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comparison bulk-operations.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-bulk-operations" name="Bulk Operations" version="0.1.0">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="frontmatter" />
6 <command><![CDATA[
7 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/mart/$association/$object_category/$taxon?rows=$rows&fetch_objects=true' > $output
8 ]]></command>
9 <inputs>
10 <param name="taxon" type="text" format="txt" multiple="false" label="Taxon (e.g. NCBITaxon:9606)"/>
11 <param name="object_category" type="text" format="txt" multiple="false" label="Object Category (e.g. phenotype, disease)"/>
12 <param name="association" type="select" multiple="false" display="radio" label="Type">
13 <option value="gene">Gene</option>
14 <option value="disease">Disease</option>
15 <option value="case">Case</option>
16 </param>
17 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
18 </inputs>
19 <expand macro="outputs" />
20 <tests>
21 <!--NOTE: these take way too long to run because fo the large amount of data involved-->
22 <!--<test>-->
23 <!--<param name="type" value="gene"/>-->
24 <!--<param name="taxon" value="NCBITaxon:9606"/>-->
25 <!--<param name="rows" value="1"/>-->
26 <!--<param name="object_category" value="phenotype"/>-->
27 <!--<output name="output" file="gene-mart-for-phenotype.json"/>-->
28 <!--</test>-->
29 <!--<test>-->
30 <!--<param name="type" value="disease"/>-->
31 <!--<param name="taxon" value="NCBITaxon:9606"/>-->
32 <!--<param name="rows" value="1"/>-->
33 <!--<param name="object_category" value="phenotype"/>-->
34 <!--<output name="output" file="disease-mart-for-phenotype.json"/>-->
35 <!--</test>-->
36 <!--<test>-->
37 <!--<param name="type" value="case"/>-->
38 <!--<param name="taxon" value="NCBITaxon:9606"/>-->
39 <!--<param name="rows" value="1"/>-->
40 <!--<param name="object_category" value="phenotype"/>-->
41 <!--<output name="output" file="case-mart-for-phenotype.json"/>-->
42 <!--</test>-->
43 </tests>
44 <expand macro="citations" />
45 </tool>
46