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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ProteinInference" name="ProteinInference" version="1.12.0">
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3 <description>Protein inference based on the number of identified peptides.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ProteinInference</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>ProteinInference
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -min_peptides_per_protein ${param_min_peptides_per_protein}
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15 ${param_treat_charge_variants_separately}
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16 ${param_treat_modification_variants_separately}
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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="idXML" optional="False" label="input file" help="(-in)"/>
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21 <param name="param_min_peptides_per_protein" type="integer" min="1" optional="True" value="2" label="Minimal number of peptides needed for a protein identification" help="(-min_peptides_per_protein)"/>
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22 <param name="param_treat_charge_variants_separately" type="boolean" truevalue="-treat_charge_variants_separately true" falsevalue="-treat_charge_variants_separately false" checked="false" optional="True" label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences." help="(-treat_charge_variants_separately)"/>
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23 <param name="param_treat_modification_variants_separately" type="boolean" truevalue="-treat_modification_variants_separately true" falsevalue="-treat_modification_variants_separately false" checked="false" optional="True" label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences." help="(-treat_modification_variants_separately)"/>
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24 </inputs>
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25 <outputs>
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26 <data name="param_out" label="output file" format="idXML"/>
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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 Protein inference based on the number of identified peptides.
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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_ProteinInference.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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