Mercurial > repos > devteam > data_manager_bwa_mem_index_builder
annotate test-data/all_fasta.loc @ 7:7ba12e5d28e1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 2cc657cadd9c2e0dee930410d87c23d9cf29aed3"
| author | iuc |
|---|---|
| date | Wed, 04 Dec 2019 21:28:41 +0000 |
| parents | 58fb7cfad4c5 |
| children | 74dbe9e6c888 |
| rev | line source |
|---|---|
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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1 #This file lists the locations and dbkeys of all the fasta files |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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changeset
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2 #under the "genome" directory (a directory that contains a directory |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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changeset
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3 #for each build). The script extract_fasta.py will generate the file |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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4 #all_fasta.loc. This file has the format (white space characters are |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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changeset
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5 #TAB characters): |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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6 # |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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7 #<unique_build_id> <dbkey> <display_name> <file_path> |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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8 # |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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9 #So, all_fasta.loc could look something like this: |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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10 # |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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14 # |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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changeset
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15 #Your all_fasta.loc file should contain an entry for each individual |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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16 #fasta file. So there will be multiple fasta files for each build, |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
diff
changeset
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17 #such as with hg19 above. |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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18 # |
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58fb7cfad4c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit a2c93a8a0afeaecbb43172b44e4a7159bf43d11c"
iuc
parents:
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19 phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta |