--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PeakPickerWavelet.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,119 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="1.12.0">
+  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
+  <macros>
+    <token name="@EXECUTABLE@">PeakPickerWavelet</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PeakPickerWavelet
+
+-in ${param_in}
+-out ${param_out}
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:signal_to_noise ${param_signal_to_noise}
+-algorithm:peak_width ${param_peak_width}
+${param_estimate_peak_width}
+#if $adv_opts.adv_opts_selector=='advanced':
+    ${adv_opts.param_write_peak_meta_data}
+    -algorithm:centroid_percentage ${adv_opts.param_centroid_percentage}
+    -algorithm:fwhm_lower_bound_factor ${adv_opts.param_fwhm_lower_bound_factor}
+    -algorithm:fwhm_upper_bound_factor ${adv_opts.param_fwhm_upper_bound_factor}
+    -algorithm:optimization:iterations ${adv_opts.param_iterations}
+    -algorithm:optimization:penalties:position ${adv_opts.param_position}
+    -algorithm:optimization:penalties:left_width ${adv_opts.param_left_width}
+    -algorithm:optimization:penalties:right_width ${adv_opts.param_right_width}
+    -algorithm:optimization:penalties:height ${adv_opts.param_height}
+    -algorithm:optimization:2d:tolerance_mz ${adv_opts.param_tolerance_mz}
+    -algorithm:optimization:2d:max_peak_distance ${adv_opts.param_max_peak_distance}
+    -algorithm:thresholds:peak_bound ${adv_opts.param_peak_bound}
+    -algorithm:thresholds:peak_bound_ms2_level ${adv_opts.param_peak_bound_ms2_level}
+    -algorithm:thresholds:correlation ${adv_opts.param_correlation}
+    -algorithm:thresholds:noise_level ${adv_opts.param_noise_level}
+    -algorithm:thresholds:search_radius ${adv_opts.param_search_radius}
+    -algorithm:wavelet_transform:spacing ${adv_opts.param_spacing}
+    ${adv_opts.param_deconvolution}
+    -algorithm:deconvolution:asym_threshold ${adv_opts.param_asym_threshold}
+    -algorithm:deconvolution:left_width ${adv_opts.param_left_width}
+    -algorithm:deconvolution:right_width ${adv_opts.param_right_width}
+    -algorithm:deconvolution:scaling ${adv_opts.param_scaling}
+    -algorithm:deconvolution:fitting:fwhm_threshold ${adv_opts.param_fwhm_threshold}
+    -algorithm:deconvolution:fitting:eps_abs ${adv_opts.param_eps_abs}
+    -algorithm:deconvolution:fitting:eps_rel ${adv_opts.param_eps_rel}
+    -algorithm:deconvolution:fitting:max_iteration ${adv_opts.param_max_iteration}
+    -algorithm:deconvolution:fitting:penalties:position ${adv_opts.param_position}
+    -algorithm:deconvolution:fitting:penalties:height ${adv_opts.param_height}
+    -algorithm:deconvolution:fitting:penalties:left_width ${adv_opts.param_left_width}
+    -algorithm:deconvolution:fitting:penalties:right_width ${adv_opts.param_right_width}
+    -algorithm:SignalToNoiseEstimationParameter:max_intensity ${adv_opts.param_max_intensity}
+    -algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+    -algorithm:SignalToNoiseEstimationParameter:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+    -algorithm:SignalToNoiseEstimationParameter:auto_mode ${adv_opts.param_auto_mode}
+    -algorithm:SignalToNoiseEstimationParameter:win_len ${adv_opts.param_win_len}
+    -algorithm:SignalToNoiseEstimationParameter:bin_count ${adv_opts.param_bin_count}
+    -algorithm:SignalToNoiseEstimationParameter:stdev_mp ${adv_opts.param_stdev_mp}
+    -algorithm:SignalToNoiseEstimationParameter:min_required_elements ${adv_opts.param_min_required_elements}
+    -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML" optional="False" label="input profile data file " help="(-in)"/>
+    <param name="param_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal to noise ratio for a peak to be picked." help="(-signal_to_noise)"/>
+    <param name="param_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks." help="(-peak_width)"/>
+    <param name="param_estimate_peak_width" type="boolean" truevalue="-algorithm:estimate_peak_width true" falsevalue="-algorithm:estimate_peak_width false" checked="false" optional="True" label="Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored." help="(-estimate_peak_width)"/>
+    <expand macro="advanced_options">
+      <param name="param_write_peak_meta_data" type="boolean" truevalue="-write_peak_meta_data true" falsevalue="-write_peak_meta_data false" checked="false" optional="True" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file.Attention: this can blow up files,as 7 arrays are stored per spectrum!" help="(-write_peak_meta_data)"/>
+      <param name="param_centroid_percentage" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid. If it is 1 the centroid position corresponds to the position of the highest intensity." help="(-centroid_percentage)"/>
+      <param name="param_fwhm_lower_bound_factor" type="float" min="0.0" optional="True" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded." help="(-fwhm_lower_bound_factor)"/>
+      <param name="param_fwhm_upper_bound_factor" type="float" min="0.0" optional="True" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width. All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded." help="(-fwhm_upper_bound_factor)"/>
+      <param name="param_iterations" type="integer" min="1" optional="True" value="400" label="maximal number of iterations for the fitting step" help="(-iterations)"/>
+      <param name="param_position" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized " help="(-position)"/>
+      <param name="param_left_width" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized." help="(-left_width)"/>
+      <param name="param_right_width" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized." help="(-right_width)"/>
+      <param name="param_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized." help="(-height)"/>
+      <param name="param_tolerance_mz" type="float" min="0.0" optional="True" value="2.2" label="mz tolerance for cluster construction" help="(-tolerance_mz)"/>
+      <param name="param_max_peak_distance" type="float" min="0.0" optional="True" value="1.2" label="maximal peak distance in mz in a cluster" help="(-max_peak_distance)"/>
+      <param name="param_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity." help="(-peak_bound)"/>
+      <param name="param_peak_bound_ms2_level" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity for MS/MS peaks." help="(-peak_bound_ms2_level)"/>
+      <param name="param_correlation" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped." help="(-correlation)"/>
+      <param name="param_noise_level" type="float" min="0.0" optional="True" value="0.1" label="noise level for the search of the peak endpoints." help="(-noise_level)"/>
+      <param name="param_search_radius" type="integer" min="0" optional="True" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help="(-search_radius)"/>
+      <param name="param_spacing" type="float" min="0.0" optional="True" value="0.001" label="spacing of the cwt." help="(-spacing)"/>
+      <param name="param_deconvolution" type="boolean" truevalue="-algorithm:deconvolution:deconvolution true" falsevalue="-algorithm:deconvolution:deconvolution false" checked="false" optional="True" label="If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;" help="(-deconvolution)"/>
+      <param name="param_asym_threshold" type="float" min="0.0" optional="True" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started." help="(-asym_threshold)"/>
+      <param name="param_left_width" type="float" min="0.0" optional="True" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step." help="(-left_width)"/>
+      <param name="param_right_width" type="float" min="0.0" optional="True" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step." help="(-right_width)"/>
+      <param name="param_scaling" type="float" min="0.0" optional="True" value="0.12" label="Initial scaling of the cwt used in the seperation of heavily overlapping peaks. The initial value is used for charge 1, for higher charges it is adapted to scaling/charge." help="(-scaling)"/>
+      <param name="param_fwhm_threshold" type="float" min="0.0" optional="True" value="0.7" label="If the fwhm of a peak is higher than fwhm_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started." help="(-fwhm_threshold)"/>
+      <param name="param_eps_abs" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the absolute error gets smaller than this value the fitting is stopped." help="(-eps_abs)"/>
+      <param name="param_eps_rel" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the relative error gets smaller than this value the fitting is stopped." help="(-eps_rel)"/>
+      <param name="param_max_iteration" type="integer" min="1" optional="True" value="10" label="maximal number of iterations for the fitting step" help="(-max_iteration)"/>
+      <param name="param_position" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule." help="(-position)"/>
+      <param name="param_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized." help="(-height)"/>
+      <param name="param_left_width" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized." help="(-left_width)"/>
+      <param name="param_right_width" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized." help="(-right_width)"/>
+      <param name="param_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)." help="(-max_intensity)"/>
+      <param name="param_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor)"/>
+      <param name="param_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile)"/>
+      <param name="param_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode)"/>
+      <param name="param_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len)"/>
+      <param name="param_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count)"/>
+      <param name="param_stdev_mp" type="float" min="0.01" max="999.0" optional="True" value="3.0" label="multiplier for stdev" help="(-stdev_mp)"/>
+      <param name="param_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements)"/>
+      <param name="param_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output peak file " format="mzML"/>
+  </outputs>
+  <help>**What it does**
+
+Finds mass spectrometric peaks in profile mass spectra.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html
+
+@REFERENCES@
+</help>
+</tool>