Mercurial > repos > iuc > irissv
annotate test-data/all_fasta.loc @ 3:3242dbeea69c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7
author | iuc |
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date | Sat, 18 May 2024 20:34:13 +0000 |
parents | 1d4f065fa0ef |
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30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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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:
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changeset
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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
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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
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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:
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5 #TAB characters): |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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6 # |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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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
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8 # |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
changeset
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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
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10 # |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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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:
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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:
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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:
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14 # |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff
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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:
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changeset
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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:
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17 #such as with hg19 above. |
30fc9f2bcbe4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
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18 # |
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1d4f065fa0ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
iuc
parents:
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19 iris iris iris ${__HERE__}/genome.fa.gz |