--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MRMMapper.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,57 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="MRMMapper" name="MRMMapper" version="2.0.0">
+  <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
+  <macros>
+    <token name="@EXECUTABLE@">MRMMapper</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MRMMapper
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_tr:
+  -tr $param_tr
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_precursor_tolerance:
+  -precursor_tolerance $param_precursor_tolerance
+#end if
+#if $param_product_tolerance:
+  -product_tolerance $param_product_tolerance
+#end if
+#if $param_no_strict:
+  -no-strict
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#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="mzml" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in) "/>
+    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
+    <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance) "/>
+    <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance) "/>
+    <param name="param_no_strict" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/>
+    <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="mzml"/>
+  </outputs>
+  <help>**What it does**
+
+MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html</help>
+  <expand macro="references"/>
+</tool>