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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="1.12.0">
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3 <description>Compute confidence scores for OpenSwath results</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</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>OpenSwathConfidenceScoring
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11
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12 -in ${param_in}
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13 -lib ${param_lib}
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14 -out ${param_out}
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15 -trafo ${param_trafo}
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16 -decoys ${param_decoys}
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17 -transitions ${param_transitions}
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18 -threads \${GALAXY_SLOTS:-24}
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19 #if $adv_opts.adv_opts_selector=='advanced':
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20 -GLM:intercept ${adv_opts.param_intercept}
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21 -GLM:delta_rt ${adv_opts.param_delta_rt}
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22 -GLM:dist_int ${adv_opts.param_dist_int}
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23 #end if
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24 </command>
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25 <inputs>
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26 <param name="param_in" type="data" format="featureXML" optional="False" label="Input file (OpenSwath results)" help="(-in)"/>
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27 <param name="param_lib" type="data" format="" optional="False" label="Assay library" help="(-lib)"/>
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28 <param name="param_trafo" type="data" format="" optional="True" label="Retention time transformation" help="(-trafo)"/>
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29 <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for "all")" help="(-decoys)"/>
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30 <param name="param_transitions" type="integer" min="0" optional="True" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for "all")" help="(-transitions)"/>
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31 <expand macro="advanced_options">
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32 <param name="param_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept)"/>
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33 <param name="param_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt)"/>
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34 <param name="param_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int)"/>
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35 </expand>
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36 </inputs>
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37 <outputs>
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38 <data name="param_out" label="Output file (results with confidence scores)" format="featureXML"/>
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39 </outputs>
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40 <help>**What it does**
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41
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42 Compute confidence scores for OpenSwath results
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43
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44
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45 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html
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46
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47 @REFERENCES@
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48 </help>
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49 </tool>
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