Mercurial > repos > iuc > nextclade

annotate all_fasta.loc.sample @ 15:daddf188c13f 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/nextclade commit 9187a8743503c4a28471fc801ba9dca850890be1"
author iuc
date Mon, 28 Feb 2022 10:50:06 +0000
parents 615f484bdb4a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
5 #TAB characters):
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
6 #
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
8 #
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
10 #
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
14 #
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
17 #such as with hg19 above.
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
18 #