--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMRM.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,65 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="2.0.0">
+  <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
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_algorithm_min_rt_distance:
+  -algorithm:min_rt_distance $param_algorithm_min_rt_distance
+#end if
+#if $param_algorithm_min_signal_to_noise_ratio:
+  -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_min_num_peaks_per_feature:
+  -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature
+#end if
+    #if $adv_opts.param_algorithm_write_debug_files:
+  -algorithm:write_debug_files
+#end if
+    #if $adv_opts.param_algorithm_resample_traces:
+  -algorithm:resample_traces
+#end if
+    #if $adv_opts.param_algorithm_write_debuginfo:
+  -algorithm:write_debuginfo
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
+    <param name="param_algorithm_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_algorithm_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" help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise"/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_algorithm_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_algorithm_write_debug_files" type="boolean" truevalue="-algorithm:write_debug_files" falsevalue="" 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_algorithm_resample_traces" type="boolean" truevalue="-algorithm:resample_traces" falsevalue="" 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_algorithm_write_debuginfo" type="boolean" truevalue="-algorithm:write_debuginfo" falsevalue="" 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" 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</help>
+  <expand macro="references"/>
+</tool>