diff tandem_to_pepxml.xml @ 14:9d6e0ad4d600 draft

Docker support and update for protk 1.4

--- a/tandem_to_pepxml.xml	Tue Jul 01 11:06:33 2014 -0400
+++ b/tandem_to_pepxml.xml	Thu Mar 26 19:53:53 2015 -0400
@@ -1,25 +1,38 @@
-<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.0.1">
+<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.0">
 	<requirements>
-	    <requirement type="package" version="1.3.0">protk</requirement>
-	    <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
-   </requirements>
+         <container type="docker">iracooke/protk-1.4.1</container>
+	    <requirement type="package" version="1.4">protk</requirement>
+	    <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
+    </requirements>
 
-  <description>Converts a tandem result file to pepXML</description>
+	<description>Converts a tandem result file to pepXML</description>
 
-<command>
-	tandem_to_pepxml.rb $input_file -o $output 
-</command>
+	<command>
+		tandem_to_pepxml.rb $input_file -o $output 
+	</command>
+
+	<inputs>
+		<param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
+	</inputs>
 
-<inputs>
-	<param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
-</inputs>
+	<outputs>
+		<data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
+	</outputs>
+
+	<help>
+		Convert X!Tandem results to pepXML
+	</help>
 
-<outputs>
-	<data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
-</outputs>
-
-<help>
-	Convert X!Tandem results to pepXML
-</help>
+	<tests>
+		<!-- Just test that the tool runs and produces vaguely correct output -->
+		<test>
+		    <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/>
+		    <output name="output" format="raw_pepxml">
+		        <assert_contents>
+					<has_text text="SQVFQLESTFDV" />
+		        </assert_contents>
+		    </output>
+		</test>
+	</tests>
 
 </tool>