Mercurial > repos > yhoogstrate > crossmap

annotate tool-data/all_fasta.loc.sample @ 1:e6efe37b456a draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
author yhoogstrate
date Fri, 28 Aug 2015 03:44:05 -0400
parents bfcdabc062ca
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
5 #TAB characters):
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
6 #
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
8 #
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
10 #
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
14 #
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
17 #such as with hg19 above.
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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18 #