Mercurial > repos > iuc > arriba_draw_fusions

annotate test-data/all_fasta.loc @ 5:c49d6a069ce3 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 10:37:40 +0000
parents ea76fa4f1526
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
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2 #under the "genome" directory (a directory that contains a directory
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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3 #for each build). The script extract_fasta.py will generate the file
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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5 #TAB characters):
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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6 #
ea76fa4f1526 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>
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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8 #
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
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9 #So, all_fasta.loc could look something like this:
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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10 #
ea76fa4f1526 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
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
ea76fa4f1526 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
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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14 #
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
ea76fa4f1526 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,
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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17 #such as with hg19 above.
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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18 #
ea76fa4f1526 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
iuc
parents:
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19 genome_id dbkey genome_name ${__HERE__}/genome.fasta.gz