Mercurial > repos > iracooke > tpp_prophets

diff protxml_to_table.xml @ 18:84b47300a4c8 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:46:16 -0400
parents b68f292b2904
children
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line diff
--- a/protxml_to_table.xml	Mon Jan 05 05:37:56 2015 -0500
+++ b/protxml_to_table.xml	Tue Oct 20 20:46:16 2015 -0400
@@ -1,37 +1,37 @@
-<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.0.1">
-	<requirements>
-            <container type="docker">simonalpha/protk:1.4.0</container>
-	    <requirement type="package" version="1.3">protk</requirement>
-   </requirements>
-
-	<description>Converts a ProtXML file to a table</description>
-
-	<command>
-		protxml_to_table.rb 
-	  	$invert_probs
-
-		$input_file 
-		-o $output 
-	</command>
-
-	<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>
-
-
-	<outputs>
-		<data format="tabular" name="output" />
-	</outputs>
-
-
-  <help>
-
+<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.1">
+    <description>Converts a ProtXML file to a table</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+    </requirements>
+    <command>
+        protxml_to_table.rb
+          $invert_probs
+        $input_file
+        -o $output
+    </command>
+    <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>
+    <outputs>
+        <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>
 **What it does**
 
 Converts a ProtXML file to a tab separated table 
 
-  </help>
-
+    </help>
 </tool>