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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="1.12.0">
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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 ${param_in}
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13 -tr ${param_tr}
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14 -out ${param_out}
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15 ${param_short_format}
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16 -best_scoring_peptide ${param_best_scoring_peptide}
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17 -threads \${GALAXY_SLOTS:-24}
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18 </command>
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19 <inputs>
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20 <param name="param_in" type="data" format="featureXML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
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21 <param name="param_tr" type="data" format="" optional="False" label="TraML transition file" help="(-tr)"/>
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22 <param name="param_short_format" type="boolean" truevalue="-short_format true" falsevalue="-short_format false" 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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23 <param name="param_best_scoring_peptide" type="text" size="20" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide)"/>
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24 </inputs>
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25 <outputs>
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26 <data name="param_out" label="tsv output file (mProphet compatible)" format="tabular"/>
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27 </outputs>
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28 <help>**What it does**
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29
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30 Converts a featureXML to a mProphet tsv.
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31
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32
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33 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html
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34
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35 @REFERENCES@
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36 </help>
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37 </tool>
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