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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="RTEvaluation" name="RTEvaluation" version="1.12.0">
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3 <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">RTEvaluation</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>RTEvaluation
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -sequences_file ${param_sequences_file}
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15 ${param_latex}
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16 -p_value_dim_1 ${param_p_value_dim_1}
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17 -p_value_dim_2 ${param_p_value_dim_2}
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18 -threads \${GALAXY_SLOTS:-24}
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19 </command>
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20 <inputs>
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21 <param name="param_in" type="data" format="idXML" optional="False" label="input file" help="(-in)"/>
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22 <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)"/>
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23 <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)"/>
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24 <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)"/>
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25 <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)"/>
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26 </inputs>
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27 <outputs>
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28 <data name="param_out" label="output file " format="tabular"/>
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29 </outputs>
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30 <help>**What it does**
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31
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32 Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
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33
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34
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35 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html
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36
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37 @REFERENCES@
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38 </help>
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39 </tool>
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