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comparison imgt_loader.xml @ 10:768e258f8dba draft

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author davidvanzessen
date Mon, 19 Dec 2016 09:37:34 -0500
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9:efa1f5a17b6e 10:768e258f8dba
1 <tool id="imgt_loader_igg" name="IMGT Loader" version="1.0">
2 <description> </description>
3 <command interpreter="bash">
4 imgt_loader/imgt_loader.sh $in_file $out_file "tmp"
5 </command>
6 <inputs>
7 <param name="in_file" type="data" label="Archive with files" />
8 </inputs>
9 <outputs>
10 <data format="tabular" name="out_file" label="IMGT Loader on ${in_file.name}"/>
11 </outputs>
12 <help>
13 **INPUT**
14
15 This tool accepts an IMGT/HIGHV-QUEST ZIP file
16
17 **OUTPUT**
18
19 The following data is used for ARGalaxy
20
21 +-----------------+----------------------------------------------+
22 | Column name | Column contents |
23 +-----------------+----------------------------------------------+
24 | ID | The Sequence ID provided by the sequencer. |
25 +-----------------+----------------------------------------------+
26 | VDJ Frame | In-frame/Out-frame |
27 +-----------------+----------------------------------------------+
28 | Top V Gene | The best matching V gene found. |
29 +-----------------+----------------------------------------------+
30 | Top D Gene | The best matching D gene found. |
31 +-----------------+----------------------------------------------+
32 | Top J Gene | The best matching J gene found. |
33 +-----------------+----------------------------------------------+
34 | CDR3 Seq | The CDR3 region. |
35 +-----------------+----------------------------------------------+
36 | CDR3 Length | The length of the CDR3 region. |
37 +-----------------+----------------------------------------------+
38 | CDR3 Seq DNA | The CDR3 sequence region. |
39 +-----------------+----------------------------------------------+
40 | CDR3 Length DNA | The length of the CDR3 sequence region. |
41 +-----------------+----------------------------------------------+
42 | Functionality | If sequence is productive/unproductive |
43 +-----------------+----------------------------------------------+
44
45
46 </help>
47
48 </tool>