Mercurial > repos > bgruening > nanopolish_methylation

annotate tool-data/all_fasta.loc.sample @ 8:90a922f32523 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author bgruening
date Thu, 30 Nov 2023 17:58:25 +0000
parents be95355fef8d
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
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1 #This file lists the locations and dbkeys of all the fasta files
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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2 #under the "genome" directory (a directory that contains a directory
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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3 #for each build). The script extract_fasta.py will generate the file
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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4 #all_fasta.loc. This file has the format (white space characters are
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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5 #TAB characters):
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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6 #
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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8 #
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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9 #So, all_fasta.loc could look something like this:
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
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10 #
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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14 #
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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15 #Your all_fasta.loc file should contain an entry for each individual
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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16 #fasta file. So there will be multiple fasta files for each build,
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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17 #such as with hg19 above.
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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18 #
be95355fef8d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 23969530e590419a54d93156c5791e75a94a3837"
bgruening
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19 #Arabidopsis_thaliana Arabidopsis_thaliana_TAIR10 Arabidopsis_thaliana: TAIR 10 /export/home1/users/biocomp/chbernar/galaxy_testing/tool-data/from_personal_data/Fasta/TAIR10.fa