Merge pull request #3145 from antgonza/add-nanopore-ebi

add nanopore to ebi submissions

Author: charles-cowart

qiita_pet/support_files/doc/source/gettingstartedguide/index.rst

@@ -281,22 +281,24 @@ In order to submit your data to EBI, certain fields are required in your prepara
 
 For all valid values for instrument_model per platform, view the values in the table below:
 
-+-----------------+----------------------------------------------------------------------------------------------------------+
-| Platform        | Valid instrument_model options                                                                           |
-+=================+==========================================================================================================+
-| ``LS454``       |  ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, |
-|                 |  ``454 GS Junior`` or ``unspecified``                                                                    |
-+-----------------+----------------------------------------------------------------------------------------------------------+
-| ``Illumina``    |  ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``,       |
-|                 |  ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``,                       |
-|                 |  ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``,    |
-|                 |  ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``,           |
-|                 |  ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or `unspecified``                           |
-+-----------------+----------------------------------------------------------------------------------------------------------+
-| ``Ion_Torrent`` |  ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL``                  |
-+-----------------+----------------------------------------------------------------------------------------------------------+
-| ``PacBio_SMRT`` |  ``PacBio RS``, ``PacBio RS II``, ``Sequel ``, ``Sequel II``                                             |
-+-----------------+----------------------------------------------------------------------------------------------------------+
++---------------------+----------------------------------------------------------------------------------------------------------+
+| Platform            | Valid instrument_model options                                                                           |
++=====================+==========================================================================================================+
+| ``LS454``           |  ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, |
+|                     |  ``454 GS Junior`` or ``unspecified``                                                                    |
++---------------------+----------------------------------------------------------------------------------------------------------+
+| ``Illumina``        |  ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``,       |
+|                     |  ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``,                       |
+|                     |  ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``,    |
+|                     |  ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``,           |
+|                     |  ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or ``unspecified``                          |
++---------------------+----------------------------------------------------------------------------------------------------------+
+| ``Ion_Torrent``     |  ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL``                  |
++---------------------+----------------------------------------------------------------------------------------------------------+
+| ``PacBio_SMRT``     |  ``PacBio RS``, ``PacBio RS II``, ``Sequel``, ``Sequel II``                                              |
++---------------------+----------------------------------------------------------------------------------------------------------+
+| ``Oxford_Nanopore`` |  ``GridION``                                                                                             |
++---------------------+----------------------------------------------------------------------------------------------------------+
 
 
 Required fields for pre-processing target gene data

qiita_ware/ebi.py

@@ -113,6 +113,7 @@ class EBISubmission(object):
                                     'NEXTSEQ 500',
                                     'NEXTSEQ 550',
                                     'UNSPECIFIED'],
+                       'OXFORD_NANOPORE': ['GRIDION'],
                        'PACBIO_SMRT': ['PACBIO RS',
                                        'PACBIO RS II',
                                        'SEQUEL',