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1 <tool id="report_clonality_t-cells" name="Report Clonality T-Cells" version="1.0">
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2 <description> </description>
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3 <command interpreter="bash">
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3
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4 r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
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5 </command>
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6 <inputs>
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7 <param name="in_file" format="tabular" type="data" label="Data to Process" />
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8 <param name="clonaltype_select" type="select" label="Clonal Type Definition">
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9 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
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10 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
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11 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
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12 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
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13 <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
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14 </param>
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3
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15
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16 <param name="species" type="select" label="Species">
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17 <option value="human">Human</option>
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18 <option value="mouse">Mouse</option>
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19 </param>
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20
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21 <param name="locus" type="select" label="Locus">
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22 <option value="trb">TRB</option>
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23 <option value="tra">TRA</option>
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24 <option value="trg">TRG</option>
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25 <option value="trd">TRD</option>
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26 </param>
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27
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28 <param name="selection" type="select" label="Selection">
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29 <option value="unique">Unique (Based on clonaltype)</option>
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30 <option value="all">All</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data format="html" name="out_file" />
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35 </outputs>
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36 <help>
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37 Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J)
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38 </help>
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39 </tool>
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