Mercurial > repos > iuc > coverm_contig

annotate test-data/all_fasta.loc @ 5:b9c38856e540 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 339c91447e45305efa0eed6952ef391db8e5d207
author iuc
date Sun, 12 Nov 2023 14:30:50 +0000
parents 6941d0d453ba
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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1 #This is a sample file distributed with Galaxy that enables tools
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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2 #to use a directory of sequence data files. You will need
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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3 #to create these data files and then create a fasta_indexes.loc file
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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4 #similar to this one (store it in this directory) that points to
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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5 #the directories in which those files are stored. The fasta_indexes.loc
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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6 #file has this format (white space characters are TAB characters):
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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7 #
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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9 #
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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10 #So, for example, if you had hg19 Canonical indexed stored in
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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11 #
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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12 # /depot/data2/galaxy/hg19/,
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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13 #
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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14 #then the all_fasta.loc entry would look like this:
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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15 #
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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17 #
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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18 #and your /depot/data2/galaxy/hg19/ directory
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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19 #would contain hg19canon.fasta files.
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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20 #
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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21 #Your fasta_indexes.loc file should include an entry per line for
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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22 #each index set you have stored. The file in the path does actually
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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23 #exist, but it should never be directly used. Instead, the name serves
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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24 #as a prefix for the index file. For example:
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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25 #
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/hg18canon.fasta
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/hg18full.fasta
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/hg19full.fasta
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b9c38856e540 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 339c91447e45305efa0eed6952ef391db8e5d207
iuc
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30 500kb_value 50kb_dbkey 500kb_name ${__HERE__}/500kb.fna
b9c38856e540 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 339c91447e45305efa0eed6952ef391db8e5d207
iuc
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31 1mbp_value 1mbp_dbkey 1mbp_name ${__HERE__}/1mbp.fna
b9c38856e540 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 339c91447e45305efa0eed6952ef391db8e5d207
iuc
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32 1mbp