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comparison associations.xml @ 0:028a3ffc17b4 draft

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planemo upload commit b095175f34e78ceded24a6e1da99b328f50db86d
author nathandunn
date Fri, 23 Jun 2017 15:04:12 -0400
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children 66ece4fd024f
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-1:000000000000 0:028a3ffc17b4
1 <tool id="planteome-associations" name="Associations" version="0.1.0">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="frontmatter" />
6 <command><![CDATA[
7 #if $type == 'find'
8 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/?rows=$rows&fetch_objects=true&subject=$subject' > $output
9 #else if $type == 'from'
10 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$subject?rows=$rows&fetch_objects=true' > $output
11 #else if $type == 'to'
12 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$object?rows=$rows&fetch_objects=true' > $output
13 #else if $type == 'between'
14 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output
15 #end if
16 ]]></command>
17 <inputs>
18 <param name="subject" type="text" format="txt" multiple="false" label="Subject"/>
19 <param name="object" type="text" format="txt" multiple="false" label="Object"/>
20 <param name="type" type="select" multiple="false" display="radio" label="Type">
21 <option value="find">Find (subject)</option>
22 <option value="from">From (subject)</option>
23 <option value="to">To (object)</option>
24 <option value="between">Between (subject -> object)</option>
25 </param>
26 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
27 </inputs>
28 <expand macro="outputs" />
29 <tests>
30 <test>
31 <param name="subject" value="NCBIGene:84570"/>
32 <param name="type" value="find"/>
33 <output name="output" file="find-associations-for-subject.json"/>
34 </test>
35 <test>
36 <param name="subject" value="NCBIGene:84570"/>
37 <param name="type" value="from"/>
38 <output name="output" file="from-associations-for-subject.json"/>
39 </test>
40 <test>
41 <param name="object" value="MP:0013765"/>
42 <param name="type" value="to"/>
43 <output name="output" file="to-associations-for-object.json"/>
44 </test>
45 <test>
46 <param name="subject" value="MGI:1342287"/>
47 <param name="object" value="MP:0013765"/>
48 <param name="type" value="between"/>
49 <output name="output" file="between-associations.json"/>
50 </test>
51 </tests>
52 <expand macro="citations" />
53 </tool>
54