Mercurial > repos > rnateam > sortmerna
comparison tool-data/rRNA_databases.loc.sample @ 1:b482293b2987 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty
author | iuc |
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date | Wed, 05 Aug 2015 02:50:43 -0400 |
parents | a8ac09e937f3 |
children | cd8c76234b0c |
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0:a8ac09e937f3 | 1:b482293b2987 |
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1 #This is a sample file distributed with Galaxy that is used to define a | 1 #This is a sample file distributed with Galaxy that is used to define a |
2 #list of public ribosomal databases, using three columns tab separated | 2 #list of public ribosomal databases for SortMeRNA, using the following format |
3 #(longer whitespace are TAB characters): | 3 #(white space characters are TAB characters): |
4 # | 4 # |
5 #<unique_id> <database_caption> <base_name_path> | 5 #<unique_id> <database_caption> <fasta_file_path> |
6 # | 6 # |
7 #It is important that the actual database name does not have a space in it, | 7 #So, for example, if your database is rfam-5.8s-id98 and the path to your FASTA |
8 #and that the first tab that appears in the line is right before the path. | 8 #file is /data/rRNA_databases/rfam-5.8s-id98.fasta, then the rRNA_databases.loc |
9 #entry would look like this: | |
9 # | 10 # |
10 #So, for example, if your database is rfam-5.8s and the path to your base name | 11 #rfam-5.8s-id98 Rfam 5.8S eukarya /data/rRNA_databases/rfam-5.8s-id98.fasta |
11 #is /data/rRNA_databases/rfam-5.8s, then the rRNA_databases.loc entry would look like this: | |
12 # | 12 # |
13 #rfam-5.8s Rfam 5.8S eukarya /data/rRNA_databases/rfam-5.8s | 13 #For each rRNA database, you need to create the index files using the |
14 #indexdb_rna program provided by SortMeRNA. You need to specify as index | |
15 #basename the path of the FASTA file without extension. For example, for the | |
16 #previous database the command is: | |
14 # | 17 # |
15 #Since SortMeRNA comes bundled with eight ribosomal databases, which are ready | 18 # indexdb_rna --ref /data/rRNA_databases/rfam-5.8s-id98.fasta,/data/rRNA_databases/rfam-5.8s-id98 |
16 #for use after the tool installation, this sample file is in fact an actual file | |
17 #to save the user the trouble of setting it. | |
18 # | 19 # |
19 rfam-5.8s Rfam 5.8S eukarya $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta | 20 #Since SortMeRNA comes bundled with eight ribosomal databases, you can use them |
20 rfam-5s Rfam 5S archaea/bacteria $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta | 21 #by creating the actual index files as explained above and uncommenting the |
21 silva-arc-16s SILVA 16S archaea $SORTMERNADIR/rRNA_databases/silva-arc-16s-database-id95.fasta | 22 #following lines. |
22 silva-arc-23s SILVA 16S bacteria $SORTMERNADIR/rRNA_databases/silva-arc-23s-database-id98.fasta | 23 #rfam-5.8s-id98 Rfam 5.8S eukarya $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta |
23 silva-bac-16s SILVA 16S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-16s-database-id85.fasta | 24 #rfam-5s-id98 Rfam 5S archaea/bacteria $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta |
24 silva-bac-23s SILVA 23S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-23s-database-id98.fasta | 25 #silva-arc-16s-id95 SILVA v.119 16S archaea $SORTMERNADIR/rRNA_databases/silva-arc-16s-id95.fasta |
25 silva-euk-18s SILVA 18S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-18s-database-id95.fasta | 26 #silva-arc-23s-id98 SILVA v.119 23S archaea $SORTMERNADIR/rRNA_databases/silva-arc-23s-id98.fasta |
26 silva-euk-28s SILVA 28S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-28s-database-id98.fasta | 27 #silva-bac-16s-id90 SILVA v.119 16S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-16s-id90.fasta |
28 #silva-bac-23s-id98 SILVA v.119 23S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-23s-id98.fasta | |
29 #silva-euk-18s-id95 SILVA v.119 18S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-18s-id95.fasta | |
30 #silva-euk-28s-id98 SILVA v.119 28S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta |