# HG changeset patch
# User iuc
# Date 1438715698 14400
# Node ID 42509ccf8f598b2f5dcb0a7eb802f60fd27d25e7
# Parent  6f23678fc6e9e31ab4c3226974413c8b0f136a5f
Uploaded

diff -r 6f23678fc6e9 -r 42509ccf8f59 readme.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.md	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,46 @@
+=========
+SortMeRNA
+=========
+
+SortMeRNA, a fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
+
+For more information, please see http://bioinfo.lifl.fr/RNA/sortmerna/.
+
+
+============
+Installation
+============
+
+It is recommended to install this wrapper via the `Galaxy Tool Shed`.
+
+.. _`Galaxy Tool Shed`:  https://testtoolshed.g2.bx.psu.edu/view/bgruening/sortmerna
+
+
+=======
+History
+=======
+- 0.1: First version of the wrapper from Jean-Frédéric
+- 1.9.0: First version with data tables, new dependency definition, generall restructuring
+
+
+===============================
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sortmerna.xml	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,260 @@
+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.0.0">
+    <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
+    <requirements>
+        <requirement type='package' version="2.0">sortmerna</requirement>
+    </requirements>
+    <stdio>
+        <regex match="This program builds a Burst trie on an input rRNA database"
+            source="both"
+            level="fatal"
+            description="Buildtrie program failed to execute." />
+        <regex match="The database name"
+            source="both"
+            level="fatal"
+            description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
+    </stdio>
+    <version_command>
+<![CDATA[
+sortmerna --version 2>&1|grep 'SortMeRNA version'
+]]>
+    </version_command>
+    <command>
+<![CDATA[
+    #set $ref = ''
+    #set $sep=''
+    #if str( $databases_type.databases_selector ) == 'history':
+        #for $db in $databases_type.database_name
+            #set $ref += $sep + str($db) + ',' + $os.path.splitext($os.path.basename(str($db)))[0]
+            #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])
+        #for $db in $databases_type.input_databases.value
+            #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0]
+            #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
+    #end if
+    $strand_search
+    $aligned_fastx.aligned_fastx_selector
+    #if $aligned_fastx.aligned_fastx_selector == '--fastx'
+        #if $aligned_fastx.other
+            --other other_file
+        #end if
+    #end if
+    $aligned_sam.aligned_sam_selector
+    #if $aligned_sam.aligned_sam_selector == '--sam'
+        $aligned_sam.sq
+    #end if
+    $aligned_blast
+    $log
+    -a \${GALAXY_SLOTS:-1}
+]]>
+    </command>
+    <inputs>
+        <param format="fasta,fastq" name="input_reads" type="data" label="Querying sequences" help="In FASTA or FASTQ format (--reads)"/>
+        <conditional name="sequencing_type">
+            <param name="sequencing_type_selector" type="select" label="Sequencing type">
+                <option value="not_paired">Reads are not paired</option>
+                <option value="paired">Reads are paired</option>
+            </param>
+            <when value="paired">
+                <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
+                    <option value="">leave the reads split between aligned and rejected files</option>
+                    <option value="--paired-in">output both reads to aligned file (--paired-in)</option>
+                    <option value="--paired-out">output both reads to rejected file (--paired-out)</option>
+                </param>
+            </when>
+        </conditional>
+
+        <param name="strand_search" type="select" label="Which strands to search" display="radio">
+            <option value="">Search both strands</option>
+            <option value="-F">Search only the forward strand (-F)</option>
+            <option value="-R">Search only the reverse-complementary strand (-R)</option>
+        </param>
+
+        <conditional name="databases_type">
+            <param name="databases_selector" type="select" label="Databases to query"
+                help="Public rRNA databases provided with SortMeRNA have been indexed.
+                    On the contrary, personal databases must be indexed each time SortMeRNA is launched.
+                    Please be patient, this may take some time depending on the size of the given database.">
+                <option value="cached" selected="true">Public ribosomal databases</option>
+                <option value="history">Databases from your history</option>
+            </param>
+            <when value="cached">
+                <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
+                    <options from_data_table="rRNA_databases" />
+                    <validator type="no_options" message="Select at least one database"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases"
+                    help="Your databases will be indexed first, which may take up to several minutes."/>
+            </when>
+        </conditional>
+
+        <!-- Outputs -->
+        <conditional name="aligned_fastx">
+            <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format">
+                <option value="--fastx">Yes (--fastx)</option>
+                <option value="">No</option>
+            </param>
+            <when value="--fastx">
+                <param name="other" type="boolean" label="Include rejected reads file" help="(--other)" />
+            </when>
+            <when value="" />
+        </conditional>
+        <conditional name="aligned_sam">
+            <param name="aligned_sam_selector" type="select" label="Include alignments in SAM format">
+                <option value="--sam">Yes (--sam)</option>
+                <option value="">No</option>
+            </param>
+            <when value="--sam">
+                <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
+            </when>
+            <when value="" />
+        </conditional>
+        <param name="aligned_blast" type="select" label="Include alignments in BLAST-like format">
+            <option value="--blast 0">pairwise (--blast 0)</option>
+            <option value="--blast 1">tabular BLAST -m 8 format (--blast 1)</option>
+            <option value="--blast 2">tabular + column for CIGAR (--blast 2)</option>
+            <option value="--blast 3">tabular + columns for CIGAR and query coverage (--blast 3)</option>
+            <option value="" selected="true">No</option>
+        </param>
+        <param name="log" type="boolean" checked="False" truevalue="--log" falsevalue="" label="Generate statistics file"
+               help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
+        </param>
+    </inputs>
+    <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>
+        </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>
+        </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>
+        </data>
+        <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
+            label="Alignments on ${on_string} (SAM)">
+            <filter>aligned_blast</filter>
+            <change_format>
+                <when input="aligned_blast" value="--blast 0" format="txt" />
+            </change_format>
+        </data>
+        <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
+            <filter>log</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_reads" value="read_small.fastq" />
+            <param name="sequencing_type_selector" value="not_paired" />
+            <param name="strand_search" value="" />
+            <param name="databases_selector" value="history" />
+            <param name="database_name" value="ref_small.fasta" />
+            <param name="other" value="True" />
+            <param name="log" value="" />
+            <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
+            <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
+            <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
+        </test>
+        <test>
+            <param name="input_reads" value="read_small.fasta" />
+            <param name="sequencing_type_selector" value="not_paired" />
+            <param name="strand_search" value="" />
+            <param name="databases_selector" value="history" />
+            <param name="database_name" value="ref_small.fasta" />
+            <param name="other" value="True" />
+            <param name="log" value="" />
+            <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
+            <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
+            <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments
+from metatransriptomic data produced by next-generation sequencers.
+It is capable of handling large RNA databases and sorting out all fragments
+matching to the database with high accuracy and specificity.
+
+.. _SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
+
+
+**Input**
+
+The input is one file of reads in FASTA or FASTQ format and any number of rRNA databases to search against.
+If the user has two foward-reverse paired-sequencing reads files, they may use
+the script "merge_paired_reads.sh" to interleave the reads into one file, preserving their order.
+
+If the sequencing type for the reads is paired-ended, the user has two options under
+"Sequencing type" to filter the reads and preserve their order in the file.
+For a further example of each option, please refer to Section 4.2.3 in the `SortMeRNA User Manual`_.
+
+.. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
+
+
+**Output**
+
+The output will follow the same format (FASTA or FASTQ) as the reads. Optionally, a statistic file for the rRNA content of reads, as well as rRNA subunit distribution can be generated.
+
+
+**rRNA databases**
+
+SortMeRNA is distributed with 8 representative rRNA databases, which were
+all constructed from the SILVA SSU,LSU (version 111) and the RFAM 5/5.8S
+(version 11.0) databases using the tool UCLUST.
+
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+| Representative database  | id % | average id% | # seq (clustered) | Origin                 |  # seq (original) |
++==========================+======+=============+===================+========================+===================+
+| SILVA 16S bacteria       |   85 |        91.6 |              8174 | SILVA SSU Ref NR v.111 |            244077 |
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+| SILVA 16S archaea        |   95 |        96.7 |              3845 | SILVA SSU Ref NR v.111 |             10919 |
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+| SILVA 18S eukarya        |   95 |        96.7 |              4512 | SILVA SSU Ref NR v.111 |             31862 |
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+| SILVA 23S bacteria       |   98 |        99.4 |              3055 | SILVA LSU Ref v.111    |             19580 |
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+| SILVA 23s archaea        |   98 |        99.5 |               164 | SILVA LSU Ref v.111    |               405 |
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+| SILVA 28S eukarya        |   98 |        99.1 |              4578 | SILVA LSU Ref v.111    |              9321 |
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+| Rfam 5S archaea/bacteria |   98 |        99.2 |             59513 | RFAM                   |            116760 |
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+| Rfam 5.8S eukarya        |   98 |        98.9 |             13034 | RFAM                   |            225185 |
++--------------------------+------+-------------+-------------------+------------------------+-------------------+
+
+id %: members of the cluster must have identity at least 'id %' identity with the representative sequence
+
+average id %: average identity of a cluster member to the representative sequence
+
+The user may also choose to use their own rRNA databases.
+
+.. class:: warningmark
+
+Note that your personal databases are indexed each time, and that
+this may take some time depending on the size of the given database.
+]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts611</citation>
+        <citation type="doi">10.1093/nar/gks1219</citation>
+        <citation type="doi">10.1093/nar/gks1005</citation>
+        <citation type="doi">10.1093/bioinformatics/btq461</citation>
+        <citation type="doi">10.1038/nbt.2198</citation>
+    </citations>
+</tool>
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/readme.md
--- a/sortmerna/readme.md	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-=========
-SortMeRNA
-=========
-
-SortMeRNA, a fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
-
-For more information, please see http://bioinfo.lifl.fr/RNA/sortmerna/.
-
-
-============
-Installation
-============
-
-It is recommended to install this wrapper via the `Galaxy Tool Shed`.
-
-.. _`Galaxy Tool Shed`:  https://testtoolshed.g2.bx.psu.edu/view/bgruening/sortmerna
-
-
-=======
-History
-=======
-- 0.1: First version of the wrapper from Jean-Frédéric
-- 1.9.0: First version with data tables, new dependency definition, generall restructuring
-
-
-===============================
-Wrapper Licence (MIT/BSD style)
-===============================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/sortmerna.xml
--- a/sortmerna/sortmerna.xml	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,260 +0,0 @@
-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.0.0">
-    <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
-    <requirements>
-        <requirement type='package' version="2.0">sortmerna</requirement>
-    </requirements>
-    <stdio>
-        <regex match="This program builds a Burst trie on an input rRNA database"
-            source="both"
-            level="fatal"
-            description="Buildtrie program failed to execute." />
-        <regex match="The database name"
-            source="both"
-            level="fatal"
-            description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
-    </stdio>
-    <version_command>
-<![CDATA[
-sortmerna --version 2>&1|grep 'SortMeRNA version'
-]]>
-    </version_command>
-    <command>
-<![CDATA[
-    #set $ref = ''
-    #set $sep=''
-    #if str( $databases_type.databases_selector ) == 'history':
-        #for $db in $databases_type.database_name
-            #set $ref += $sep + str($db) + ',' + $os.path.splitext($os.path.basename(str($db)))[0]
-            #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])
-        #for $db in $databases_type.input_databases.value
-            #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0]
-            #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
-    #end if
-    $strand_search
-    $aligned_fastx.aligned_fastx_selector
-    #if $aligned_fastx.aligned_fastx_selector == '--fastx'
-        #if $aligned_fastx.other
-            --other other_file
-        #end if
-    #end if
-    $aligned_sam.aligned_sam_selector
-    #if $aligned_sam.aligned_sam_selector == '--sam'
-        $aligned_sam.sq
-    #end if
-    $aligned_blast
-    $log
-    -a \${GALAXY_SLOTS:-1}
-]]>
-    </command>
-    <inputs>
-        <param format="fasta,fastq" name="input_reads" type="data" label="Querying sequences" help="In FASTA or FASTQ format (--reads)"/>
-        <conditional name="sequencing_type">
-            <param name="sequencing_type_selector" type="select" label="Sequencing type">
-                <option value="not_paired">Reads are not paired</option>
-                <option value="paired">Reads are paired</option>
-            </param>
-            <when value="paired">
-                <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
-                    <option value="">leave the reads split between aligned and rejected files</option>
-                    <option value="--paired-in">output both reads to aligned file (--paired-in)</option>
-                    <option value="--paired-out">output both reads to rejected file (--paired-out)</option>
-                </param>
-            </when>
-        </conditional>
-
-        <param name="strand_search" type="select" label="Which strands to search" display="radio">
-            <option value="">Search both strands</option>
-            <option value="-F">Search only the forward strand (-F)</option>
-            <option value="-R">Search only the reverse-complementary strand (-R)</option>
-        </param>
-
-        <conditional name="databases_type">
-            <param name="databases_selector" type="select" label="Databases to query"
-                help="Public rRNA databases provided with SortMeRNA have been indexed.
-                    On the contrary, personal databases must be indexed each time SortMeRNA is launched.
-                    Please be patient, this may take some time depending on the size of the given database.">
-                <option value="cached" selected="true">Public ribosomal databases</option>
-                <option value="history">Databases from your history</option>
-            </param>
-            <when value="cached">
-                <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
-                    <options from_data_table="rRNA_databases" />
-                    <validator type="no_options" message="Select at least one database"/>
-                </param>
-            </when>
-            <when value="history">
-                <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases"
-                    help="Your databases will be indexed first, which may take up to several minutes."/>
-            </when>
-        </conditional>
-
-        <!-- Outputs -->
-        <conditional name="aligned_fastx">
-            <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format">
-                <option value="--fastx">Yes (--fastx)</option>
-                <option value="">No</option>
-            </param>
-            <when value="--fastx">
-                <param name="other" type="boolean" label="Include rejected reads file" help="(--other)" />
-            </when>
-            <when value="" />
-        </conditional>
-        <conditional name="aligned_sam">
-            <param name="aligned_sam_selector" type="select" label="Include alignments in SAM format">
-                <option value="--sam">Yes (--sam)</option>
-                <option value="">No</option>
-            </param>
-            <when value="--sam">
-                <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
-            </when>
-            <when value="" />
-        </conditional>
-        <param name="aligned_blast" type="select" label="Include alignments in BLAST-like format">
-            <option value="--blast 0">pairwise (--blast 0)</option>
-            <option value="--blast 1">tabular BLAST -m 8 format (--blast 1)</option>
-            <option value="--blast 2">tabular + column for CIGAR (--blast 2)</option>
-            <option value="--blast 3">tabular + columns for CIGAR and query coverage (--blast 3)</option>
-            <option value="" selected="true">No</option>
-        </param>
-        <param name="log" type="boolean" checked="False" truevalue="--log" falsevalue="" label="Generate statistics file"
-               help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
-        </param>
-    </inputs>
-    <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>
-        </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>
-        </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>
-        </data>
-        <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
-            label="Alignments on ${on_string} (SAM)">
-            <filter>aligned_blast</filter>
-            <change_format>
-                <when input="aligned_blast" value="--blast 0" format="txt" />
-            </change_format>
-        </data>
-        <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
-            <filter>log</filter>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_reads" value="read_small.fastq" />
-            <param name="sequencing_type_selector" value="not_paired" />
-            <param name="strand_search" value="" />
-            <param name="databases_selector" value="history" />
-            <param name="database_name" value="ref_small.fasta" />
-            <param name="other" value="True" />
-            <param name="log" value="" />
-            <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
-            <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
-            <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
-        </test>
-        <test>
-            <param name="input_reads" value="read_small.fasta" />
-            <param name="sequencing_type_selector" value="not_paired" />
-            <param name="strand_search" value="" />
-            <param name="databases_selector" value="history" />
-            <param name="database_name" value="ref_small.fasta" />
-            <param name="other" value="True" />
-            <param name="log" value="" />
-            <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
-            <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
-            <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-**What it does**
-
-SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments
-from metatransriptomic data produced by next-generation sequencers.
-It is capable of handling large RNA databases and sorting out all fragments
-matching to the database with high accuracy and specificity.
-
-.. _SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
-
-
-**Input**
-
-The input is one file of reads in FASTA or FASTQ format and any number of rRNA databases to search against.
-If the user has two foward-reverse paired-sequencing reads files, they may use
-the script "merge_paired_reads.sh" to interleave the reads into one file, preserving their order.
-
-If the sequencing type for the reads is paired-ended, the user has two options under
-"Sequencing type" to filter the reads and preserve their order in the file.
-For a further example of each option, please refer to Section 4.2.3 in the `SortMeRNA User Manual`_.
-
-.. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
-
-
-**Output**
-
-The output will follow the same format (FASTA or FASTQ) as the reads. Optionally, a statistic file for the rRNA content of reads, as well as rRNA subunit distribution can be generated.
-
-
-**rRNA databases**
-
-SortMeRNA is distributed with 8 representative rRNA databases, which were
-all constructed from the SILVA SSU,LSU (version 111) and the RFAM 5/5.8S
-(version 11.0) databases using the tool UCLUST.
-
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-| Representative database  | id % | average id% | # seq (clustered) | Origin                 |  # seq (original) |
-+==========================+======+=============+===================+========================+===================+
-| SILVA 16S bacteria       |   85 |        91.6 |              8174 | SILVA SSU Ref NR v.111 |            244077 |
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-| SILVA 16S archaea        |   95 |        96.7 |              3845 | SILVA SSU Ref NR v.111 |             10919 |
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-| SILVA 18S eukarya        |   95 |        96.7 |              4512 | SILVA SSU Ref NR v.111 |             31862 |
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-| SILVA 23S bacteria       |   98 |        99.4 |              3055 | SILVA LSU Ref v.111    |             19580 |
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-| SILVA 23s archaea        |   98 |        99.5 |               164 | SILVA LSU Ref v.111    |               405 |
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-| SILVA 28S eukarya        |   98 |        99.1 |              4578 | SILVA LSU Ref v.111    |              9321 |
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-| Rfam 5S archaea/bacteria |   98 |        99.2 |             59513 | RFAM                   |            116760 |
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-| Rfam 5.8S eukarya        |   98 |        98.9 |             13034 | RFAM                   |            225185 |
-+--------------------------+------+-------------+-------------------+------------------------+-------------------+
-
-id %: members of the cluster must have identity at least 'id %' identity with the representative sequence
-
-average id %: average identity of a cluster member to the representative sequence
-
-The user may also choose to use their own rRNA databases.
-
-.. class:: warningmark
-
-Note that your personal databases are indexed each time, and that
-this may take some time depending on the size of the given database.
-]]>
-    </help>
-
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/bts611</citation>
-        <citation type="doi">10.1093/nar/gks1219</citation>
-        <citation type="doi">10.1093/nar/gks1005</citation>
-        <citation type="doi">10.1093/bioinformatics/btq461</citation>
-        <citation type="doi">10.1038/nbt.2198</citation>
-    </citations>
-</tool>
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/read_small.fasta
--- a/sortmerna/test-data/read_small.fasta	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->read1
-GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/read_small.fastq
--- a/sortmerna/test-data/read_small.fastq	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@read1
-GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
-+read1
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/ref_small.fasta
--- a/sortmerna/test-data/ref_small.fasta	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->EncFa169 count=1; cluster_weight=27830; cluster=EncFa169; cluster_score=1.000000; cluster_center=True;
-AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGCTTCTTTCCTCCCGAGTGCTTGCACTCAATTGGAAAGAGGAGTGGCGGACGGGTGAGTAACACGTGGGTAACCTACCCATCAGAGGGGGATAACACTTGGAAACAGGTGCTAATACCGCATAACAGTTTATGCCGCATGGCATAAGAGTGAAAGGCGCTTTCGGGTGTCGCTGATGGATGGACCCGCGGTGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCCACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACAAGGACGTTAGTAACTGAACGTCCCCTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTGGAGGGTTTCCGCCCTTCAGTGCTGCAGCAAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTTTGACCACTCTAGAGATAGAGCTTTCCCTTCGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTGTTAGTTGCCATCATTTAGTTGGGCACTCTAGCGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGGAAGTACAACGAGTCGCTAGACCGCGAGGTCATGCAAATCTCTTAAAGCTTCTCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGTGAGGTAACCTTTTTGGAGCCAGCCGCCTAAGGTGGGATAGATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCT
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/sortmerna_wrapper_accept1.fastq
--- a/sortmerna/test-data/sortmerna_wrapper_accept1.fastq	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@read1
-GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
-+read1
-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/sortmerna_wrapper_accept2.fasta
--- a/sortmerna/test-data/sortmerna_wrapper_accept2.fasta	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->read1
-GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/sortmerna_wrapper_other1.fastq
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/sortmerna_wrapper_other2.fasta
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/sortmerna_wrapper_sam1.sam
--- a/sortmerna/test-data/sortmerna_wrapper_sam1.sam	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-@HD	VN:1.0	SO:unsorted
-@PG	ID:sortmerna	VN:1.0	CL:sortmerna --ref /tmp/tmpY80cK0/files/000/dataset_2.dat,dataset_2 --reads /tmp/tmpY80cK0/files/000/dataset_1.dat --aligned aligned --fastx --other other_file.dat dat -a 1 
-read1	0	EncFa169	645	255	2S87M	*	0	0	GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:169	NM:i:1
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/test-data/sortmerna_wrapper_sam2.sam
--- a/sortmerna/test-data/sortmerna_wrapper_sam2.sam	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-@HD	VN:1.0	SO:unsorted
-@PG	ID:sortmerna	VN:1.0	CL:sortmerna --ref /tmp/tmpY80cK0/files/000/dataset_7.dat,dataset_7 --reads /tmp/tmpY80cK0/files/000/dataset_6.dat --aligned aligned --fastx --other other_file.dat dat -a 1 
-read1	0	EncFa169	645	255	2S87M	*	0	0	GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC	*	AS:i:169	NM:i:1
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/tool-data/rRNA_databases.loc.sample
--- a/sortmerna/tool-data/rRNA_databases.loc.sample	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +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	$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-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	$SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/tool_data_table_conf.xml.sample
--- a/sortmerna/tool_data_table_conf.xml.sample	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<tables>
-    <!-- Locations of public ribosomal databases -->
-    <table name="rRNA_databases" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/rRNA_databases.loc" />
-    </table>
-</tables>
diff -r 6f23678fc6e9 -r 42509ccf8f59 sortmerna/tool_dependencies.xml
--- a/sortmerna/tool_dependencies.xml	Tue Aug 04 15:13:04 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="sortmerna" version="2.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
-                <action type="autoconf"/>
-                <action type="set_environment">
-                    <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed.
-        </readme>
-    </package>
-</tool_dependency>
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/read_small.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/read_small.fasta	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,2 @@
+>read1
+GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/read_small.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/read_small.fastq	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,4 @@
+@read1
+GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
++read1
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/ref_small.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref_small.fasta	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,2 @@
+>EncFa169 count=1; cluster_weight=27830; cluster=EncFa169; cluster_score=1.000000; cluster_center=True;
+AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGCTTCTTTCCTCCCGAGTGCTTGCACTCAATTGGAAAGAGGAGTGGCGGACGGGTGAGTAACACGTGGGTAACCTACCCATCAGAGGGGGATAACACTTGGAAACAGGTGCTAATACCGCATAACAGTTTATGCCGCATGGCATAAGAGTGAAAGGCGCTTTCGGGTGTCGCTGATGGATGGACCCGCGGTGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCCACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACAAGGACGTTAGTAACTGAACGTCCCCTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTGGAGGGTTTCCGCCCTTCAGTGCTGCAGCAAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTTTGACCACTCTAGAGATAGAGCTTTCCCTTCGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTGTTAGTTGCCATCATTTAGTTGGGCACTCTAGCGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGGAAGTACAACGAGTCGCTAGACCGCGAGGTCATGCAAATCTCTTAAAGCTTCTCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGTGAGGTAACCTTTTTGGAGCCAGCCGCCTAAGGTGGGATAGATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCT
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/sortmerna_wrapper_accept1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortmerna_wrapper_accept1.fastq	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,4 @@
+@read1
+GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
++read1
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/sortmerna_wrapper_accept2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortmerna_wrapper_accept2.fasta	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,2 @@
+>read1
+GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/sortmerna_wrapper_other1.fastq
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/sortmerna_wrapper_other2.fasta
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/sortmerna_wrapper_sam1.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortmerna_wrapper_sam1.sam	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:unsorted
+@PG	ID:sortmerna	VN:1.0	CL:sortmerna --ref /tmp/tmpY80cK0/files/000/dataset_2.dat,dataset_2 --reads /tmp/tmpY80cK0/files/000/dataset_1.dat --aligned aligned --fastx --other other_file.dat dat -a 1 
+read1	0	EncFa169	645	255	2S87M	*	0	0	GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:169	NM:i:1
diff -r 6f23678fc6e9 -r 42509ccf8f59 test-data/sortmerna_wrapper_sam2.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortmerna_wrapper_sam2.sam	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:unsorted
+@PG	ID:sortmerna	VN:1.0	CL:sortmerna --ref /tmp/tmpY80cK0/files/000/dataset_7.dat,dataset_7 --reads /tmp/tmpY80cK0/files/000/dataset_6.dat --aligned aligned --fastx --other other_file.dat dat -a 1 
+read1	0	EncFa169	645	255	2S87M	*	0	0	GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC	*	AS:i:169	NM:i:1
diff -r 6f23678fc6e9 -r 42509ccf8f59 tool-data/rRNA_databases.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rRNA_databases.loc.sample	Tue Aug 04 15:14:58 2015 -0400
@@ -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 16S bacteria	$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	$SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta
diff -r 6f23678fc6e9 -r 42509ccf8f59 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of public ribosomal databases -->
+    <table name="rRNA_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/rRNA_databases.loc" />
+    </table>
+</tables>
diff -r 6f23678fc6e9 -r 42509ccf8f59 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="sortmerna" version="2.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
+                <action type="autoconf"/>
+                <action type="set_environment">
+                    <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed.
+        </readme>
+    </package>
+</tool_dependency>