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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="RTEvaluation" name="RTEvaluation" version="2.0.0">
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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 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_sequences_file:
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19 -sequences_file $param_sequences_file
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20 #end if
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21 #if $param_latex:
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22 -latex
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23 #end if
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24 #if $param_p_value_dim_1:
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25 -p_value_dim_1 $param_p_value_dim_1
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26 #end if
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27 #if $param_p_value_dim_2:
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28 -p_value_dim_2 $param_p_value_dim_2
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29 #end if
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30 -threads \${GALAXY_SLOTS:-24}
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31 #if $adv_opts.adv_opts_selector=='advanced':
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32 #if $adv_opts.param_force:
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33 -force
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34 #end if
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35 #end if
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36 </command>
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37 <inputs>
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38 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
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39 <param name="param_sequences_file" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-sequences_file) <br>All peptides that are not a substring of a sequence in this file are considered as false"/>
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40 <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) "/>
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41 <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) "/>
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42 <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) "/>
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43 <expand macro="advanced_options">
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44 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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45 </expand>
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46 </inputs>
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47 <outputs>
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48 <data name="param_out" format="tabular"/>
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49 </outputs>
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50 <help>**What it does**
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51
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52 Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
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53
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54
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55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html</help>
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56 <expand macro="references"/>
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57 </tool>
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