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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="RTPredict" name="RTPredict" version="1.12.0">
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3 <description>Predicts retention times for peptides using a model trained by RTModel.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">RTPredict</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>RTPredict
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11
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12 -in_id ${param_in_id}
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13 -in_text ${param_in_text}
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14 -svm_model ${param_svm_model}
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15 -total_gradient_time ${param_total_gradient_time}
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16 -threads \${GALAXY_SLOTS:-24}
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17 -out_id:file ${param_file}
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18 -out_id:positive ${param_positive}
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19 -out_id:negative ${param_negative}
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20 -out_text:file ${param_file}
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21 #if $adv_opts.adv_opts_selector=='advanced':
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22 -max_number_of_peptides ${adv_opts.param_max_number_of_peptides}
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23 ${adv_opts.param_rewrite_peptideidentification_rtmz}
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24 #end if
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25 </command>
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26 <inputs>
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27 <param name="param_in_id" type="data" format="idXML" optional="True" label="Peptides with precursor information" help="(-in_id)"/>
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28 <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text)"/>
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29 <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by RTModel)" help="(-svm_model)"/>
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30 <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="The time (in seconds) of the gradient (peptide RT prediction)" help="(-total_gradient_time)"/>
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31 <expand macro="advanced_options">
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32 <param name="param_max_number_of_peptides" type="integer" value="100000" label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)." help="(-max_number_of_peptides)"/>
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33 <param name="param_rewrite_peptideidentification_rtmz" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz true" falsevalue="-out_id:rewrite_peptideidentification_rtmz false" checked="false" optional="True" label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" help="(-rewrite_peptideidentification_rtmz)"/>
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34 </expand>
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35 </inputs>
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36 <outputs>
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37 <data name="param_file" label="Output file with peptide RT prediction" format="idXML"/>
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38 <data name="param_positive" label="Output file in idXML format containing positive predictions for peptide separation prediction - requires 'out_id:negative' to be present as well." format="idXML"/>
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39 <data name="param_negative" label="Output file in idXML format containing negative predictions for peptide separation prediction - requires 'out_id:positive' to be present as well." format="idXML"/>
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40 <data name="param_file" label="Output file with predicted RT values" format="tabular"/>
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41 </outputs>
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42 <help>**What it does**
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43
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44 Predicts retention times for peptides using a model trained by RTModel.
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45
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46
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47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html
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48
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49 @REFERENCES@
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50 </help>
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51 </tool>
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