Mercurial > repos > nathandunn > biolinkmonarchinitiative

comparison associations.xml @ 2:88e1bd76b069 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
author nathandunn
date Thu, 22 Jun 2017 15:28:43 -0400
parents 4f6fba8332ec
children
comparison
equal deleted inserted replaced
1:8fdad43e4250 2:88e1bd76b069
1 <tool id="monarch-associations" name="Associations" version="0.1.0"> 1 <tool id="monarch-associations" name="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 #if $type == 'find' 7 #if $type == 'find'
8 curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/?rows=$rows&fetch_objects=true&subject=$subject' > $output 8 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/?rows=$rows&fetch_objects=true&subject=$subject' > $output
9 #else if $type == 'from' 9 #else if $type == 'from'
10 curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$subject?rows=$rows&fetch_objects=true' > $output 10 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$subject?rows=$rows&fetch_objects=true' > $output
11 #else if $type == 'to' 11 #else if $type == 'to'
12 curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$object?rows=$rows&fetch_objects=true' > $output 12 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$object?rows=$rows&fetch_objects=true' > $output
13 #else if $type == 'between' 13 #else if $type == 'between'
14 curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output 14 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output
15 #end if 15 #end if
16 ]]></command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <param name="subject" type="text" format="txt" multiple="false" label="Subject"/> 18 <param name="subject" type="text" format="txt" multiple="false" label="Subject"/>
19 <param name="object" type="text" format="txt" multiple="false" label="Object"/> 19 <param name="object" type="text" format="txt" multiple="false" label="Object"/>
23 <option value="to">To (object)</option> 23 <option value="to">To (object)</option>
24 <option value="between">Between (subject -> object)</option> 24 <option value="between">Between (subject -> object)</option>
25 </param> 25 </param>
26 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/> 26 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
27 </inputs> 27 </inputs>
28 <outputs> 28 <expand macro="outputs" />
29 <data name="output" format="json"/>
30 </outputs>
31 <tests> 29 <tests>
32 <test> 30 <test>
33 <param name="subject" value="NCBIGene:84570"/> 31 <param name="subject" value="NCBIGene:84570"/>
34 <param name="type" value="find"/> 32 <param name="type" value="find"/>
35 <output name="output" file="find-associations-for-subject.json"/> 33 <output name="output" file="find-associations-for-subject.json"/>
49 <param name="object" value="MP:0013765"/> 47 <param name="object" value="MP:0013765"/>
50 <param name="type" value="between"/> 48 <param name="type" value="between"/>
51 <output name="output" file="between-associations.json"/> 49 <output name="output" file="between-associations.json"/>
52 </test> 50 </test>
53 </tests> 51 </tests>
54 <help><![CDATA[ 52 <expand macro="citations" />
55 Pulls data from Monarch Initiative BioLink API web services as JSON.
56 https://api.monarchinitiative.org/api/
57 ]]></help>
58 <citations>
59 <citation type="doi">doi:10.5281/zenodo.56412</citation>
60 </citations>
61 </tool> 53 </tool>
62 54