<?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="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.0.0">
    <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
    <macros>
      <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>FalseDiscoveryRate

#if $param_in:
  -in $param_in
#end if
#if $param_in_target:
  -in_target $param_in_target
#end if
#if $param_in_decoy:
  -in_decoy $param_in_decoy
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_proteins_only:
  -proteins_only
#end if
#if $param_peptides_only:
  -peptides_only
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_algorithm_no_qvalues:
  -algorithm:no_qvalues
#end if
#if $param_algorithm_use_all_hits:
  -algorithm:use_all_hits
#end if
#if $param_algorithm_split_charge_variants:
  -algorithm:split_charge_variants
#end if
#if $param_algorithm_treat_runs_separately:
  -algorithm:treat_runs_separately
#end if
#if $param_algorithm_add_decoy_peptides:
  -algorithm:add_decoy_peptides
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) Either specify '-in' alone or 'in_target' together with 'in_decoy' as input" label="Identification input file containing a search against a concatenated sequence database" name="param_in" optional="True" type="data"/>
      <param format="xml" help="(-in_target) " label="Identification input file containing a search against a target-only database" name="param_in_target" optional="True" type="data"/>
      <param format="xml" help="(-in_decoy) " label="Identification input file containing a search against a decoy-only database" name="param_in_decoy" optional="True" type="data"/>
      <param checked="false" falsevalue="" help="(-proteins_only) " label="If set only the FDR on protein level is calculated" name="param_proteins_only" optional="True" truevalue="-proteins_only" type="boolean"/>
      <param checked="false" falsevalue="" help="(-peptides_only) " label="If set only the FDR on peptide (PSM) level is calculated" name="param_peptides_only" optional="True" truevalue="-peptides_only" type="boolean"/>
      <param checked="false" falsevalue="" help="(-no_qvalues) " label="If 'true' strict FDRs will be calculated instead of q-values (the default)" name="param_algorithm_no_qvalues" optional="True" truevalue="-algorithm:no_qvalues" type="boolean"/>
      <param checked="false" falsevalue="" help="(-use_all_hits) " label="If 'true' not only the first hit, but all are used (peptides only)" name="param_algorithm_use_all_hits" optional="True" truevalue="-algorithm:use_all_hits" type="boolean"/>
      <param checked="false" falsevalue="" help="(-split_charge_variants) " label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" name="param_algorithm_split_charge_variants" optional="True" truevalue="-algorithm:split_charge_variants" type="boolean"/>
      <param checked="false" falsevalue="" help="(-treat_runs_separately) " label="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)" name="param_algorithm_treat_runs_separately" optional="True" truevalue="-algorithm:treat_runs_separately" type="boolean"/>
      <param checked="false" falsevalue="" help="(-add_decoy_peptides) The q-value is set to the closest target score" label="If 'true' decoy peptides will be written to output file, too" name="param_algorithm_add_decoy_peptides" optional="True" truevalue="-algorithm:add_decoy_peptides" type="boolean"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
    </outputs>
    <help>Estimates the false discovery rate on peptide and protein level using decoy searches.


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