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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.0.0">
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3 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</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>OpenSwathRewriteToFeatureXML
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11
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12 #if $param_csv:
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13 -csv $param_csv
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14 #end if
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15 #if $param_featureXML:
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16 -featureXML $param_featureXML
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_FDR_cutoff:
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22 -FDR_cutoff $param_FDR_cutoff
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23 #end if
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24 -threads \${GALAXY_SLOTS:-24}
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25 #if $adv_opts.adv_opts_selector=='advanced':
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26 #if $adv_opts.param_force:
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27 -force
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28 #end if
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29 #end if
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30 </command>
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31 <inputs>
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32 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: "all_peakgroups.xls"" help="(-csv) "/>
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33 <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/>
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34 <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
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35 <expand macro="advanced_options">
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36 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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37 </expand>
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38 </inputs>
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39 <outputs>
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40 <data name="param_out" format="featurexml"/>
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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 Combines featureXML and mProphet tsv to FDR filtered featureXML.
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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_OpenSwathRewriteToFeatureXML.html</help>
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48 <expand macro="references"/>
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49 </tool>
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