# HG changeset patch
# User bebatut
# Date 1446029428 14400
# Node ID 16dacde7336cf90e70c69270df43b9f89c5c9046
# Parent  87327d15b04513ecd30371c53cce8b547677a769
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty

diff -r 87327d15b045 -r 16dacde7336c sortmerna.xml
--- a/sortmerna.xml	Wed Oct 28 06:41:11 2015 -0400
+++ b/sortmerna.xml	Wed Oct 28 06:50:28 2015 -0400
@@ -53,7 +53,7 @@
         #if $sam.test:
             --aligned $sam_alignment_file
             --sam
-            $sq_tag
+            $sam.sq_tag
         #end if
 
         #if $blast.test:
diff -r 87327d15b045 -r 16dacde7336c tool-data/sortmerna_rRNA_databases.loc
--- a/tool-data/sortmerna_rRNA_databases.loc	Wed Oct 28 06:41:11 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#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
diff -r 87327d15b045 -r 16dacde7336c tool-data/sortmerna_rRNA_databases.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sortmerna_rRNA_databases.loc.sample	Wed Oct 28 06:50:28 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