<tool id="openms_peak_list_preprocessor" version="0.1" name="Peak List Preprocessor">
  <description>
    Wizard to apply multiple OpenMS signal preprocessing tools for peak lists.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <configfiles>
    <configfile name="setup_input">cp '$input' 'output.mzML'</configfile>
    <configfile name="rename">mv 'output.mzML' 'input.mzML'</configfile>
    <configfile name="copy_output">mv 'output.mzML' '$output'</configfile>
    <configfile name="resampler_config">[simple_options]
#if $resample.do
in=input.mzML
out=output.mzML
sampling_rate=$resample.sampling_rate
#end if
</configfile>
    <configfile name="noise_filter_config">[simple_options]
#set $noise_filter_type = str($noise.type)
in=input.mzML
out=output.mzML
#if $noise_filter_type == 'NoiseFilterGaussian'

#end if
#if $noise_filter_type == 'NoiseFilterSGolay'

#end if
    </configfile>
    <configfile name="baseline_config">[simple_options]
in=input.mzML
out=output.mzML
#if $baseline.do

#end if
    </configfile>
    <configfile name="peak_picker_config">[simple_options]
#set $peak_picker_type = str($peak_picker.type)
in=input.mzML
out=output.mzML
#if $peak_picker_type == 'PeakPickerHiRes'
algorithm!signal_to_noise=$peak_picker.signal_to_noise
algorithm!ms1_only=$peak_picker.ms1_only
#end if
#if $peak_picker_type == 'PeakPickerWavelet'
algorithm!signal_to_noise=$peak_picker.signal_to_noise
#if $peak_picker.peak_width.estimate
algorithm!estimate_peak_width=true
#else
algorithm!estimate_peak_width=false
algorithm!peak_width=$peak_picker.peak_width.peak_width
#end if
#end if
    </configfile>
    <configfile name="mass_corrector_config">[simple_options]
in=input.mzML
out=output.mzML
    </configfile>
    <configfile name="spectra_filter_config">[simple_options]
in=input.mzML
out=output.mzML
#set $spectra_filter_type = str($spectra_filter.type)
    </configfile>
  </configfiles>
  <command interpreter="python">
    openms_wrapper.py 
    --executable '__SHELL__' --config $setup_input
    #if $resample.do
    --executable '__SHELL__' --config $rename
    --executable 'Resampler' --config $resampler_config
    #end if
    #set $noise_filter_type = str($noise.type)
    #if $noise_filter_type != "none"
    --executable '__SHELL__' --config $rename
    --executable '$noise_filter_type' --config $noise_filter_config
    #end if
    #if $baseline.do
    --executable '__SHELL__' --config $rename    
    --executable 'BaselineFilter' --config $baseline_config
    #end if
    #set $peak_picker_type = str($peak_picker.type)
    #if $peak_picker_type != "none"
    --executable '__SHELL__' --config $rename
    --executable '$peak_picker_type' --config $peak_picker_config
    #if $peak_picker_type == "PeakPickerHiRes"
    #if $peak_picker.use_high_res_mass_corrector
    --executable '__SHELL__' --config $rename    
    --executable 'HighResPrecursorMassCorrector' --config $mass_corrector_config
    #end if
    #end if
    #end if
    #set $spectra_filter_type = str($spectra_filter.type)
    #if $spectra_filter_type != "none"
    --executable '__SHELL__' --config $rename
    --executable '$spectra_filter_type' --config $spectra_filter_config
    #end if
    --executable '__SHELL__' --config $copy_output
  </command>
  <inputs>
    <!-- TODO: Maybe even have a conversion step here. -->
    <param format="mzML" name="input" type="data" label="Input Peak List (mzML)"/>
    <conditional name="resample">
      <param name="do" type="boolean" label="Resample" help="If you want to use the Savitzky Golay filter, or Baseline filter with non equally spaced profile data, e.g. TOF data, you have should generate equally spaced data by resampling.">        
      </param>
      <when value="false">
      </when>
      <when value="true">
        <expand macro="sampling_rate_param" />
      </when>
    </conditional>
    <conditional name="noise">
      <param name="type" type="select" label="Noise Filter" help="">
        <option value="none" select="true">None</option>
        <option value="NoiseFilterGaussian">Gaussian</option>
        <option value="NoiseFilterSGolay">Savitzky Golay</option>
      </param>
      <when value="none">
      </when>
      <when value="NoiseFilterGaussian">
      </when>
      <when value="NoiseFilterSGolay">
      </when>
    </conditional>
    <conditional name="baseline">
      <param name="do" type="boolean" label="Apply Baseline Filter" help="Executes the top-hat filter to remove the baseline of an MS experiment." />
      <when value="false">
      </when>
      <when value="true">
      </when>
    </conditional>
    <conditional name="peak_picker">
      <param name="type" type="select" label="Peak Picker" help="">
        <option value="none" select="true">None</option>
        <option value="PeakPickerHiRes">High Resolution</option>
        <option value="PeakPickerWavelet">Wavelet</option>
      </param>
      <when value="none">
      </when>
      <when value="PeakPickerHiRes">
        <param name="signal_to_noise" label="Signal-to-noise Ratio" help="Minimal signal to noise ratio for a peak to be picked. (0.0 disables SNT estimation!)" value="1.0" type="float" />
        <param name="ms1_only" type="boolean" label="MS1 Only" truevalue="true" falsevalue="false" />
        <param name="use_high_res_mass_corrector" label="Correct precursor m/z on centroided high resolution data." checked="false" type="boolean" />
      </when>
      <when value="PeakPickerWavelet">
        <param name="signal_to_noise" label="Signal-to-noise Ratio" help="Minimal signal to noise ratio for a peak to be picked." value="1.0" type="float" />
        <conditional name="peak_width">
          <param name="estimate" label="Estimate Peak Width" type="boolean" checked="false" />
          <when value="true">
          </when>
          <when value="false">
            <param name="peak_width" type="float" value="0.15" help="Approximate fwhm of the peaks." label="Peak Width" />
          </when>
        </conditional>        
      </when>
    </conditional>
    <conditional name="spectra_filter">
      <param name="type" type="select" label="Apply Spectra Filter" help="">
        <option value="none" select="true">None</option>
        <option value="SpectraFilterNLargest">N Largest</option>
        <option value="SpectraFilterNormalizer">Normalizer</option>
        <option value="SpectraFilterScaler">Scaler</option>
        <option value="SpectraFilterBernNorm">Bern et. al. normalization</option>
        <option value="SpectraFilterMarkerMower">Marker Mower</option>
        <option value="SpectraFilterParentPeakMower">Parent Peak Mower</option>
        <option value="SpectraFilterSqrtMower">Square Root Mower</option>
        <option value="SpectraFilterThresholdMower">Threshold Mower</option>
        <option value="SpectraFilterWindowMower">Window Mower</option>
      </param>
      <when value="none">
      </when>
      <when value="SpectraFilterNLargest">
        <!-- 1 param -->
      </when>
      <when value="SpectraFilterNormalizer">
        <!-- 1 param -->
      </when>
      <when value="SpectraFilterScaler">
        <!-- 3 params -->
      </when>
      <when value="SpectraFilterBernNorm">
      </when>
      <when value="SpectraFilterMarkerMower">
      </when>
      <when value="SpectraFilterParentPeakMower">
        <!-- Tons of params -->
      </when>
      <when value="SpectraFilterSqrtMower">
      </when>
      <when value="SpectraFilterThresholdMower">
        <!-- 1 param -->
      </when>
      <when value="SpectraFilterWindowMower">
        <!-- 2 params -->
      </when>
    </conditional>    
  </inputs>
  <outputs>
    <data format="mzml" name="output" />
  </outputs>
  <help>
**What it does**

**Citation**

For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms    
  </help>
</tool>