annotate test-data/all_gff.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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the GFF files
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
2 #This file has the format (white space characters are
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
3 #TAB characters):
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
4 #
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
5 #<unique_build_id> <dbkey> <display_name> <file_path>
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
6 #
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
7 #So, all_gff.loc could look something like this:
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
8 #
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
9 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/annotation/apiMel3/apiMel3.gff
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
10 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/annotation/hg19/hg19canon.gff
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
11 #hg19full hg19 Human (Homo sapiens): hg19 Representative transcripts /path/to/annotation/hg19/hg19_representative_tx.gff
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
12 #
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
13 #Your all_gff.loc file should contain an entry for each different annotation.
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
14 #So there can be multiple gff files for each build, such as with hg19 above.
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents:
diff changeset
15 testid testdbkey testdisplay ${__HERE__}/a.bed