# HG changeset patch
# User iuc
# Date 1438757366 14400
# Node ID e6727cef3083944fd6404dd0ceb08a45bef3a5c1
# Parent  42509ccf8f598b2f5dcb0a7eb802f60fd27d25e7
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty

diff -r 42509ccf8f59 -r e6727cef3083 sortmerna.xml
--- a/sortmerna.xml	Tue Aug 04 15:14:58 2015 -0400
+++ b/sortmerna.xml	Wed Aug 05 02:49:26 2015 -0400
@@ -28,6 +28,7 @@
             #set $sep = ':'
         #end for
         indexdb_rna --ref $ref
+        &&
     #else:
         ## databases path is not directly accessible, must match by hand with LOC file contents
         #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
@@ -36,7 +37,6 @@
             #set $sep = ':'
         #end for
     #end if
-    &&
     sortmerna --ref $ref --reads $input_reads --aligned aligned
     #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
         $sequencing_type.paired_type
@@ -134,18 +134,18 @@
     <outputs>
         <data format_source="input_reads" name="output_fastx" from_work_dir="aligned.dat"
             label="Aligned reads on ${on_string} (${input_reads.datatype.file_ext})">
-            <filter>aligned_fastx.aligned_fastx_selector</filter>
+            <filter>aligned_fastx['aligned_fastx_selector']</filter>
         </data>
         <data format_source="input_reads" name="output_other" from_work_dir="other_file.dat"
             label="Rejected reads on ${on_string} (${input_reads.datatype.file_ext})">
-            <filter>aligned_fastx.aligned_fastx_selector and aligned_fastx.other</filter>
+            <filter>aligned_fastx['aligned_fastx_selector'] and aligned_fastx['other']</filter>
         </data>
         <data format="sam" name="output_sam" from_work_dir="aligned.sam"
             label="Alignments on ${on_string} (SAM)">
-            <filter>aligned_sam.aligned_sam_selector</filter>
+            <filter>aligned_sam['aligned_sam_selector']</filter>
         </data>
         <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
-            label="Alignments on ${on_string} (SAM)">
+            label="Alignments on ${on_string} (BLAST)">
             <filter>aligned_blast</filter>
             <change_format>
                 <when input="aligned_blast" value="--blast 0" format="txt" />
diff -r 42509ccf8f59 -r e6727cef3083 tool-data/rRNA_databases.loc.sample
--- a/tool-data/rRNA_databases.loc.sample	Tue Aug 04 15:14:58 2015 -0400
+++ b/tool-data/rRNA_databases.loc.sample	Wed Aug 05 02:49:26 2015 -0400
@@ -23,7 +23,7 @@
 #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 16S bacteria	$SORTMERNADIR/rRNA_databases/silva-arc-23s-id98.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