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1 <tool id="imgt_loader_igg" name="IMGT Loader" version="1.0">
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2 <description> </description>
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3 <command interpreter="bash">
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4 imgt_loader/imgt_loader.sh $in_file $out_file "tmp"
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5 </command>
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6 <inputs>
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7 <param name="in_file" type="data" label="Archive with files" />
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8 </inputs>
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9 <outputs>
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10 <data format="tabular" name="out_file" label="IMGT Loader on ${in_file.name}"/>
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11 </outputs>
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12 <help>
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13 **INPUT**
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14
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15 This tool accepts an IMGT/HIGHV-QUEST ZIP file
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16
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17 **OUTPUT**
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18
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19 The following data is used for ARGalaxy
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20
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21 +-----------------+----------------------------------------------+
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22 | Column name | Column contents |
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23 +-----------------+----------------------------------------------+
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24 | ID | The Sequence ID provided by the sequencer. |
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25 +-----------------+----------------------------------------------+
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26 | VDJ Frame | In-frame/Out-frame |
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27 +-----------------+----------------------------------------------+
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28 | Top V Gene | The best matching V gene found. |
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29 +-----------------+----------------------------------------------+
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30 | Top D Gene | The best matching D gene found. |
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31 +-----------------+----------------------------------------------+
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32 | Top J Gene | The best matching J gene found. |
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33 +-----------------+----------------------------------------------+
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34 | CDR3 Seq | The CDR3 region. |
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35 +-----------------+----------------------------------------------+
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36 | CDR3 Length | The length of the CDR3 region. |
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37 +-----------------+----------------------------------------------+
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38 | CDR3 Seq DNA | The CDR3 sequence region. |
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39 +-----------------+----------------------------------------------+
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40 | CDR3 Length DNA | The length of the CDR3 sequence region. |
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41 +-----------------+----------------------------------------------+
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42 | Functionality | If sequence is productive/unproductive |
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43 +-----------------+----------------------------------------------+
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44
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45
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46 </help>
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47
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48 </tool>
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