--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMRM.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,47 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="1.12.0">
+  <description>Detects two-dimensional features in LC-MS data.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FeatureFinderMRM</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FeatureFinderMRM
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:min_rt_distance ${param_min_rt_distance}
+-algorithm:min_signal_to_noise_ratio ${param_min_signal_to_noise_ratio}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -algorithm:min_num_peaks_per_feature ${adv_opts.param_min_num_peaks_per_feature}
+    ${adv_opts.param_write_debug_files}
+    ${adv_opts.param_resample_traces}
+    ${adv_opts.param_write_debuginfo}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML" optional="False" label="input file" help="(-in)"/>
+    <param name="param_min_rt_distance" type="float" min="0.0" optional="True" value="10.0" label="Minimal distance of MRM features in seconds." help="(-min_rt_distance)"/>
+    <param name="param_min_signal_to_noise_ratio" type="float" min="0.0" optional="True" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise." help="(-min_signal_to_noise_ratio)"/>
+    <expand macro="advanced_options">
+      <param name="param_min_num_peaks_per_feature" type="integer" min="1" optional="True" value="5" label="Minimal number of peaks which are needed for a single feature" help="(-min_num_peaks_per_feature)"/>
+      <param name="param_write_debug_files" type="boolean" truevalue="-algorithm:write_debug_files true" falsevalue="-algorithm:write_debug_files false" checked="false" optional="True" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help="(-write_debug_files)"/>
+      <param name="param_resample_traces" type="boolean" truevalue="-algorithm:resample_traces true" falsevalue="-algorithm:resample_traces false" checked="false" optional="True" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help="(-resample_traces)"/>
+      <param name="param_write_debuginfo" type="boolean" truevalue="-algorithm:write_debuginfo true" falsevalue="-algorithm:write_debuginfo false" checked="false" optional="True" label="If set to true, debug messages are written, the output can be somewhat lengthy." help="(-write_debuginfo)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file" format="featureXML"/>
+  </outputs>
+  <help>**What it does**
+
+Detects two-dimensional features in LC-MS data.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html
+
+@REFERENCES@
+</help>
+</tool>