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1 <tool id="immunerepertoirecombined_imgt" name="Immunerepertoire combined" version="1.0">
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2 <description>pipeline for IMGT</description>
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3 <command interpreter="bash">
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4 combined.sh
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5 #for $i, $f in enumerate($patients)
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6 ${f.id}
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7 #for $j, $g in enumerate($f.samples)
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8 ${g.sample}
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9 #end for
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10 #end for
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11 "$clonaltype_select" $out_file $out_file.files_path
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12 </command>
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13 <inputs>
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14 <repeat name="patients" title="Patients" min="1" default="1">
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15 <repeat name="samples" title="Sample" min="1" default="1">
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16 <param name="sample" type="data" label="Sample to Process" />
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17 </repeat>
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18 <param name="id" type="text" label="ID" />
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19 </repeat>
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20 <param name="clonaltype_select" type="select" label="Clonal Type Definition">
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21 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
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22 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
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23 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
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24 <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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25 <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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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="html" name="out_file" />
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30 </outputs>
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31 <help>
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32 The entire Immune Repertoire pipeline as a single tool, input several FASTA files, give them an ID and it will BLAST, parse, merge and plot them.
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33 </help>
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34 <requirements>
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35 <requirement type="package" version="1.0.0">igBlastn</requirement>
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36 </requirements>
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37 </tool>
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38
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