--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathChromatogramExtractor.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,110 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.0.0">
+  <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
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_tr:
+  -tr $param_tr
+#end if
+#if $param_rt_norm:
+  -rt_norm $param_rt_norm
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_min_upper_edge_dist:
+  -min_upper_edge_dist $param_min_upper_edge_dist
+#end if
+#if $param_mz_window:
+  -mz_window $param_mz_window
+#end if
+#if $param_rt_window:
+  -rt_window $param_rt_window
+#end if
+#if $param_is_swath:
+  -is_swath
+#end if
+#if $param_ppm:
+  -ppm
+#end if
+#if $param_extract_MS1:
+  -extract_MS1
+#end if
+#if $param_extraction_function:
+  -extraction_function
+  #if " " in str($param_extraction_function):
+    "$param_extraction_function"
+  #else
+    $param_extraction_function
+  #end if
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_model_type:
+  -model:type
+  #if " " in str($param_model_type):
+    "$param_model_type"
+  #else
+    $param_model_type
+  #end if
+#end if
+#if $param_model_symmetric_regression:
+  -model:symmetric_regression
+#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="mzml" 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_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
+    <param name="param_rt_norm" type="data" format="trafoxml" 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," help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side"/>
+    <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," help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
+    <param name="param_is_swath" type="boolean" truevalue="-is_swath" falsevalue="" 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" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
+    <param name="param_extract_MS1" type="boolean" truevalue="-extract_MS1" falsevalue="" 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_model_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_model_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
+    <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**
+
+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</help>
+  <expand macro="references"/>
+</tool>