Mercurial > repos > iuc > crossmap_vcf

annotate tool-data/all_fasta.loc.sample @ 11:b17b9f3a148a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 11:59:28 +0000
parents 3fc985b6afdd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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2 #under the "genome" directory (a directory that contains a directory
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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diff changeset
3 #for each build). The script extract_fasta.py will generate the file
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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diff changeset
5 #TAB characters):
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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6 #
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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diff changeset
8 #
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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9 #So, all_fasta.loc could look something like this:
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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10 #
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
14 #
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
17 #such as with hg19 above.
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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18 #