# HG changeset patch
# User rnateam
# Date 1496256932 14400
# Node ID cd8c76234b0c61ce4d598a87b39b22514eeb36d2
# Parent  1bdb57965c6fc78fd6d145f2799e8b900e4e5c80
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5

diff -r 1bdb57965c6f -r cd8c76234b0c macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed May 31 14:55:32 2017 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0" ?>
+<macros>
+    <token name="@VERSION@">2.1b</token>
+</macros>
\ No newline at end of file
diff -r 1bdb57965c6f -r cd8c76234b0c readme.md
--- a/readme.md	Thu May 11 10:28:11 2017 -0400
+++ b/readme.md	Wed May 31 14:55:32 2017 -0400
@@ -15,6 +15,8 @@
 
 .. _`Galaxy Tool Shed`:  https://testtoolshed.g2.bx.psu.edu/view/bgruening/sortmerna
 
+To install the databases, we recommend to use the dedicated data manager available in the `Galaxy Tool Shed`
+
 
 =======
 History
diff -r 1bdb57965c6f -r cd8c76234b0c sortmerna.xml
--- a/sortmerna.xml	Thu May 11 10:28:11 2017 -0400
+++ b/sortmerna.xml	Wed May 31 14:55:32 2017 -0400
@@ -1,7 +1,10 @@
-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.2">
+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.3">
     <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="2.1b">sortmerna</requirement>
+        <requirement type="package" version="@VERSION@">sortmerna</requirement>
     </requirements>
     <stdio>
         <regex match="This program builds a Burst trie on an input rRNA database"
@@ -33,16 +36,16 @@
         #end for
     #else if str( $databases_type.databases_selector ) == 'cached_to_index'
         ## 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])
+        #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
         #for $db in $databases_type.input_databases.value
-            #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] + '-reindexed'
+            #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] + '-reindexed'
             #set $sep = ':'
         #end for
     #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])
+        #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
         #for $db in $databases_type.input_databases.value
-            #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0]
+            #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db]
             #set $sep = ':'
         #end for
     #end if
diff -r 1bdb57965c6f -r cd8c76234b0c tool-data/rRNA_databases.loc.sample
--- a/tool-data/rRNA_databases.loc.sample	Thu May 11 10:28:11 2017 -0400
+++ b/tool-data/rRNA_databases.loc.sample	Wed May 31 14:55:32 2017 -0400
@@ -1,30 +1,1 @@
-#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	$SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta
+#<unique_id>  <database_caption>  <name>  <fasta_file_path>
diff -r 1bdb57965c6f -r cd8c76234b0c tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Thu May 11 10:28:11 2017 -0400
+++ b/tool_data_table_conf.xml.sample	Wed May 31 14:55:32 2017 -0400
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of public ribosomal databases -->
     <table name="rRNA_databases" comment_char="#">
-        <columns>value, name, path</columns>
+        <columns>value, name, dbkey, path</columns>
         <file path="tool-data/rRNA_databases.loc" />
     </table>
 </tables>
diff -r 1bdb57965c6f -r cd8c76234b0c tool_dependencies.xml
--- a/tool_dependencies.xml	Thu May 11 10:28:11 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="sortmerna" version="2.1b">
-        <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
-                    <action type="shell_command"><![CDATA[
-                        ./build.sh --prefix=$INSTALL_DIR
-                    ]]>
-                    </action>
-                    <action type="shell_command">make install</action>
-                    <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
-                    <action type="move_directory_files">
-                        <source_directory>rRNA_databases/</source_directory>
-                        <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
-                    </action>
-                    <action type="set_environment">
-                        <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
-                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    </action>
-                </actions>
-                <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
-                    <action type="shell_command"><![CDATA[
-                        export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./build.sh --prefix=$INSTALL_DIR && make install
-                    ]]>
-                    </action>
-                    <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
-                    <action type="move_directory_files">
-                        <source_directory>rRNA_databases/</source_directory>
-                        <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
-                    </action>
-                    <action type="set_environment">
-                        <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
-                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    </action>
-                </actions>
-            </actions_group>
-        </install>
-        <readme>
-        SortMeRNA requires g++ 4.8 or later.
-
-        Note: the Clang compiler on Mac (distributed through Xcode) does not
-        support multithreading. The user is recommended to install the original
-        GCC compiler via MacPorts
-        </readme>
-    </package>
-</tool_dependency>