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1 <tool id="kinamine_java" name="Kinamine_7_to_7" version="0.5.0">
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2 <description>Extracts phosphorylated motifs</description>
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3 <requirements>
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4 <requirement type="package" version="8.0.1440.1">Java</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 mkdir -p output &&
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8 java -Djava.awt.headless=true -cp '$__tool_directory__/Kinamine.jar' kinamine.KinaMine $FDRreport $reference output $fdr
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9 ]]></command>
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10 <inputs>
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11 <param format="txt" name="FDRreport" type="data" label="Distinct Peptide Report"/>
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12 <param format="fasta" name="reference" type="data" label="FASTA reference genome"/>
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13 <param name="fdr" type="integer" value"1" min="1" max="100" label="FDR"/>
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14 <param name="outGroup" type="text" value"kinase" label="Kinase Name"/>
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15 </inputs>
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16 <outputs>
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17 <data format="csv" name="Substrates" from_work_dir="output_Substrates.csv" label="${outGroup}_Substrates.csv"/>
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18 <data format="csv" name="SBF" from_work_dir="output2_Substrate Background Frequency.csv" label="$[outGroup]_Substrate Background Frequency"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="FDRreport" ftype="txt" value="FDRreport.csv"/>
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23 <param name="reference" ftype="fasta" value="reference.fasta"/>
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24 <param name="SBF" ftype="csv" value="SBF.csv"/>
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25 <output name="SDtable" file="SDtable.csv"/>
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26 <output name="EPM" file="EPM.csv"/>
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27 <output name="Characterization" file="Characterization.csv"/>
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28 </test>
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29 </tests>
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30
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31
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32 <help><![CDATA[
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33 This takes a Distinct Peptide Report and extracts from it all phospho-motifs that were discovered at a threshold above a given FDR value. This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook.
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34
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35 ===========
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36 Inputs
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37 ===========
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38 **Distinct Peptide Report**
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39 This is... ask Minervo
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40
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41 **FASTA reference**
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42 This should be a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants
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43
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44 ]]></help>
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45 <citations>
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46 <citation type="doi">10.1021/ja507164a</citation>
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47 </citations>
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48 </tool>
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49
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