# HG changeset patch
# User galaxyp
# Date 1537570143 14400
# Node ID 992b0d5a7c6fbb8261a81897796d12cbc5359872
# Parent  9575b93e03f75e91e04aa07372e950ea74768853
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a9276f2d097976168059eb91e18cf280ef7a45bb

diff -r 9575b93e03f7 -r 992b0d5a7c6f thermo_converter.xml
--- a/thermo_converter.xml	Fri Sep 14 18:03:57 2018 -0400
+++ b/thermo_converter.xml	Fri Sep 21 18:49:03 2018 -0400
@@ -11,7 +11,7 @@
 ThermoRawFileParser.sh
     -i=input.raw
     -o=./
-    -f=1
+    -f=$output_format
     #if $metadata:
         --metadata=1
     #end if
@@ -21,9 +21,17 @@
         <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" />
         <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False"
             label="Output metadata" help="" />
+        <param name="output_format" type="select" label="Choose an output format">
+            <option value="0">mgf</option>
+            <option value="1" selected="True">mzml</option>
+        </param>
     </inputs>
     <outputs>
-        <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}" />
+        <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}">
+            <change_format>
+                <when input="output_format" value="0" format="mgf" />
+            </change_format>
+        </data>
         <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata">
             <filter>metadata</filter>
         </data>
@@ -35,6 +43,13 @@
                 <has_text text="ThermoRawFileParser.sh"/>
             </assert_command>
         </test>
+        <test>
+            <param name="input" value="fake_input.txt"/>
+            <param name="output_format" value="0"/>
+            <assert_command>
+                <has_text text="-f=0"/>
+            </assert_command>
+        </test>
     </tests>
     <help>
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