 34 <output name="output" file="genotypes-for-genotype.json"/>
37 </test> 35 </test>
38 <test> 36 <test>
39 <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/> 37 <param name="input" value="dbSNPIndividual:12141"/>
40 <param name="association" value="phenotypes"/> 38 <param name="association" value="phenotypes"/>
41 <output name="output" file="phenotypes-for-genotype.json"/> 39 <output name="output" file="phenotypes-for-genotype.json"/>
42 </test> 40 </test>
43 </tests> 41 </tests>
44 <help><![CDATA[ 42 <expand macro="citations" />
45 Pulls data from Monarch Initiative BioLink API web services as JSON.
46 https://api.monarchinitiative.org/api/
47 ]]></help>
48 <citations>
49 <citation type="doi">doi:10.5281/zenodo.56412</citation>
50 </citations>
51 </tool> 43 </tool>