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annotate test-data/all_gff.loc @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 9f6bd4c9479f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9f6bd4c9479f "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 GFF files
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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2 #This file has the format (white space characters are
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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3 #TAB characters):
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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4 #
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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5 #<unique_build_id> <dbkey> <display_name> <file_path>
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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6 #
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
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7 #So, all_gff.loc could look something like this:
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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8 #
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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9 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/annotation/apiMel3/apiMel3.gff
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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10 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/annotation/hg19/hg19canon.gff
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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11 #hg19full hg19 Human (Homo sapiens): hg19 Representative transcripts /path/to/annotation/hg19/hg19_representative_tx.gff
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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12 #
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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13 #Your all_gff.loc file should contain an entry for each different annotation.
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
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14 #So there can be multiple gff files for each build, such as with hg19 above.
9f6bd4c9479f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
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15 testid testdbkey testdisplay ${__HERE__}/a.bed