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comparison tool-data/rRNA_databases.loc.sample @ 1:b482293b2987 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty
author iuc
date Wed, 05 Aug 2015 02:50:43 -0400
parents a8ac09e937f3
children cd8c76234b0c
comparison
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0:a8ac09e937f3 1:b482293b2987
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