Mercurial > repos > iracooke > tpp_prophets

diff protxml_to_table.xml @ 14:d90c8bc10a9c draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:55:19 -0400
parents 4c66453a168e
children 0746a2ae9e04
line wrap: on
line diff
--- a/protxml_to_table.xml	Tue Jul 01 11:16:41 2014 -0400
+++ b/protxml_to_table.xml	Thu Mar 26 19:55:19 2015 -0400
@@ -1,12 +1,14 @@
-<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.0.1">
+<tool id="protxml_to_table_1" name="ProtXML 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>
 
 	<description>Converts a ProtXML file to a table</description>
 
 	<command>
 		protxml_to_table.rb 
+	  	$invert_probs
 
 		$input_file 
 		-o $output 
@@ -15,7 +17,7 @@
 	<inputs>	
 		
 		<param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/>
-
+	    <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
 	</inputs>
 
 
@@ -23,6 +25,18 @@
 		<data format="tabular" name="output" />
 	</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_pproph_protproph.prot.xml" format="protxml"/>
+	      <output name="output" format="tabular">
+	          <assert_contents>
+	              <has_text text="AVQKYLTAHEQSK" />
+	          </assert_contents>
+	      </output>
+	  </test>
+	</tests>
+
 
   <help>