# HG changeset patch
# User galaxyp
# Date 1503053372 14400
# Node ID 33e3f62dcf237cf7f3d44ade117b558b71afdae2
# Parent  07121f8410b9307728be5c0ca0c88e5a3da7147d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ba082ee3343087740aaa741120b1f575646183a4

diff -r 07121f8410b9 -r 33e3f62dcf23 FileMerger.xml
--- a/FileMerger.xml	Mon Aug 07 14:33:57 2017 -0400
+++ b/FileMerger.xml	Fri Aug 18 06:49:32 2017 -0400
@@ -26,16 +26,6 @@
   -rt_concat:gap $param_rt_concat_gap
 #end if
 
-#if $rep_param_rt_concat_trafo_out:
--rt_concat:trafo_out
-  #for token in $rep_param_rt_concat_trafo_out:
-    #if " " in str(token):
-      "$token.param_rt_concat_trafo_out"
-    #else
-      $token.param_rt_concat_trafo_out
-    #end if
-  #end for
-#end if
 #if $param_raw_rt_auto:
   -raw:rt_auto
 #end if
@@ -74,8 +64,8 @@
     <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/>
     <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value &gt; 0 is set"/>
     <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/>
-    <repeat name="rep_param_raw_rt_custom" min="0" max="1" title="param_raw_rt_custom">
-      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
+    <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom">
+      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="Custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
         <sanitizer>
           <valid initial="string.printable">
             <remove value="'"/>
@@ -91,8 +81,7 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="featurexml"/>
-    <data name="param_rt_concat_trafo_out" format="trafoxml"/>
+    <data name="param_out" format="mzml"/>
   </outputs>
   <help>Merges several MS files into one file.