--- a/FeatureFinderMRM.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FeatureFinderMRM.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,47 +1,65 @@
-<?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
+<?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="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="references"/>
+    <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 $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':
-    -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}
+    #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_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.
+    <inputs>
+      <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param help="(-min_rt_distance) " label="Minimal distance of MRM features in seconds" min="0.0" name="param_algorithm_min_rt_distance" optional="True" type="float" value="10.0"/>
+      <param help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise" label="Minimal S/N ratio a peak must have to be taken into account" min="0.0" name="param_algorithm_min_signal_to_noise_ratio" optional="True" type="float" value="2.0"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-min_num_peaks_per_feature) " label="Minimal number of peaks which are needed for a single feature" min="1" name="param_algorithm_min_num_peaks_per_feature" optional="True" type="integer" value="5"/>
+        <param checked="false" falsevalue="" help="(-write_debug_files) " label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" name="param_algorithm_write_debug_files" optional="True" truevalue="-algorithm:write_debug_files" type="boolean"/>
+        <param checked="false" falsevalue="" help="(-resample_traces) " 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" name="param_algorithm_resample_traces" optional="True" truevalue="-algorithm:resample_traces" type="boolean"/>
+        <param checked="false" falsevalue="" help="(-write_debuginfo) " label="If set to true, debug messages are written, the output can be somewhat lengthy" name="param_algorithm_write_debuginfo" optional="True" truevalue="-algorithm:write_debuginfo" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+    </outputs>
+    <help>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>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html</help>
+  </tool>