Mercurial > repos > devteam > fasta_compute_length

annotate test-data/all_fasta.loc @ 6:5cbde03c1103 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
author devteam
date Thu, 03 Oct 2024 12:11:55 +0000
parents 2051602a5f97
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
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2 #under the "genome" directory (a directory that contains a directory
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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3 #for each build). The script extract_fasta.py will generate the file
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
diff changeset
5 #TAB characters):
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
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6 #
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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8 #
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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9 #So, all_fasta.loc could look something like this:
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
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10 #
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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14 #
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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17 #such as with hg19 above.
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
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18 #
2051602a5f97 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6ba0996437dfa7c51f3c2d2ded79dd85ad099b65"
devteam
parents:
diff changeset
19 test_id test_dbkey test display name ${__HERE__}/merged.fa