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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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4 r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" "$species"
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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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15 <param name="species" type="select" label="Human or Mouse (Does nothing)">
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16 <option value="human">Human</option>
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17 <option value="mouse">Mouse</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="html" name="out_file" />
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22 </outputs>
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23 <help>
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24 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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25 </help>
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26 </tool>
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