Mercurial > repos > davidvanzessen > imgt_loader
diff imgt_loader.xml @ 0:bd23170af386 draft default tip
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| author | davidvanzessen |
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| date | Fri, 18 Aug 2017 10:41:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imgt_loader.xml Fri Aug 18 10:41:51 2017 -0400 @@ -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>