Mercurial > repos > iuc > coverm_contig
annotate test-data/all_fasta.loc @ 3:c2a5823e4763 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
| author | iuc |
|---|---|
| date | Wed, 26 Jul 2023 07:35:24 +0000 |
| parents | 6941d0d453ba |
| children | b9c38856e540 |
| rev | line source |
|---|---|
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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1 #This is a sample file distributed with Galaxy that enables tools |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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2 #to use a directory of sequence data files. You will need |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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3 #to create these data files and then create a fasta_indexes.loc file |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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4 #similar to this one (store it in this directory) that points to |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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5 #the directories in which those files are stored. The fasta_indexes.loc |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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6 #file has this format (white space characters are TAB characters): |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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7 # |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path> |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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9 # |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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10 #So, for example, if you had hg19 Canonical indexed stored in |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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11 # |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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12 # /depot/data2/galaxy/hg19/, |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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13 # |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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14 #then the all_fasta.loc entry would look like this: |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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15 # |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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17 # |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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18 #and your /depot/data2/galaxy/hg19/ directory |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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19 #would contain hg19canon.fasta files. |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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20 # |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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21 #Your fasta_indexes.loc file should include an entry per line for |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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22 #each index set you have stored. The file in the path does actually |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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23 #exist, but it should never be directly used. Instead, the name serves |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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24 #as a prefix for the index file. For example: |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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25 # |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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changeset
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/hg18canon.fasta |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/hg18full.fasta |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/hg19full.fasta |
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6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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30 test1tg01 "TestGenome" ${__HERE__}/reference.fasta |