--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderCentroided.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,102 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="1.12.0">
+  <description>Detects two-dimensional features in LC-MS data.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FeatureFinderCentroided</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FeatureFinderCentroided
+
+-in ${param_in}
+-out ${param_out}
+-seeds ${param_seeds}
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:intensity:bins ${param_bins}
+-algorithm:mass_trace:mz_tolerance ${param_mz_tolerance}
+-algorithm:mass_trace:min_spectra ${param_min_spectra}
+-algorithm:mass_trace:max_missing ${param_max_missing}
+-algorithm:mass_trace:slope_bound ${param_slope_bound}
+-algorithm:isotopic_pattern:charge_low ${param_charge_low}
+-algorithm:isotopic_pattern:charge_high ${param_charge_high}
+-algorithm:isotopic_pattern:mz_tolerance ${param_mz_tolerance}
+-algorithm:seed:min_score ${param_min_score}
+-algorithm:feature:min_score ${param_min_score}
+-algorithm:feature:reported_mz ${param_reported_mz}
+-algorithm:user-seed:rt_tolerance ${param_rt_tolerance}
+-algorithm:user-seed:mz_tolerance ${param_mz_tolerance}
+-algorithm:user-seed:min_score ${param_min_score}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -out_mzq ${adv_opts.param_out_mzq}
+    -algorithm:debug:pseudo_rt_shift ${adv_opts.param_pseudo_rt_shift}
+    -algorithm:isotopic_pattern:intensity_percentage ${adv_opts.param_intensity_percentage}
+    -algorithm:isotopic_pattern:intensity_percentage_optional ${adv_opts.param_intensity_percentage_optional}
+    -algorithm:isotopic_pattern:optional_fit_improvement ${adv_opts.param_optional_fit_improvement}
+    -algorithm:isotopic_pattern:mass_window_width ${adv_opts.param_mass_window_width}
+    -algorithm:isotopic_pattern:abundance_12C ${adv_opts.param_abundance_12C}
+    -algorithm:isotopic_pattern:abundance_14N ${adv_opts.param_abundance_14N}
+    -algorithm:fit:max_iterations ${adv_opts.param_max_iterations}
+    -algorithm:feature:min_isotope_fit ${adv_opts.param_min_isotope_fit}
+    -algorithm:feature:min_trace_score ${adv_opts.param_min_trace_score}
+    -algorithm:feature:min_rt_span ${adv_opts.param_min_rt_span}
+    -algorithm:feature:max_rt_span ${adv_opts.param_max_rt_span}
+    -algorithm:feature:rt_shape ${adv_opts.param_rt_shape}
+    -algorithm:feature:max_intersection ${adv_opts.param_max_intersection}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML" optional="False" label="input file" help="(-in)"/>
+    <param name="param_seeds" type="data" format="featureXML" optional="True" label="User specified seed list" help="(-seeds)"/>
+    <param name="param_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map." help="(-bins)"/>
+    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!" help="(-mz_tolerance)"/>
+    <param name="param_min_spectra" type="integer" min="1" optional="True" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace." help="(-min_spectra)"/>
+    <param name="param_max_missing" type="integer" min="0" optional="True" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below 'min_spectra'!" help="(-max_missing)"/>
+    <param name="param_slope_bound" type="float" min="0.0" optional="True" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to seperate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot." help="(-slope_bound)"/>
+    <param name="param_charge_low" type="integer" min="1" optional="True" value="1" label="Lowest charge to search for." help="(-charge_low)"/>
+    <param name="param_charge_high" type="integer" min="1" optional="True" value="4" label="Highest charge to search for." help="(-charge_high)"/>
+    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!" help="(-mz_tolerance)"/>
+    <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum seed score a peak has to reach to be used as seed.#br#The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.#br#If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score." help="(-min_score)"/>
+    <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="Feature score threshold for a feature to be reported.#br#The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks." help="(-min_score)"/>
+    <param name="param_reported_mz" type="select" optional="True" value="monoisotopic" label="The mass type that is reported for features.#br#'maximum' returns the m/z value of the highest mass trace.#br#'average' returns the intensity-weighted average m/z value of all contained peaks.#br#'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model." help="(-reported_mz)">
+      <option value="maximum">maximum</option>
+      <option value="average">average</option>
+      <option value="monoisotopic">monoisotopic</option>
+    </param>
+    <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position." help="(-rt_tolerance)"/>
+    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position." help="(-mz_tolerance)"/>
+    <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case." help="(-min_score)"/>
+    <expand macro="advanced_options">
+      <param name="param_pseudo_rt_shift" type="float" min="1.0" optional="True" value="500.0" label="Pseudo RT shift used when ." help="(-pseudo_rt_shift)"/>
+      <param name="param_intensity_percentage" type="float" min="0.0" max="100.0" optional="True" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present." help="(-intensity_percentage)"/>
+      <param name="param_intensity_percentage_optional" type="float" min="0.0" max="100.0" optional="True" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing." help="(-intensity_percentage_optional)"/>
+      <param name="param_optional_fit_improvement" type="float" min="0.0" max="100.0" optional="True" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak." help="(-optional_fit_improvement)"/>
+      <param name="param_mass_window_width" type="float" min="1.0" max="200.0" optional="True" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions." help="(-mass_window_width)"/>
+      <param name="param_abundance_12C" type="float" min="0.0" max="100.0" optional="True" value="98.93" label="Rel. abundance of the light carbon. Modify if labeled." help="(-abundance_12C)"/>
+      <param name="param_abundance_14N" type="float" min="0.0" max="100.0" optional="True" value="99.632" label="Rel. abundance of the light nitrogen. Modify if labeled." help="(-abundance_14N)"/>
+      <param name="param_max_iterations" type="integer" min="1" optional="True" value="500" label="Maximum number of iterations of the fit." help="(-max_iterations)"/>
+      <param name="param_min_isotope_fit" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum isotope fit of the feature before model fitting." help="(-min_isotope_fit)"/>
+      <param name="param_min_trace_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Trace score threshold.#br#Traces below this threshold are removed after the model fitting.#br#This parameter is important for features that overlap in m/z dimension." help="(-min_trace_score)"/>
+      <param name="param_min_rt_span" type="float" min="0.0" max="1.0" optional="True" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting." help="(-min_rt_span)"/>
+      <param name="param_max_rt_span" type="float" min="0.5" optional="True" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have." help="(-max_rt_span)"/>
+      <param name="param_rt_shape" type="select" optional="True" value="symmetric" label="Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used." help="(-rt_shape)">
+        <option value="symmetric">symmetric</option>
+        <option value="asymmetric">asymmetric</option>
+      </param>
+      <param name="param_max_intersection" type="float" min="0.0" max="1.0" optional="True" value="0.35" label="Maximum allowed intersection of features." help="(-max_intersection)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file" format="featureXML"/>
+    <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/>
+  </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_FeatureFinderCentroided.html
+
+@REFERENCES@
+</help>
+</tool>