# HG changeset patch
# User fabad
# Date 1462224571 14400
# Node ID dcfcb9a2836003e450823e28ee6313bbcf2a91da
# Parent  48c6cb07caf3e8a0fc7505d8ea8744810059e980
Uploaded

diff -r 48c6cb07caf3 -r dcfcb9a28360 sparql_uniprot.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sparql_uniprot.xml	Mon May 02 17:29:31 2016 -0400
@@ -0,0 +1,56 @@
+<tool id="sparql_uniprot" name="Uniprot Sparql" version="0.1.0">
+  <description>Perform a search into uniprot database using its sparql interface.</description>
+  <requirements>
+    <requirement type="python-module" version="1.7.6">SPARQLWrapper</requirement>
+  </requirements>
+  <command interpreter="python">sparql_uniprot.py "${protein}" "${proteinName}" "${geneName}" "${organismName}" "${diseaseAnnotation}" "${domainName}" "${similarityAnnotation}" "${locationAnnotation}" "${functionAnnotation}" "${pharmaceuticalAnnotation}" "${output}"</command>
+  <inputs>
+    <param name="protein" type="text" label="Uniprot Identifier"/>
+
+    <param name="proteinName" type="text" label="Protein Name">
+	<!-- sanitizer para que nos deje usar el caracter $ -->
+	<sanitizer sanitize="False"/>
+    </param>
+
+    <param name="geneName" type="text" label="Gene Name">
+	<sanitizer sanitize="False"/>
+    </param>
+
+    <param name="organismName" type="text" label="Organism">
+	<sanitizer sanitize="False"/>
+    </param>
+
+    <param name="diseaseAnnotation" type="text" label="Disease Annotation">
+	<sanitizer sanitize="False"/>
+    </param>
+
+    <param name="domainName" type="text" label="Domain">
+	<sanitizer sanitize="False"/>
+    </param>
+
+    <param name="similarityAnnotation" type="text" label="Similarity Annotation">
+	<sanitizer sanitize="False"/>
+    </param>
+
+    <param name="locationAnnotation" type="text" label="Location Annotation">
+	<sanitizer sanitize="False"/>
+    </param>
+
+    <param name="functionAnnotation" type="text" label="Function Annotation">
+	<sanitizer sanitize="False"/>
+    </param>
+
+    <param name="pharmaceuticalAnnotation" type="text" label="Pharmaceutical Annotation">
+	<sanitizer sanitize="False"/>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <help>
+	With this tool you can search proteins using regular expressions by the following fields: uniprot identifier, protein name, gene name , organism name, disease annotation, domain name, similarity annotation, location annotation, function annotation or pharmaceutical annotationText. You can fill the fields you want and the tool will return all the data found in uniprot by filling the other fields. Results will be stored in a tabular format. If you want to search the exact match of a field you should use ^parameter$, for example ^insulin$.
+  </help>
+
+</tool>