Mercurial > repos > bebatut > sortmerna
diff tool-data/rRNA_databases.loc.sample @ 15:baab049d3aff draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
| author | bebatut |
|---|---|
| date | Wed, 10 Feb 2016 04:02:18 -0500 |
| parents | |
| children | 1a4662c2d6db |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rRNA_databases.loc.sample Wed Feb 10 04:02:18 2016 -0500 @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of public ribosomal databases for SortMeRNA, using the following format +#(white space characters are TAB characters): +# +#<unique_id> <database_caption> <fasta_file_path> +# +#So, for example, if your database is rfam-5.8s-id98 and the path to your FASTA +#file is /data/rRNA_databases/rfam-5.8s-id98.fasta, then the rRNA_databases.loc +#entry would look like this: +# +#rfam-5.8s-id98 Rfam 5.8S eukarya /data/rRNA_databases/rfam-5.8s-id98.fasta +# +#For each rRNA database, you need to create the index files using the +#indexdb_rna program provided by SortMeRNA. You need to specify as index +#basename the path of the FASTA file without extension. For example, for the +#previous database the command is: +# +# indexdb_rna --ref /data/rRNA_databases/rfam-5.8s-id98.fasta,/data/rRNA_databases/rfam-5.8s-id98 +# +#Since SortMeRNA comes bundled with eight ribosomal databases, you can use them +#by creating the actual index files as explained above and uncommenting the +#following lines. +#rfam-5.8s-id98 Rfam 5.8S eukarya $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta +#rfam-5s-id98 Rfam 5S archaea/bacteria $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta +#silva-arc-16s-id95 SILVA v.119 16S archaea $SORTMERNADIR/rRNA_databases/silva-arc-16s-id95.fasta +#silva-arc-23s-id98 SILVA v.119 23S archaea $SORTMERNADIR/rRNA_databases/silva-arc-23s-id98.fasta +#silva-bac-16s-id90 SILVA v.119 16S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-16s-id90.fasta +#silva-bac-23s-id98 SILVA v.119 23S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-23s-id98.fasta +#silva-euk-18s-id95 SILVA v.119 18S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-18s-id95.fasta +#silva-euk-28s-id98 SILVA v.119 28S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta