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author davidvanzessen
date Mon, 05 Sep 2016 10:59:47 -0400
parents f90fbc15b35a
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<tool id="imgt_loader_igg" name="IMGT Loader" version="1.0">
	<description> </description>
	<command interpreter="bash">
		imgt_loader/imgt_loader.sh $in_file $out_file "tmp"
	</command>
	<inputs>
        <param name="in_file" type="data" label="Archive with files" />
	</inputs>
	<outputs>
		<data format="tabular" name="out_file" label="IMGT Loader on ${in_file.name}"/>
	</outputs>
	<help>
**INPUT**

This tool accepts an IMGT/HIGHV-QUEST ZIP file

**OUTPUT**

The following data is used for ARGalaxy

+-----------------+----------------------------------------------+
| Column name     | Column contents                              |
+-----------------+----------------------------------------------+
| ID              | The Sequence ID provided by the sequencer.   |
+-----------------+----------------------------------------------+
| VDJ Frame       | In-frame/Out-frame                           |
+-----------------+----------------------------------------------+
| Top V Gene      | The best matching V gene found.              |
+-----------------+----------------------------------------------+
| Top D Gene      | The best matching D gene found.              |
+-----------------+----------------------------------------------+
| Top J Gene      | The best matching J gene found.              |
+-----------------+----------------------------------------------+
| CDR3 Seq        | The CDR3 region.                             |
+-----------------+----------------------------------------------+
| CDR3 Length     | The length of the CDR3 region.               |
+-----------------+----------------------------------------------+
| CDR3 Seq DNA    | The CDR3 sequence region.                    |
+-----------------+----------------------------------------------+
| CDR3 Length DNA | The length of the CDR3 sequence region.      |
+-----------------+----------------------------------------------+
| Functionality   | If sequence is productive/unproductive       |
+-----------------+----------------------------------------------+


	</help>

</tool>