Mercurial > repos > iuc > bedtools
annotate tool-data/dbkeys.loc.sample @ 20:df56e1b12d0c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a
author | iuc |
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date | Wed, 10 Jan 2018 19:21:33 -0500 |
parents | 44867b59dbf2 |
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44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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1 #This file lists the locations and dbkeys of all the genome files |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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2 #See here for details: http://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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3 #You can add elements to this data table using the data_manager_fetch_genome_dbkeys_all_fasta data manager. |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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4 #Alternatively, index files created using samtools faidx (http://www.htslib.org/doc/faidx.html) contain 3 extra columns, but work fine. |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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5 #This file has the format (white space characters are TAB characters): |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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6 # |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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7 #<dbkey> <display_name> <file_path> |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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8 # |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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9 #So, dbkeys.loc could look something like this: |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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10 # |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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11 #apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.len |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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12 #hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.len |
44867b59dbf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
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13 # |