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<?xml version='1.0' encoding='UTF-8'?>
<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="1.12.0">
  <description>Assembles metabolite features from singleton mass traces.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderMetabo</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderMetabo

-in ${param_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:common:noise_threshold_int ${param_noise_threshold_int}
-algorithm:common:chrom_peak_snr ${param_chrom_peak_snr}
-algorithm:common:chrom_fwhm ${param_chrom_fwhm}
-algorithm:mtd:mass_error_ppm ${param_mass_error_ppm}
${param_reestimate_mt_sd}
${param_enabled}
-algorithm:epd:width_filtering ${param_width_filtering}
-algorithm:ffm:charge_lower_bound ${param_charge_lower_bound}
-algorithm:ffm:charge_upper_bound ${param_charge_upper_bound}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:mtd:trace_termination_criterion ${adv_opts.param_trace_termination_criterion}
    -algorithm:mtd:trace_termination_outliers ${adv_opts.param_trace_termination_outliers}
    -algorithm:mtd:min_sample_rate ${adv_opts.param_min_sample_rate}
    -algorithm:mtd:min_trace_length ${adv_opts.param_min_trace_length}
    -algorithm:mtd:max_trace_length ${adv_opts.param_max_trace_length}
    -algorithm:epd:min_fwhm ${adv_opts.param_min_fwhm}
    -algorithm:epd:max_fwhm ${adv_opts.param_max_fwhm}
    ${adv_opts.param_masstrace_snr_filtering}
    -algorithm:ffm:local_rt_range ${adv_opts.param_local_rt_range}
    -algorithm:ffm:local_mz_range ${adv_opts.param_local_mz_range}
    ${adv_opts.param_report_summed_ints}
    ${adv_opts.param_disable_isotope_filtering}
    -algorithm:ffm:isotope_model ${adv_opts.param_isotope_model}
    -algorithm:ffm:isotope_noisemodel ${adv_opts.param_isotope_noisemodel}
    ${adv_opts.param_use_smoothed_intensities}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="input centroided mzML file" help="(-in)"/>
    <param name="param_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise." help="(-noise_threshold_int)"/>
    <param name="param_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have." help="(-chrom_peak_snr)"/>
    <param name="param_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)." help="(-chrom_fwhm)"/>
    <param name="param_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)." help="(-mass_error_ppm)"/>
    <param name="param_reestimate_mt_sd" type="boolean" truevalue="-algorithm:mtd:reestimate_mt_sd true" falsevalue="-algorithm:mtd:reestimate_mt_sd false" checked="true" optional="True" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage." help="(-reestimate_mt_sd)"/>
    <param name="param_enabled" type="boolean" truevalue="-algorithm:epd:enabled true" falsevalue="-algorithm:epd:enabled false" checked="true" optional="True" label="Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection." help="(-enabled)"/>
    <param name="param_width_filtering" type="select" optional="True" value="fixed" label="Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution." help="(-width_filtering)">
      <option value="off">off</option>
      <option value="fixed">fixed</option>
      <option value="auto">auto</option>
    </param>
    <param name="param_charge_lower_bound" type="integer" value="1" label="Lowest charge state to consider" help="(-charge_lower_bound)"/>
    <param name="param_charge_upper_bound" type="integer" value="3" label="Highest charge state to consider" help="(-charge_upper_bound)"/>
    <expand macro="advanced_options">
      <param name="param_trace_termination_criterion" type="select" optional="True" value="outlier" label="Termination criterion for the extension of mass traces. In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold." help="(-trace_termination_criterion)">
        <option value="outlier">outlier</option>
        <option value="sample_rate">sample_rate</option>
      </param>
      <param name="param_trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached." help="(-trace_termination_outliers)"/>
      <param name="param_min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak." help="(-min_sample_rate)"/>
      <param name="param_min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)." help="(-min_trace_length)"/>
      <param name="param_max_trace_length" type="float" value="300.0" label="Minimum expected length of a mass trace (in seconds)." help="(-max_trace_length)"/>
      <param name="param_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto." help="(-min_fwhm)"/>
      <param name="param_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto." help="(-max_fwhm)"/>
      <param name="param_masstrace_snr_filtering" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering true" falsevalue="-algorithm:epd:masstrace_snr_filtering false" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing." help="(-masstrace_snr_filtering)"/>
      <param name="param_local_rt_range" type="float" value="10.0" label="RT range where to look for coeluting mass traces" help="(-local_rt_range)"/>
      <param name="param_local_mz_range" type="float" value="6.5" label="MZ range where to look for isotopic mass traces" help="(-local_mz_range)"/>
      <param name="param_report_summed_ints" type="boolean" truevalue="-algorithm:ffm:report_summed_ints true" falsevalue="-algorithm:ffm:report_summed_ints false" checked="false" optional="True" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone." help="(-report_summed_ints)"/>
      <param name="param_disable_isotope_filtering" type="boolean" truevalue="-algorithm:ffm:disable_isotope_filtering true" falsevalue="-algorithm:ffm:disable_isotope_filtering false" checked="false" optional="True" label="Disable isotope filtering." help="(-disable_isotope_filtering)"/>
      <param name="param_isotope_model" type="select" optional="True" value="metabolites" label="Change type of isotope model." help="(-isotope_model)">
        <option value="metabolites">metabolites</option>
        <option value="peptides">peptides</option>
      </param>
      <param name="param_isotope_noisemodel" type="select" optional="True" value="5%RMS" label="SVM isotope models were trained with either 2% or 5% RMS error. Select the appropriate noise model according to the quality of measurement or MS device." help="(-isotope_noisemodel)">
        <option value="5%RMS">5%RMS</option>
        <option value="2%RMS">2%RMS</option>
      </param>
      <param name="param_use_smoothed_intensities" type="boolean" truevalue="-algorithm:ffm:use_smoothed_intensities true" falsevalue="-algorithm:ffm:use_smoothed_intensities false" checked="true" optional="True" label="Use LOWESS intensities instead of raw intensities." help="(-use_smoothed_intensities)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="output featureXML file with metabolite features" format="featureXML"/>
  </outputs>
  <help>**What it does**

Assembles metabolite features from singleton mass traces.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html

@REFERENCES@
</help>
</tool>