Mercurial > repos > mikel-egana-aranguren > sadi_generic

comparison galaxy-dist/tools/SADI/sadi_generic.xml @ 2:977c838e3442 draft default tip

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New dir structure, README improved, tests added and RDF merge tool created
author mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
date Fri, 25 Apr 2014 14:41:12 +0200
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1:bb17b69a74c5 2:977c838e3442
1 <tool id="sadi_generic" name="SADI services generic caller" version="0.0.1">
2 <description>Send any input RDF to any SADI service</description>
3
4 <command>${__tool_data_path__}/shared/errwrap.sh java -Xmx2000M -Xms250M -jar ${__tool_data_path__}/shared/jars/sadi_generic_client.jar $url $input > $output </command>
5
6 <inputs>
7 <param name="url" type="text" size="250" label="Service URL">
8 <sanitizer sanitize="False"/><!-- Disable sanitizer for URLs with e.g. tilde character -->
9 </param>
10 <param name="input" type="data" format="rdf" label="RDF input for SADI service"/>
11 </inputs>
12 <outputs>
13 <data format="rdf" name="output" />
14 </outputs>
15 <tests>
16 <test>
17 <param name="url" type="text" size="200" value="http://sadiframework.org/examples/hello" label="Service URL"/>
18 <param name="input" type="data" format="rdf" label="hello-input.rdf"/>
19 <!--<output name="output" file="test_hello_output.rdf" ftype="rdf"/>-->
20
21 <output name="output">
22 <assert_contents>
23 <is_valid_xml />
24 <has_text text="http://sadiframework.org/examples/hello.owl#GreetedIndividual" />
25 </assert_contents>
26 </output>
27 </test>
28 <test>
29 <param name="url" type="text" size="200" value="http://sadiframework.org/examples/pdb2uniprot" label="Service URL"/>
30 <param name="input" type="data" format="rdf" label="pdb2uniprot-input.rdf"/>
31 <!-- <output name="output" file="" ftype="rdf"/> -->
32
33 <output name="output">
34 <assert_contents>
35 <is_valid_xml />
36 <has_text text="http://sadiframework.org/examples/pdb2uniprot.owl#OutputClass" />
37 </assert_contents>
38 </output>
39 </test>
40 <test>
41 <param name="url" type="text" size="200" value="http://sadiframework.org/examples/uniprotInfo" label="Service URL"/>
42 <param name="input" type="data" format="rdf" label="uniprotInfot-input.rdf"/>
43 <!-- <output name="output" file="" ftype="rdf"/> -->
44
45 <output name="output">
46 <assert_contents>
47 <is_valid_xml />
48 <has_text text="http://sadiframework.org/examples/uniprotInfo.owl#AnnotatedUniProtRecord" />
49 </assert_contents>
50 </output>
51 </test>
52 <test>
53 <param name="url" type="text" size="200" value="http://dev.biordf.net/~kawas/cgi-bin/getdbSNPRecordByUniprotID" label="Service URL"/>
54 <param name="input" type="data" format="rdf" label="dbSNPUniprotInput.rdf"/>
55 <!-- <output name="output" file="" ftype="rdf"/> -->
56
57 <output name="output">
58 <assert_contents>
59 <is_valid_xml />
60 <has_text text="http://purl.oclc.org/SADI/LSRN/dbSNP_Identifier" />
61 </assert_contents>
62 </output>
63 </test>
64 <test>
65 <param name="url" type="text" size="200" value="http://localhost:9090#" label="Service URL"/>
66 <param name="input" type="data" format="rdf" label="hello-input-localhost-SADI.rdf"/>
67 <output name="output" file="hello-output-localhost-SADI.rdf" ftype="rdf"/>
68 </test>
69
70
71
72 </tests>
73
74 <help>
75
76 **What it does**
77
78 Given an RDF input and a SADI service URL, infers whether the RDF complies with the service's input OWL Class and if so executes it, obtaining an ouput RDF from the SADI service.
79
80 **About**
81
82 More information and contact: http://github.com/mikel-egana-aranguren/SADI-Galaxy
83
84 </help>
85 </tool>