diff pepxml_to_table.xml @ 14:d90c8bc10a9c draft

Docker support and update for protk 1.4

--- a/pepxml_to_table.xml	Tue Jul 01 11:16:41 2014 -0400
+++ b/pepxml_to_table.xml	Thu Mar 26 19:55:19 2015 -0400
@@ -1,7 +1,8 @@
-<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.1">
+<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.0">
 
 	<requirements>
-	    <requirement type="package" version="1.3">protk</requirement>
+            <container type="docker">iracooke/protk-1.4.1</container>
+	    <requirement type="package" version="1.4">protk</requirement>
    </requirements>
 
 
@@ -10,18 +11,33 @@
 
 
 <!-- Note .. the input file is assumed to be the first argument -->
-<command>pepxml_to_table.rb $input_file -o $output</command>
+<command>pepxml_to_table.rb $input_file -o $output $invert_probs</command>
 
 
 <inputs>
 
 	<param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml"  multiple="false" label="Input File" help="A pepXML file"/>
+    <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
 
 </inputs>
 <outputs>
 	<data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" />
 </outputs>
 
+	
+	<tests>
+	  <!-- Just test that the tool runs and produces vaguely correct output -->
+	  <test>
+	      <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/>
+	      <output name="output" format="csv">
+	          <assert_contents>
+	              <has_text text="ANTNNYAPKSSR" />
+	          </assert_contents>
+	      </output>
+	  </test>
+	</tests>
+
+
 <help>
 	Convert a pepXML file to Tab delimited text
 </help>