Mercurial > repos > bebatut > sortmerna
comparison tool-data/sortmerna_rRNA_databases.loc.sample @ 1:16dacde7336c draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
| author | bebatut |
|---|---|
| date | Wed, 28 Oct 2015 06:50:28 -0400 |
| parents | |
| children | 817fb14fc739 |
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| 0:87327d15b045 | 1:16dacde7336c |
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| 1 #This is a sample file distributed with Galaxy that is used to define a | |
| 2 #list of public ribosomal databases for SortMeRNA, using the following format | |
| 3 #(white space characters are TAB characters): | |
| 4 # | |
| 5 #<unique_id> <database_caption> <fasta_file_path> | |
| 6 # | |
| 7 #So, for example, if your database is rfam-5.8s-id98 and the path to your FASTA | |
| 8 #file is /data/rRNA_databases/rfam-5.8s-id98.fasta, then the rRNA_databases.loc | |
| 9 #entry would look like this: | |
| 10 # | |
| 11 #rfam-5.8s-id98 Rfam 5.8S eukarya /data/rRNA_databases/rfam-5.8s-id98.fasta | |
| 12 # | |
| 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: | |
| 17 # | |
| 18 # indexdb_rna --ref /data/rRNA_databases/rfam-5.8s-id98.fasta,/data/rRNA_databases/rfam-5.8s-id98 | |
| 19 # | |
| 20 #Since SortMeRNA comes bundled with eight ribosomal databases, you can use them | |
| 21 #by creating the actual index files as explained above and uncommenting the | |
| 22 #following lines. | |
| 23 | |
| 24 rfam-5.8s-id98 Rfam 5.8S eukarya tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta | |
| 25 rfam-5s-id98 Rfam 5S archaea/bacteria tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta | |
| 26 silva-arc-16s-id95 SILVA v.119 16S archaea tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta | |
| 27 silva-arc-23s-id98 SILVA v.119 23S archaea tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta | |
| 28 silva-bac-16s-id90 SILVA v.119 16S bacteria tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta | |
| 29 silva-bac-23s-id98 SILVA v.119 23S bacteria tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta | |
| 30 silva-euk-18s-id95 SILVA v.119 18S eukarya tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta | |
| 31 silva-euk-28s-id98 SILVA v.119 28S eukarya tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta |