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<?xml version='1.0' encoding='UTF-8'?>
<tool id="RTEvaluation" name="RTEvaluation" version="1.12.0">
  <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

-in ${param_in}
-out ${param_out}
-sequences_file ${param_sequences_file}
${param_latex}
-p_value_dim_1 ${param_p_value_dim_1}
-p_value_dim_2 ${param_p_value_dim_2}
-threads \${GALAXY_SLOTS:-24} 
</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.#br#All peptides that are not a substring of a sequence in this file are considered as false" help="(-sequences_file)"/>
    <param name="param_latex" type="boolean" truevalue="-latex true" falsevalue="-latex false" 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 filter" 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 filter" help="(-p_value_dim_2)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file " 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

@REFERENCES@
</help>
</tool>