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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ConvertTSVToTraML" name="ConvertTSVToTraML" version="2.0.0">
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3 <description>Converts an OpenSWATH transition TSV file to a TraML file</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ConvertTSVToTraML</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>ConvertTSVToTraML
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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 -threads \${GALAXY_SLOTS:-24}
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19 #if $adv_opts.adv_opts_selector=='advanced':
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20 #if $adv_opts.param_force:
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21 -force
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22 #end if
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23 #if $adv_opts.param_algorithm_retentionTimeInterpretation:
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24 -algorithm:retentionTimeInterpretation
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25 #if " " in str($adv_opts.param_algorithm_retentionTimeInterpretation):
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26 "$adv_opts.param_algorithm_retentionTimeInterpretation"
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27 #else
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28 $adv_opts.param_algorithm_retentionTimeInterpretation
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29 #end if
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30 #end if
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31 #if $adv_opts.param_algorithm_override_group_label_check:
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32 -algorithm:override_group_label_check
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33 #end if
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34 #end if
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35 </command>
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36 <inputs>
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37 <param name="param_in" type="data" format="tabular" optional="False" label="Input OpenSWATH transition TSV file or SpectraST MRM file" help="(-in) <br> See http://www.openms.de/current_doxygen/html/UTILS_ConvertTSVToTraML.html for format"/>
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38 <expand macro="advanced_options">
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39 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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40 <param name="param_algorithm_retentionTimeInterpretation" type="select" optional="True" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) ">
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41 <option value="iRT">iRT</option>
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42 <option value="seconds">seconds</option>
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43 <option value="minutes">minutes</option>
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44 </param>
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45 <param name="param_algorithm_override_group_label_check" type="boolean" truevalue="-algorithm:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>
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46 </expand>
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47 </inputs>
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48 <outputs>
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49 <data name="param_out" format="traml"/>
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50 </outputs>
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51 <help>**What it does**
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52
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53 Converts an OpenSWATH transition TSV file to a TraML file
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54
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55
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56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConvertTSVToTraML.html</help>
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57 <expand macro="references"/>
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58 </tool>
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