--- a/EICExtractor.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/EICExtractor.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,55 +1,104 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="EICExtractor" name="EICExtractor" version="1.12.0">
-  <description>Extracts intensities from dedicates positions in a LC/MS map</description>
-  <macros>
-    <token name="@EXECUTABLE@">EICExtractor</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>EICExtractor
+<?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: [Quantitation]-->
+  <tool id="EICExtractor" name="EICExtractor" version="2.0.0">
+    <description>Extracts intensities from dedicates positions in a LC/MS map</description>
+    <macros>
+      <token name="@EXECUTABLE@">EICExtractor</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>EICExtractor
 
--in ${param_in}
--in_header ${param_in_header}
--pos ${param_pos}
--rt_tol ${param_rt_tol}
--mz_tol ${param_mz_tol}
--rt_collect ${param_rt_collect}
--out ${param_out}
--threads \${GALAXY_SLOTS:-24} 
-${param_enabled}
+-in
+  #for token in $param_in:
+    $token
+  #end for
+-in_header
+  #for token in $param_in_header:
+    $token
+  #end for
+#if $param_pos:
+  -pos $param_pos
+#end if
+#if $param_rt_tol:
+  -rt_tol $param_rt_tol
+#end if
+#if $param_mz_tol:
+  -mz_tol $param_mz_tol
+#end if
+#if $param_rt_collect:
+  -rt_collect $param_rt_collect
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_auto_rt_enabled:
+  -auto_rt:enabled
+#end if
+#if $param_auto_rt_out_debug_TIC:
+  -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    -out_separator ${adv_opts.param_out_separator}
-    -auto_rt:FHWM ${adv_opts.param_FHWM}
-    -auto_rt:SNThreshold ${adv_opts.param_SNThreshold}
-    -auto_rt:out_debug_TIC ${adv_opts.param_out_debug_TIC}
+    #if $adv_opts.param_out_separator:
+  -out_separator     &quot;$adv_opts.param_out_separator&quot;
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_auto_rt_FHWM:
+  -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM
+#end if
+    #if $adv_opts.param_auto_rt_SNThreshold:
+  -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input raw data file" help="(-in)"/>
-    <param name="param_in_header" type="data" format="txt" optional="True" size="20" label="[for Waters data only] Read additional information from _HEADER.TXT. Provide one for each raw input file." help="(-in_header)"/>
-    <param name="param_pos" type="data" format="" optional="False" label="Input config file stating where to find signal" help="(-pos)"/>
-    <param name="param_rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol)"/>
-    <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol)"/>
-    <param name="param_rt_collect" type="integer" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help="(-rt_collect)"/>
-    <param name="param_enabled" type="boolean" truevalue="-auto_rt:enabled true" falsevalue="-auto_rt:enabled false" checked="false" optional="True" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations." help="(-enabled)"/>
-    <expand macro="advanced_options">
-      <param name="param_out_separator" type="text" size="20" value="," label="Separator character for output CSV file." help="(-out_separator)"/>
-      <param name="param_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]. Gaussian smoothing filter with this width is applied to TIC." help="(-FHWM)"/>
-      <param name="param_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking. Higher thesholds will result in less peaks." help="(-SNThreshold)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output quantitation file (multiple columns for each input compound)" format="tabular"/>
-    <data name="param_out_debug_TIC" label="Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions" format="mzML"/>
-  </outputs>
-  <help>**What it does**
-
-Extracts intensities from dedicates positions in a LC/MS map
+    <inputs>
+      <param format="mzml" help="(-in) " label="Input raw data file" 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="txt" help="(-in_header) Provide one for each raw input file" label="[for Waters data only] Read additional information from _HEADER.TXT" multiple="true" name="param_in_header" optional="True" size="30" type="data">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param format="tabular" help="(-pos) " label="Input config file stating where to find signal" name="param_pos" optional="False" type="data"/>
+      <param help="(-rt_tol) " label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" name="param_rt_tol" type="float" value="3.0"/>
+      <param help="(-mz_tol) " label="m/z tolerance in [ppm] for finding a peak" name="param_mz_tol" type="float" value="10.0"/>
+      <param help="(-rt_collect) " label="# of scans up &amp; down in RT from highest point for ppm estimation in result" name="param_rt_collect" type="integer" value="1"/>
+      <param checked="false" falsevalue="" help="(-enabled) " label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" name="param_auto_rt_enabled" optional="True" truevalue="-auto_rt:enabled" type="boolean"/>
+      <expand macro="advanced_options">
+        <param help="(-out_separator) " label="Separator character for output CSV file" name="param_out_separator" size="30" type="text" value=",">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC" label="Expected full width at half-maximum of each raw RT peak in [s]" name="param_auto_rt_FHWM" type="float" value="5.0"/>
+        <param help="(-SNThreshold) Higher thesholds will result in less peaks" label="S/N threshold for a smoothed raw peak to pass peak picking" name="param_auto_rt_SNThreshold" type="float" value="5.0"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="param_out"/>
+      <data format="mzml" name="param_auto_rt_out_debug_TIC"/>
+    </outputs>
+    <help>Extracts intensities from dedicates positions in a LC/MS map
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html</help>
+  </tool>