Mercurial > repos > brinkmanlab > mauve_contig_mover
annotate all_fasta.loc.sample @ 7:4c4838703fa8 draft default tip
planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit d396bc9f82b351c35ae4940ebfbb6a43e6e7215a
author | brinkmanlab |
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date | Thu, 25 Aug 2022 21:03:33 +0000 |
parents | 38fbb67f0dac |
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rev | line source |
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38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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1 #This file lists the locations and dbkeys of all the fasta files |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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changeset
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2 #under the "genome" directory (a directory that contains a directory |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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3 #for each build). The script extract_fasta.py will generate the file |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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4 #all_fasta.loc. This file has the format (white space characters are |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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5 #TAB characters): |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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changeset
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6 # |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path> |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
|
8 # |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
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9 #So, all_fasta.loc could look something like this: |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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changeset
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10 # |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
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14 # |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
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15 #Your all_fasta.loc file should contain an entry for each individual |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
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16 #fasta file. So there will be multiple fasta files for each build, |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
diff
changeset
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17 #such as with hg19 above. |
38fbb67f0dac
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit e26f08ccc754d9bab560cdab7ea78203cc92ec9f"
brinkmanlab
parents:
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changeset
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18 # |