<?xml version='1.0' encoding='UTF-8'?>
<tool id="RTEvaluation" name="RTEvaluation" version="2.0.0">
  <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
  <macros>
    <token name="@EXECUTABLE@">RTEvaluation</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>RTEvaluation

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_sequences_file:
  -sequences_file $param_sequences_file
#end if
#if $param_latex:
  -latex
#end if
#if $param_p_value_dim_1:
  -p_value_dim_1 $param_p_value_dim_1
#end if
#if $param_p_value_dim_2:
  -p_value_dim_2 $param_p_value_dim_2
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
    <param name="param_sequences_file" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-sequences_file) &lt;br&gt;All peptides that are not a substring of a sequence in this file are considered as false"/>
    <param name="param_latex" type="boolean" truevalue="-latex" falsevalue="" checked="false" optional="True" label="indicates whether the output file format of the table should be latex or csv" help="(-latex) "/>
    <param name="param_p_value_dim_1" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Significance level of first dimension RT filte" help="(-p_value_dim_1) "/>
    <param name="param_p_value_dim_2" type="float" min="0.0" max="1.0" optional="True" value="0.05" label="Significance level of second dimension RT filte" help="(-p_value_dim_2) "/>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
  </outputs>
  <help>**What it does**

Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html</help>
  <expand macro="references"/>
</tool>