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<?xml version='1.0' encoding='UTF-8'?>
<tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="1.12.0">
  <description>Detects features in MS1 data based on peptide identifications.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderIdentification

-in ${param_in}
-id ${param_id}
-out ${param_out}
-lib_out ${param_lib_out}
-chrom_out ${param_chrom_out}
-trafo_out ${param_trafo_out}
-reference_rt ${param_reference_rt}
-rt_window ${param_rt_window}
-mz_window ${param_mz_window}
-isotope_pmin ${param_isotope_pmin}
-elution_model ${param_elution_model}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    ${adv_opts.param_unweighted_fit}
    ${adv_opts.param_no_imputation}
    -model_check:boundaries ${adv_opts.param_boundaries}
    -model_check:width ${adv_opts.param_width}
    -model_check:asymmetry ${adv_opts.param_asymmetry}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="Input file (LC-MS raw data)" help="(-in)"/>
    <param name="param_id" type="data" format="idXML" optional="False" label="Input file (peptide identifications)" help="(-id)"/>
    <param name="param_reference_rt" type="select" optional="True" value="score" label="Method for selecting the reference RT, if there are multiple IDs for a peptide and charge ('score': RT of the best-scoring ID; 'intensity': RT of the ID with the most intense precursor; 'median': median RT of all IDs; 'all': no single reference, use RTs of all IDs, 'adapt': adapt RT windows based on IDs)" help="(-reference_rt)">
      <option value="score">score</option>
      <option value="intensity">intensity</option>
      <option value="median">median</option>
      <option value="all">all</option>
      <option value="adapt">adapt</option>
    </param>
    <param name="param_rt_window" type="float" min="0.0" optional="True" value="180.0" label="RT window size (in sec.) for chromatogram extraction." help="(-rt_window)"/>
    <param name="param_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window)"/>
    <param name="param_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Minimum probability for an isotope to be included in the assay for a peptide." help="(-isotope_pmin)"/>
    <param name="param_elution_model" type="select" optional="True" value="none" label="Elution model to fit to features" help="(-elution_model)">
      <option value="none">none</option>
      <option value="symmetric">symmetric</option>
      <option value="asymmetric">asymmetric</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_unweighted_fit" type="boolean" truevalue="-unweighted_fit true" falsevalue="-unweighted_fit false" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit)"/>
      <param name="param_no_imputation" type="boolean" truevalue="-no_imputation true" falsevalue="-no_imputation false" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the OpenSWATH intensity" help="(-no_imputation)"/>
      <param name="param_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries)"/>
      <param name="param_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width)"/>
      <param name="param_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file (features)" format="featureXML"/>
    <data name="param_lib_out" label="Output file (assay library)" format="data"/>
    <data name="param_chrom_out" label="Output file (chromatograms)" format="mzML"/>
    <data name="param_trafo_out" label="Output file (RT transformation)" format="data"/>
  </outputs>
  <help>**What it does**

Detects features in MS1 data based on peptide identifications.


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

@REFERENCES@
</help>
</tool>