# HG changeset patch
# User galaxyp
# Date 1431566384 14400
# Node ID 60a33af520420948e84592aa045f4b69eb394079
# Parent  75537a09e9fad7fd6b40f33f1ee61bf0264d7f9f
Uploaded

diff -r 75537a09e9fa -r 60a33af52042 OpenSwathWorkflow.xml
--- a/OpenSwathWorkflow.xml	Wed May 13 18:33:49 2015 -0400
+++ b/OpenSwathWorkflow.xml	Wed May 13 21:19:44 2015 -0400
@@ -27,11 +27,10 @@
 #if $param_tr_irt:
   -tr_irt $param_tr_irt
 #end if
-#if $param_out_features:
-  -out_features $param_out_features
-#end if
-#if $param_out_tsv:
-  -out_tsv     "$param_out_tsv"
+#if $output_fmt == 'tsv':
+  -out_tsv "$out_tsv"
+#else:
+  -out_features "$out_features"
 #end if
 #if $param_out_chrom:
   -out_chrom $param_out_chrom
@@ -239,13 +238,9 @@
       <option value="csv">csv</option>
     </param>
     <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
-    <param name="param_out_tsv" type="text" size="30" label="TSV output file (mProphet compatible)" help="(-out_tsv) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="output_fmt" type="select" label="Select feature list output format">
+      <option value="featurexml">FeatureXML</option>
+      <option value="tsv">TSV output file (mProphet compatible)</option>
     </param>
     <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/>
     <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/>
@@ -345,7 +340,12 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out_features" format="featurexml"/>
+    <data name="out_features" format="featurexml">
+      <filter>output_fmt == 'featurexml'</filter>
+    </data>
+    <data name="out_tsv" format="tabular">
+      <filter>output_fmt == 'tsv'</filter>
+    </data>
     <data name="param_out_chrom" format="mzml"/>
   </outputs>
   <help>**What it does**