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annotate OpenSwathRewriteToFeatureXML.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.0.0">
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5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>OpenSwathRewriteToFeatureXML
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15 #if $param_csv:
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16 -csv $param_csv
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17 #end if
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18 #if $param_featureXML:
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19 -featureXML $param_featureXML
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_FDR_cutoff:
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25 -FDR_cutoff $param_FDR_cutoff
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26 #end if
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27 -threads \${GALAXY_SLOTS:-24}
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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28 #if $adv_opts.adv_opts_selector=='advanced':
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29 #if $adv_opts.param_force:
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30 -force
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31 #end if
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32 #end if
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33 </command>
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34 <inputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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35 <param format="tabular" help="(-csv) " label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" name="param_csv" optional="True" type="data"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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36 <param format="xml" help="(-featureXML) " label="input featureXML file" name="param_featureXML" optional="False" type="data"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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37 <param help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" label="FDR cutoff (" name="param_FDR_cutoff" type="float" value="-1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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38 <expand macro="advanced_options">
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39 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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40 </expand>
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41 </inputs>
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42 <outputs>
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43 <data format="xml" name="param_out"/>
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44 </outputs>
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45 <help>Combines featureXML and mProphet tsv to FDR filtered featureXML.
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48 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html</help>
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49 </tool>