--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EICExtractor.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,55 @@
+<?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
+
+-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}
+#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}
+#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
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html
+
+@REFERENCES@
+</help>
+</tool>