Mercurial > repos > charles_s_test > seqsero2
diff libs/sratoolkit.2.8.0-centos_linux64/schema/sra/helicos.vschema @ 3:38ad1130d077 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author | charles_s_test |
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date | Mon, 27 Nov 2017 11:21:07 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/libs/sratoolkit.2.8.0-centos_linux64/schema/sra/helicos.vschema Mon Nov 27 11:21:07 2017 -0500 @@ -0,0 +1,85 @@ +/*=========================================================================== +* +* PUBLIC DOMAIN NOTICE +* National Center for Biotechnology Information +* +* This software/database is a "United States Government Work" under the +* terms of the United States Copyright Act. It was written as part of +* the author's official duties as a United States Government employee and +* thus cannot be copyrighted. This software/database is freely available +* to the public for use. The National Library of Medicine and the U.S. +* Government have not placed any restriction on its use or reproduction. +* +* Although all reasonable efforts have been taken to ensure the accuracy +* and reliability of the software and data, the NLM and the U.S. +* Government do not and cannot warrant the performance or results that +* may be obtained by using this software or data. The NLM and the U.S. +* Government disclaim all warranties, express or implied, including +* warranties of performance, merchantability or fitness for any particular +* purpose. +* +* Please cite the author in any work or product based on this material. +* +* =========================================================================== +* +*/ + +/*========================================================================== + * NCBI Helicos Sequence Read Archive schema + */ +version 1; + +include 'ncbi/sra.vschema'; +include 'ncbi/spotname.vschema'; + + +/*-------------------------------------------------------------------------- + * functions + */ + +/* tokenize_spot_name + * scans name on input + * tokenizes into parts + */ +extern function NCBI:SRA:spot_name_token + NCBI:SRA:Helicos:tokenize_spot_name #1 ( ascii name ); + + +/* Helicos:tbl + * + * history: + * 1.0.1 - explictly base upon ancestry + * 1.0.2 - base explicitly upon latest ancestry + * 1.0.3 - base explicitly upon latest ancestry + * 1.0.4 - base explicitly upon latest ancestry + */ +table NCBI:SRA:Helicos:tbl:v2 #1.0.4 + = NCBI:SRA:tbl:sra #2.1.3 + , NCBI:tbl:base_space #2.0.3 + , NCBI:tbl:phred_quality #2.0.3 +{ + ascii platform_name + = < ascii > echo < "HELICOS" > (); + + /* NAME tokenizing and coordinates + * most work happens in skeyname table + * we still obtain REGION from name + */ + + readonly column INSDC:coord:val CHANNEL = ( INSDC:coord:val ) + NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:L > ( _out_name, out_spot_name_tok ); + readonly column INSDC:coord:val FIELD = ( INSDC:coord:val ) + NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( _out_name, out_spot_name_tok ); + NCBI:SRA:spot_name_token out_spot_name_tok + = NCBI:SRA:Helicos:tokenize_spot_name ( _out_name ); + + readonly column INSDC:coord:val CAMERA = out_x_coord; + readonly column INSDC:coord:val POS = out_y_coord; + + NCBI:SRA:spot_name_token in_spot_name_tok + = NCBI:SRA:Helicos:tokenize_spot_name ( NAME ); + + INSDC:coord:zero trim_start + = < INSDC:coord:zero > echo < 0 > (); + INSDC:coord:len trim_len = spot_len; +};