Mercurial > repos > iuc > arriba

annotate test-data/all_fasta.loc @ 5:5e03d09d5fdc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0
author iuc
date Fri, 04 Apr 2025 10:37:49 +0000
parents 98163e8ed458
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
5 #TAB characters):
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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6 #
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
8 #
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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10 #
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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14 #
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
17 #such as with hg19 above.
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
18 #
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
diff changeset
19 genome_id dbkey genome_name ${__HERE__}/genome.fasta.gz