Mercurial > repos > iuc > bedtools

annotate tool-data/dbkeys.loc.sample @ 27:a33db97b220c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1ec398a9421f016b852fe59d46961c12321ee5c8
author iuc
date Tue, 15 May 2018 14:52:10 -0400
parents 44867b59dbf2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
6 #
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
diff changeset
7 #<dbkey> <display_name> <file_path>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
diff changeset
8 #
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
diff changeset
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
parents:
diff changeset
10 #
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
13 #