--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathChromatogramExtractor.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,60 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="1.12.0">
+  <description>Extract chromatograms (XIC) from a MS2 map file.</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathChromatogramExtractor
+
+-in ${param_in}
+-tr ${param_tr}
+-rt_norm ${param_rt_norm}
+-out ${param_out}
+-min_upper_edge_dist ${param_min_upper_edge_dist}
+-mz_window ${param_mz_window}
+-rt_window ${param_rt_window}
+${param_is_swath}
+${param_ppm}
+${param_extract_MS1}
+-extraction_function ${param_extraction_function}
+-threads \${GALAXY_SLOTS:-24} 
+-model:type ${param_type}
+${param_symmetric_regression}
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
+    <param name="param_tr" type="data" format="tabular" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr)"/>
+    <param name="param_rt_norm" type="data" format="" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm)"/>
+    <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist)"/>
+    <param name="param_mz_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size, e.g. 100 ppm would extract 50 ppm on either side." help="(-mz_window)"/>
+    <param name="param_rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side." help="(-rt_window)"/>
+    <param name="param_is_swath" type="boolean" truevalue="-is_swath true" falsevalue="-is_swath false" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath)"/>
+    <param name="param_ppm" type="boolean" truevalue="-ppm true" falsevalue="-ppm false" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm)"/>
+    <param name="param_extract_MS1" type="boolean" truevalue="-extract_MS1 true" falsevalue="-extract_MS1 false" checked="false" optional="True" label="Extract the MS1 transitions based on the precursor values in the TraML file" help="(-extract_MS1)"/>
+    <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function)">
+      <option value="tophat">tophat</option>
+      <option value="bartlett">bartlett</option>
+    </param>
+    <param name="param_type" type="select" optional="True" value="linear" label="Type of model" help="(-type)">
+      <option value="linear">linear</option>
+      <option value="b_spline">b_spline</option>
+      <option value="interpolated">interpolated</option>
+    </param>
+    <param name="param_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression true" falsevalue="-model:symmetric_regression false" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file" format="mzML"/>
+  </outputs>
+  <help>**What it does**
+
+Extract chromatograms (XIC) from a MS2 map file.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html
+
+@REFERENCES@
+</help>
+</tool>