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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.0.0">
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3 <description>Converts a featureXML to a mProphet tsv.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</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>OpenSwathFeatureXMLToTSV
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11
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12 -in
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13 #for token in $param_in:
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14 $token
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15 #end for
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16 #if $param_tr:
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17 -tr $param_tr
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18 #end if
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19 #if $param_out:
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20 -out $param_out
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21 #end if
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22 #if $param_short_format:
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23 -short_format
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24 #end if
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25 #if $param_best_scoring_peptide:
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26 -best_scoring_peptide "$param_best_scoring_peptide"
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27 #end if
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28 -threads \${GALAXY_SLOTS:-24}
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29 #if $adv_opts.adv_opts_selector=='advanced':
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30 #if $adv_opts.param_force:
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31 -force
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32 #end if
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33 #end if
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34 </command>
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35 <inputs>
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36 <param name="param_in" type="data" format="featurexml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
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37 <sanitizer>
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38 <valid initial="string.printable">
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39 <remove value="'"/>
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40 <remove value="""/>
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41 </valid>
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42 </sanitizer>
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43 </param>
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44 <param name="param_tr" type="data" format="traml" optional="False" label="TraML transition file" help="(-tr) "/>
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45 <param name="param_short_format" type="boolean" truevalue="-short_format" falsevalue="" checked="false" optional="True" label="Whether to write short (one peptide per line) or long format (one transition per line)" help="(-short_format) "/>
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46 <param name="param_best_scoring_peptide" type="text" size="30" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide) ">
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47 <sanitizer>
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48 <valid initial="string.printable">
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49 <remove value="'"/>
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50 <remove value="""/>
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51 </valid>
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52 </sanitizer>
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53 </param>
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54 <expand macro="advanced_options">
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55 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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56 </expand>
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57 </inputs>
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58 <outputs>
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59 <data name="param_out" format="tabular"/>
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60 </outputs>
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61 <help>**What it does**
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62
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63 Converts a featureXML to a mProphet tsv.
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64
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65
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66 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html</help>
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67 <expand macro="references"/>
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68 </tool>
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