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

New dir structure, README improved, tests added and RDF merge tool created

<tool id="sadi_generic" name="SADI services generic caller" version="0.0.1">
	<description>Send any input RDF to any SADI service</description>
	
	<command>${__tool_data_path__}/shared/errwrap.sh java -Xmx2000M -Xms250M -jar ${__tool_data_path__}/shared/jars/sadi_generic_client.jar $url $input > $output </command>
		
	<inputs>
		<param name="url" type="text" size="250" label="Service URL">
		  <sanitizer sanitize="False"/><!-- Disable sanitizer for URLs with e.g. tilde character -->
		</param>
		<param name="input" type="data" format="rdf" label="RDF input for SADI service"/>	
	</inputs>
	<outputs>
		<data format="rdf" name="output" />
	</outputs>
	<tests>
		<test>
			<param name="url" type="text" size="200" value="http://sadiframework.org/examples/hello" label="Service URL"/>
			<param name="input" type="data" format="rdf" label="hello-input.rdf"/>
			<!--<output name="output" file="test_hello_output.rdf" ftype="rdf"/>-->
			
			<output name="output">
				<assert_contents>
					<is_valid_xml />
					<has_text text="http://sadiframework.org/examples/hello.owl#GreetedIndividual" />
				</assert_contents>
			</output>
		</test>
		<test>
			<param name="url" type="text" size="200" value="http://sadiframework.org/examples/pdb2uniprot" label="Service URL"/>
			<param name="input" type="data" format="rdf" label="pdb2uniprot-input.rdf"/>
<!-- 			<output name="output" file="" ftype="rdf"/> -->

			<output name="output">
				<assert_contents>
					<is_valid_xml />
					<has_text text="http://sadiframework.org/examples/pdb2uniprot.owl#OutputClass" />
				</assert_contents>
			</output>
		</test>
		<test>
			<param name="url" type="text" size="200" value="http://sadiframework.org/examples/uniprotInfo" label="Service URL"/>
			<param name="input" type="data" format="rdf" label="uniprotInfot-input.rdf"/>
<!-- 			<output name="output" file="" ftype="rdf"/> -->

			<output name="output">
				<assert_contents>
					<is_valid_xml />
					<has_text text="http://sadiframework.org/examples/uniprotInfo.owl#AnnotatedUniProtRecord" />
				</assert_contents>
			</output>
		</test>
		<test>
			<param name="url" type="text" size="200" value="http://dev.biordf.net/~kawas/cgi-bin/getdbSNPRecordByUniprotID" label="Service URL"/>
			<param name="input" type="data" format="rdf" label="dbSNPUniprotInput.rdf"/>
<!-- 			<output name="output" file="" ftype="rdf"/> -->

			<output name="output">
				<assert_contents>
					<is_valid_xml />
					<has_text text="http://purl.oclc.org/SADI/LSRN/dbSNP_Identifier" />
				</assert_contents>
			</output>
		</test>
		<test>
			<param name="url" type="text" size="200" value="http://localhost:9090#" label="Service URL"/>
			<param name="input" type="data" format="rdf" label="hello-input-localhost-SADI.rdf"/>
			<output name="output" file="hello-output-localhost-SADI.rdf" ftype="rdf"/>
		</test>
		
		
		
	</tests>
	
	<help>
	  
	  **What it does**
	  
	  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. 
	  
	  **About**
	  
	  More information and contact: http://github.com/mikel-egana-aranguren/SADI-Galaxy
	  
	</help>
</tool>