--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FileMerger.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,90 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="FileMerger" name="FileMerger" version="2.0.0">
+  <description>Merges several MS files into one file.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FileMerger</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FileMerger
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_annotate_file_origin:
+  -annotate_file_origin
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_raw_rt_auto:
+  -raw:rt_auto
+#end if
+
+#if $rep_param_raw_rt_custom:
+-raw:rt_custom
+  #for token in $rep_param_raw_rt_custom:
+    #if " " in str(token):
+      "$token.param_raw_rt_custom"
+    #else
+      $token.param_raw_rt_custom
+    #end if
+  #end for
+#end if
+#if $param_raw_rt_filename:
+  -raw:rt_filename
+#end if
+#if $param_raw_ms_level:
+  -raw:ms_level $param_raw_ms_level
+#end if
+#if $param_raw_user_ms_level:
+  -raw:user_ms_level
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mgf,mzml,mzxml,traml,featurexml,consensusxml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_annotate_file_origin" 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_raw_rt_auto" 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" 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 given input file">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_raw_rt_filename" type="boolean" truevalue="-raw:rt_filename" falsevalue="" checked="false" optional="True" label="If this flag is set FileMerger tries to guess the rt of the file name" help="(-rt_filename) &lt;br&gt;This option is useful for merging DTA file, which should contain the string &lt;br&gt;'rt' directly followed by a floating point number: &lt;br&gt;i.e. my_spectrum_rt2795.15.dta"/>
+    <param name="param_raw_ms_level" type="integer" value="2" label="This option is useful for use with DTA files which does not contain MS level information" help="(-ms_level) The given level is assigned to the spectra"/>
+    <param name="param_raw_user_ms_level" type="boolean" truevalue="-raw:user_ms_level" falsevalue="" checked="false" optional="True" label="If this flag is set, the MS level given above is used" help="(-user_ms_level) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="featurexml"/>
+  </outputs>
+  <help>**What it does**
+
+Merges several MS files into one file.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html</help>
+  <expand macro="references"/>
+</tool>