Mercurial > repos > iracooke > tpp_prophets

diff pepxml_to_table.xml @ 15:0746a2ae9e04 draft

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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 20:45:24 -0400
parents d90c8bc10a9c
children 1b86e378de37
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line diff
--- a/pepxml_to_table.xml	Thu Mar 26 19:55:19 2015 -0400
+++ b/pepxml_to_table.xml	Tue Oct 20 20:45:24 2015 -0400
@@ -1,45 +1,30 @@
-<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.0">
-
-	<requirements>
-            <container type="docker">iracooke/protk-1.4.1</container>
-	    <requirement type="package" version="1.4">protk</requirement>
-   </requirements>
-
-
-
-  <description>Converts a pepXML file to a tab delimited text file</description>
-
-
-<!-- Note .. the input file is assumed to be the first argument -->
-<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>
-
-
+<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.1">
+    <description>Converts a pepXML file to a tab delimited text file</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+    </requirements>
+    <!-- Note .. the input file is assumed to be the first argument -->
+    <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
+    Convert a pepXML file to Tab delimited text
 </help>
-
 </tool>