diff tools/SADI-Docker/SADI-Docker-tab2rdf.xml @ 0:54c48f9ca32b default tip

first release
author Mikel Egana <mikel.egana.aranguren@gmail.com>
date Fri, 04 Sep 2015 23:24:45 +0200
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/SADI-Docker/SADI-Docker-tab2rdf.xml	Fri Sep 04 23:24:45 2015 +0200
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+<tool id="SADI-Docker-tab2rdf" name="SADI - Tab-to-RDF" version="0.1">
+  
+  <!-- Modified by Mikel EgaƱa Aranguren, very hacky -->
+  
+  <description>Converter</description>
+  
+  	<requirements>
+	  <container type="docker">mikeleganaaranguren/sadi:v6</container>
+	</requirements>
+  <command>
+    #if $namespace.choose_namespace=="none"
+      python /sadi/tab2rdf.py $input_file $output_file $output_format none
+      #for $i in $triples
+        ${i.s_col} ${i.p_val} ${i.o_col} ${i.o_type}
+      #end for
+    #else
+      python /sadi/tab2rdf.py $input_file $output_file $output_format $namespace.choosen_namespace
+      #for $i in $triples
+        ${i.s_col} ${i.p_val} ${i.o_col} ${i.o_type}
+      #end for  
+    #end if
+  </command>
+  <inputs>
+    <param name="input_file" type="data" format="tabular" label="Input File (tabular)"/>
+    
+    <conditional name="namespace">
+      <param name="choose_namespace" type="select" label="Add namespace?">
+        <option value="none">No (The tab file includes complete URIs for each resource)</option>
+        <option value="yes_choose_namespace">Yes</option>
+      </param>
+      <when value="yes_choose_namespace">
+        <param name="choosen_namespace" type="text" size="50" value="http://localhost/" label="Namespace" />
+      </when>
+    </conditional>
+    
+    <param name="output_format" type="select" label="Output Format">
+      <option value="ntriples">N-Triples</option>
+      <option value="turtle">Turtle</option>
+      <option value="rdfxml">RDF/XML</option>
+    </param>
+    <repeat name="triples" title="Triples">
+      <param name="s_col" type="data_column" data_ref="input_file" label="Subject (column)" />
+      <param name="p_val" type="text" size="50" value="a" label="Predicate (text)">
+	<sanitizer sanitize="False"/>
+      </param>
+      <param name="o_col" type="data_column" data_ref="input_file" label="Object (column)" />
+      <param name="o_type" label="Check if this object is Literal (Keep unchecked if this object is URI)" type="boolean" truevalue="1" falsevalue="0" checked="False"/>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data name="output_file" format="rdf" label="${tool.name} on ${on_string}"/>
+  </outputs>
+  <help>
+    
+**Important note**
+
+This is a modified version of Tab2RDF, local to SADI-Docker-Galaxy (http://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy).
+
+**What it does**
+
+Sample Input::
+
+    name     age  superviser
+    Micheal  42   John
+    Anne     30   Micheal
+
+Sample Parameters::
+
+    Namespace - 'http://localhost/'
+    Triple 1 - c1 'age' c2(literal)
+    Triple 2 - c3 'supervises' c1(URI)
+
+Sample Output::
+
+    &lt;http://localhost/Michael&gt; &lt;http://localhost/age&gt; "42"
+    &lt;http://localhost/Anne&gt; &lt;http://localhost/age&gt; "30"
+    &lt;http://localhost/John&gt; &lt;http://localhost/supervises&gt; &lt;http://localhost/Micheal&gt;
+    &lt;http://localhost/Micheal&gt; &lt;http://localhost/supervises&gt; &lt;http://localhost/Anne&gt;
+
+**Output Format**
+
+Output RDF format is N-Triples by default.
+
+  </help>
+</tool>