Mercurial > repos > bebatut > sortmerna
diff tool-data/sortmerna_rRNA_databases.loc @ 0:87327d15b045 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
| author | bebatut |
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| date | Wed, 28 Oct 2015 06:41:11 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sortmerna_rRNA_databases.loc Wed Oct 28 06:41:11 2015 -0400 @@ -0,0 +1,31 @@ +#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 tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta +rfam-5s-id98 Rfam 5S archaea/bacteria tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta +silva-arc-16s-id95 SILVA v.119 16S archaea tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta +silva-arc-23s-id98 SILVA v.119 23S archaea tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta +silva-bac-16s-id90 SILVA v.119 16S bacteria tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta +silva-bac-23s-id98 SILVA v.119 23S bacteria tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta +silva-euk-18s-id95 SILVA v.119 18S eukarya tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta +silva-euk-28s-id98 SILVA v.119 28S eukarya tools/manipulate_rna/sortmerna/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta \ No newline at end of file