--- a/OpenSwathChromatogramExtractor.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/OpenSwathChromatogramExtractor.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,60 +1,110 @@
-<?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
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Targeted Experiments]-->
+  <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="references"/>
+    <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}
+-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 $param_extraction_function:
+  -extraction_function
+  #if &quot; &quot; in str($param_extraction_function):
+    &quot;$param_extraction_function&quot;
+  #else
+    $param_extraction_function
+  #end if
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_model_type:
+  -model:type
+  #if &quot; &quot; in str($param_model_type):
+    &quot;$param_model_type&quot;
+  #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" 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.
+    <inputs>
+      <param format="mzml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param format="tabular,traml" help="(-tr) " label="transition file ('TraML' or 'csv')" name="param_tr" optional="False" type="data"/>
+      <param format="trafoxml" help="(-rt_norm) " label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" name="param_rt_norm" optional="True" type="data"/>
+      <param help="(-min_upper_edge_dist) " label="Minimal distance to the edge to still consider a precursor, in Thomson" name="param_min_upper_edge_dist" type="float" value="0.0"/>
+      <param help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," min="0.0" name="param_mz_window" optional="True" type="float" value="0.05"/>
+      <param help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," name="param_rt_window" type="float" value="-1.0"/>
+      <param checked="false" falsevalue="" help="(-is_swath) " label="Set this flag if the data is SWATH data" name="param_is_swath" optional="True" truevalue="-is_swath" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-ppm) " label="m/z extraction_window is in ppm" name="param_ppm" optional="True" truevalue="-ppm" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-extract_MS1) " label="Extract the MS1 transitions based on the precursor values in the TraML file" name="param_extract_MS1" optional="True" truevalue="-extract_MS1" type="boolean"/>
+      <param help="(-extraction_function) " label="Function used to extract the signal" name="param_extraction_function" optional="True" type="select" value="tophat">
+        <option value="tophat">tophat</option>
+        <option value="bartlett">bartlett</option>
+      </param>
+      <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="linear">
+        <option value="linear">linear</option>
+        <option value="b_spline">b_spline</option>
+        <option value="interpolated">interpolated</option>
+      </param>
+      <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" name="param_model_symmetric_regression" optional="True" truevalue="-model:symmetric_regression" type="boolean"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="mzml" name="param_out"/>
+    </outputs>
+    <help>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>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html</help>
+  </tool>