Mercurial > repos > rnateam > sortmerna
annotate tool-data/rRNA_databases.loc.sample @ 1:dd73a3422870 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
| author | rnateam |
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| date | Tue, 04 Aug 2015 04:17:05 -0400 |
| parents | e18696d1bc0e |
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| rev | line source |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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1 #This is a sample file distributed with Galaxy that is used to define a |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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2 #list of public ribosomal databases, using three columns tab separated |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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3 #(longer whitespace are TAB characters): |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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4 # |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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5 #<unique_id> <database_caption> <base_name_path> |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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6 # |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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7 #It is important that the actual database name does not have a space in it, |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
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8 #and that the first tab that appears in the line is right before the path. |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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9 # |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
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10 #So, for example, if your database is rfam-5.8s and the path to your base name |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
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11 #is /data/rRNA_databases/rfam-5.8s, then the rRNA_databases.loc entry would look like this: |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
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12 # |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
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13 #rfam-5.8s Rfam 5.8S eukarya /data/rRNA_databases/rfam-5.8s |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
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14 # |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
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15 #Since SortMeRNA comes bundled with eight ribosomal databases, which are ready |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
changeset
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16 #for use after the tool installation, this sample file is in fact an actual file |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
changeset
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17 #to save the user the trouble of setting it. |
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e18696d1bc0e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff
changeset
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18 # |
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1
dd73a3422870
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
rnateam
parents:
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diff
changeset
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19 rfam-5.8s-id98 Rfam 5.8S eukarya $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta |
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dd73a3422870
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
rnateam
parents:
0
diff
changeset
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20 rfam-5s-id98 Rfam 5S archaea/bacteria $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta |
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dd73a3422870
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
rnateam
parents:
0
diff
changeset
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21 silva-arc-16s-id95 SILVA 16S archaea $SORTMERNADIR/rRNA_databases/silva-arc-16s-id95.fasta |
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dd73a3422870
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
rnateam
parents:
0
diff
changeset
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22 silva-arc-23s-id98 SILVA 16S bacteria $SORTMERNADIR/rRNA_databases/silva-arc-23s-id98.fasta |
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dd73a3422870
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
rnateam
parents:
0
diff
changeset
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23 silva-bac-16s-id90 SILVA 16S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-16s-id90.fasta |
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dd73a3422870
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
rnateam
parents:
0
diff
changeset
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24 silva-bac-23s-id98 SILVA 23S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-23s-id98.fasta |
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dd73a3422870
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
rnateam
parents:
0
diff
changeset
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25 silva-euk-18s-id95 SILVA 18S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-18s-id95.fasta |
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dd73a3422870
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
rnateam
parents:
0
diff
changeset
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26 silva-euk-28s-id98 SILVA 28S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta |