--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TOFCalibration.xml	Wed Mar 01 12:30:10 2017 -0500
@@ -0,0 +1,220 @@
+<?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: [Signal processing and preprocessing]-->
+<tool id="TOFCalibration" name="TOFCalibration" version="2.1.0">
+  <description>Applies time of flight calibration.</description>
+  <macros>
+    <token name="@EXECUTABLE@">TOFCalibration</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>TOFCalibration
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_ext_calibrants:
+  -ext_calibrants $param_ext_calibrants
+#end if
+#if $param_ref_masses:
+  -ref_masses $param_ref_masses
+#end if
+#if $param_tof_const:
+  -tof_const $param_tof_const
+#end if
+#if $param_peak_data:
+  -peak_data
+#end if
+#if $param_algorithm_PeakPicker_signal_to_noise:
+  -algorithm:PeakPicker:signal_to_noise $param_algorithm_PeakPicker_signal_to_noise
+#end if
+#if $param_algorithm_PeakPicker_peak_width:
+  -algorithm:PeakPicker:peak_width $param_algorithm_PeakPicker_peak_width
+#end if
+#if $param_algorithm_PeakPicker_estimate_peak_width:
+  -algorithm:PeakPicker:estimate_peak_width
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_centroid_percentage:
+  -algorithm:PeakPicker:centroid_percentage $adv_opts.param_algorithm_PeakPicker_centroid_percentage
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor:
+  -algorithm:PeakPicker:fwhm_lower_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor:
+  -algorithm:PeakPicker:fwhm_upper_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_optimization_iterations:
+  -algorithm:PeakPicker:optimization:iterations $adv_opts.param_algorithm_PeakPicker_optimization_iterations
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position:
+  -algorithm:PeakPicker:optimization:penalties:position $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width:
+  -algorithm:PeakPicker:optimization:penalties:left_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width:
+  -algorithm:PeakPicker:optimization:penalties:right_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height:
+  -algorithm:PeakPicker:optimization:penalties:height $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz:
+  -algorithm:PeakPicker:optimization:2d:tolerance_mz $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance:
+  -algorithm:PeakPicker:optimization:2d:max_peak_distance $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound:
+  -algorithm:PeakPicker:thresholds:peak_bound $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level:
+  -algorithm:PeakPicker:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_thresholds_correlation:
+  -algorithm:PeakPicker:thresholds:correlation $adv_opts.param_algorithm_PeakPicker_thresholds_correlation
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level:
+  -algorithm:PeakPicker:thresholds:noise_level $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius:
+  -algorithm:PeakPicker:thresholds:search_radius $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing:
+  -algorithm:PeakPicker:wavelet_transform:spacing $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_deconvolution:
+  -algorithm:PeakPicker:deconvolution:deconvolution
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold:
+  -algorithm:PeakPicker:deconvolution:asym_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width:
+  -algorithm:PeakPicker:deconvolution:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width:
+  -algorithm:PeakPicker:deconvolution:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling:
+  -algorithm:PeakPicker:deconvolution:scaling $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold:
+  -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs:
+  -algorithm:PeakPicker:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel:
+  -algorithm:PeakPicker:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration:
+  -algorithm:PeakPicker:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position:
+  -algorithm:PeakPicker:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height:
+  -algorithm:PeakPicker:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width:
+  -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width:
+  -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements
+#end if
+    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window:
+  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="input peak or raw data file" help="(-in) "/>
+    <param name="param_ext_calibrants" type="data" format="mzml" optional="False" label="input file containing the external calibrant spectra (peak or raw data)" help="(-ext_calibrants) "/>
+    <param name="param_ref_masses" type="data" format="txt" optional="False" label="input file containing reference masses of the external calibrant spectra (one per line)" help="(-ref_masses) "/>
+    <param name="param_tof_const" type="data" format="tabular" optional="False" label="File containing TOF conversion constants" help="(-tof_const) These can be either two or three constants &lt;br&gt;per set, depending on the conversion type. Either one set for all calibrant spectra  &lt;br&gt;(tab separated), or one for each spectrum. &lt;br&gt;For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)"/>
+    <param name="param_peak_data" display="radio" type="boolean" truevalue="-peak_data" falsevalue="" checked="false" optional="True" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help="(-peak_data) "/>
+    <param name="param_algorithm_PeakPicker_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_algorithm_PeakPicker_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks" help="(-peak_width) "/>
+    <param name="param_algorithm_PeakPicker_estimate_peak_width" display="radio" type="boolean" truevalue="-algorithm:PeakPicker:estimate_peak_width" falsevalue="" checked="false" optional="True" label="Flag if the average peak width shall be estimated" help="(-estimate_peak_width) Attention: when this flag is set, the peak_width is ignored"/>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_algorithm_PeakPicker_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" help="(-centroid_percentage) If it is 1 the centroid position corresponds to the position of the highest intensity"/>
+      <param name="param_algorithm_PeakPicker_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" help="(-fwhm_lower_bound_factor) All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
+      <param name="param_algorithm_PeakPicker_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" help="(-fwhm_upper_bound_factor) All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
+      <param name="param_algorithm_PeakPicker_optimization_iterations" type="integer" min="1" optional="True" value="400" label="maximal number of iterations for the fitting step" help="(-iterations) "/>
+      <param name="param_algorithm_PeakPicker_optimization_penalties_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_algorithm_PeakPicker_optimization_penalties_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_algorithm_PeakPicker_optimization_penalties_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_algorithm_PeakPicker_optimization_penalties_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_algorithm_PeakPicker_optimization_2d_tolerance_mz" type="float" min="0.0" optional="True" value="2.2" label="mz tolerance for cluster construction" help="(-tolerance_mz) "/>
+      <param name="param_algorithm_PeakPicker_optimization_2d_max_peak_distance" type="float" min="0.0" optional="True" value="1.2" label="maximal peak distance in mz in a cluste" help="(-max_peak_distance) "/>
+      <param name="param_algorithm_PeakPicker_thresholds_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity" help="(-peak_bound) "/>
+      <param name="param_algorithm_PeakPicker_thresholds_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_algorithm_PeakPicker_thresholds_correlation" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="minimal correlation of a peak and the raw signal" help="(-correlation) If a peak has a lower correlation it is skipped"/>
+      <param name="param_algorithm_PeakPicker_thresholds_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_algorithm_PeakPicker_thresholds_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_algorithm_PeakPicker_wavelet_transform_spacing" type="float" min="0.0" optional="True" value="0.001" label="Spacing of the CWT" help="(-spacing) Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
+      <param name="param_algorithm_PeakPicker_deconvolution_deconvolution" display="radio" type="boolean" truevalue="-algorithm:PeakPicker:deconvolution:deconvolution" falsevalue="" 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_algorithm_PeakPicker_deconvolution_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_algorithm_PeakPicker_deconvolution_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_algorithm_PeakPicker_deconvolution_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_algorithm_PeakPicker_deconvolution_scaling" type="float" min="0.0" optional="True" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="(-scaling) The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
+      <param name="param_algorithm_PeakPicker_deconvolution_fitting_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_algorithm_PeakPicker_deconvolution_fitting_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_algorithm_PeakPicker_deconvolution_fitting_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_algorithm_PeakPicker_deconvolution_fitting_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_algorithm_PeakPicker_deconvolution_fitting_penalties_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_algorithm_PeakPicker_deconvolution_fitting_penalties_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_algorithm_PeakPicker_deconvolution_fitting_penalties_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_algorithm_PeakPicker_deconvolution_fitting_penalties_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_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) 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)"/>
+      <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_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_algorithm_PeakPicker_SignalToNoiseEstimationParameter_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_algorithm_PeakPicker_SignalToNoiseEstimationParameter_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_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/>
+      <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/>
+      <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_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_algorithm_PeakPicker_SignalToNoiseEstimationParameter_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_algorithm_PeakPicker_SignalToNoiseEstimationParameter_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" format="mzml"/>
+  </outputs>
+  <help>Applies time of flight calibration.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html</help>
+</tool>