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annotate tool-data/all_fasta.loc.sample @ 30:179bf64d12ef draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
author yhoogstrate
date Thu, 12 Nov 2015 10:26:25 -0500
parents 7e32d2a88c07
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
5 #TAB characters):
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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6 #
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7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 7
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
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cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
8 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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10 #
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7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 7
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 7
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 7
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
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cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
14 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
17 #such as with hg19 above.
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
18 #