Mercurial > repos > davidvanzessen > argalaxy_tools

diff imgt_loader.xml @ 10:768e258f8dba draft

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author davidvanzessen
date Mon, 19 Dec 2016 09:37:34 -0500
parents afe85eb6572e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imgt_loader.xml	Mon Dec 19 09:37:34 2016 -0500
@@ -0,0 +1,48 @@
+<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>