<?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: [ID Processing]-->
  <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.0.0">
    <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
    <macros>
      <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>IDPosteriorErrorProbability

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_plot:
  -out_plot $param_out_plot
#end if
#if $param_split_charge:
  -split_charge
#end if
#if $param_top_hits_only:
  -top_hits_only
#end if
#if $param_ignore_bad_data:
  -ignore_bad_data
#end if
#if $param_prob_correct:
  -prob_correct
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_fdr_for_targets_smaller:
  -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_fit_algorithm_number_of_bins:
  -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins
#end if
    #if $adv_opts.param_fit_algorithm_incorrectly_assigned:
  -fit_algorithm:incorrectly_assigned
  #if &quot; &quot; in str($adv_opts.param_fit_algorithm_incorrectly_assigned):
    &quot;$adv_opts.param_fit_algorithm_incorrectly_assigned&quot;
  #else
    $adv_opts.param_fit_algorithm_incorrectly_assigned
  #end if
#end if
    #if $adv_opts.param_fit_algorithm_max_nr_iterations:
  -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param checked="false" falsevalue="" help="(-split_charge) Thus, for each charge state a new model will be computed" label="The search engine scores are split by charge if this flag is set" name="param_split_charge" optional="True" truevalue="-split_charge" type="boolean"/>
      <param checked="false" falsevalue="" help="(-top_hits_only) " label="If set only the top hits of every PeptideIdentification will be used" name="param_top_hits_only" optional="True" truevalue="-top_hits_only" type="boolean"/>
      <param checked="false" falsevalue="" help="(-ignore_bad_data) Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through" label="If set errors will be written but ignored" name="param_ignore_bad_data" optional="True" truevalue="-ignore_bad_data" type="boolean"/>
      <param checked="false" falsevalue="" help="(-prob_correct) " label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" name="param_prob_correct" optional="True" truevalue="-prob_correct" type="boolean"/>
      <expand macro="advanced_options">
        <param help="(-fdr_for_targets_smaller) Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run" label="Only used, when top_hits_only set" name="param_fdr_for_targets_smaller" type="float" value="0.05"/>
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param help="(-number_of_bins) Only needed if each iteration step of the EM-Algorithm will be visualized" label="Number of bins used for visualization" name="param_fit_algorithm_number_of_bins" type="integer" value="100"/>
        <param help="(-incorrectly_assigned) For 'Gauss', the Gauss distribution is used" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" name="param_fit_algorithm_incorrectly_assigned" optional="True" type="select" value="Gumbel">
          <option value="Gumbel">Gumbel</option>
          <option value="Gauss">Gauss</option>
        </param>
        <param help="(-max_nr_iterations) " label="Bounds the number of iterations for the EM algorithm when convergence is slow" name="param_fit_algorithm_max_nr_iterations" type="integer" value="1000"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
      <data format="txt" name="param_out_plot"/>
    </outputs>
    <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help>
  </tool>