annotate test-data/dbkeys.loc @ 43:07e8b80f278c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author iuc
date Fri, 01 Apr 2022 19:02:51 +0000
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07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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1 #This file lists the locations and dbkeys of all the genome files
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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2 #See here for details: http://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
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.
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
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.
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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5 #This file has the format (white space characters are TAB characters):
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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6 #
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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7 #<dbkey> <display_name> <file_path>
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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8 #
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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9 #So, dbkeys.loc could look something like this:
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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10 #
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
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11 #apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.len
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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12 #hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.len
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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13 #
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
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14 mm9 Mus Musculus ${__HERE__}/mm9.len