Mercurial > repos > iuc > data_manager_vsnp_excel

annotate test-data/all_fasta.loc @ 0:25811bd45c44 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
author iuc
date Fri, 08 May 2020 18:02:37 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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diff changeset
2 #under the "genome" directory (a directory that contains a directory
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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diff changeset
3 #for each build). The script extract_fasta.py will generate the file
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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diff changeset
5 #TAB characters):
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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6 #
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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8 #
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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9 #So, all_fasta.loc could look something like this:
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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10 #
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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14 #
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
parents:
diff changeset
17 #such as with hg19 above.
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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18 #
25811bd45c44 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_excel commit 28873701c097a136c789024151e2fb59fa1091cd"
iuc
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19 AF2122 AF2122 AF2122 ${__HERE__}/AF2122.fa