--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EICExtractor.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,104 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>EICExtractor
+
+-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':
+    #if $adv_opts.param_out_separator:
+  -out_separator     "$adv_opts.param_out_separator"
+#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" multiple="true" optional="False" size="30" label="Input raw data file" help="(-in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_in_header" type="data" format="txt" multiple="true" optional="True" size="30" label="[for Waters data only] Read additional information from _HEADER.TXT" help="(-in_header) Provide one for each raw input file">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_pos" type="data" format="tabular" 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_auto_rt_enabled" type="boolean" truevalue="-auto_rt:enabled" falsevalue="" 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="30" value="," label="Separator character for output CSV file" help="(-out_separator) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_auto_rt_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC"/>
+      <param name="param_auto_rt_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="(-SNThreshold) Higher thesholds will result in less peaks"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="tabular"/>
+    <data name="param_auto_rt_out_debug_TIC" format="mzml"/>
+  </outputs>
+  <help>**What it does**
+
+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</help>
+  <expand macro="references"/>
+</tool>