annotate tool-data/all_fasta.loc.sample @ 3:3242dbeea69c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7
author iuc
date Sat, 18 May 2024 20:34:13 +0000
parents 30fc9f2bcbe4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
5 #TAB characters):
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
6 #
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
8 #
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
10 #
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
14 #
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
17 #such as with hg19 above.
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
18 #