Mercurial > repos > rnateam > sortmerna
changeset 3:42509ccf8f59 draft
Uploaded
| author | iuc |
|---|---|
| date | Tue, 04 Aug 2015 15:14:58 -0400 |
| parents | 6f23678fc6e9 |
| children | e6727cef3083 |
| files | readme.md sortmerna.xml sortmerna/readme.md sortmerna/sortmerna.xml sortmerna/test-data/read_small.fasta sortmerna/test-data/read_small.fastq sortmerna/test-data/ref_small.fasta sortmerna/test-data/sortmerna_wrapper_accept1.fastq sortmerna/test-data/sortmerna_wrapper_accept2.fasta sortmerna/test-data/sortmerna_wrapper_other1.fastq sortmerna/test-data/sortmerna_wrapper_other2.fasta sortmerna/test-data/sortmerna_wrapper_sam1.sam sortmerna/test-data/sortmerna_wrapper_sam2.sam sortmerna/tool-data/rRNA_databases.loc.sample sortmerna/tool_data_table_conf.xml.sample sortmerna/tool_dependencies.xml test-data/read_small.fasta test-data/read_small.fastq test-data/ref_small.fasta test-data/sortmerna_wrapper_accept1.fastq test-data/sortmerna_wrapper_accept2.fasta test-data/sortmerna_wrapper_other1.fastq test-data/sortmerna_wrapper_other2.fasta test-data/sortmerna_wrapper_sam1.sam test-data/sortmerna_wrapper_sam2.sam tool-data/rRNA_databases.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 24 files changed, 381 insertions(+), 381 deletions(-) [+] |
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--- /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.
--- /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>
--- 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.
--- 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>
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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
--- 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 $SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta
--- a/sortmerna/tool_data_table_conf.xml.sample Tue Aug 04 15:13:04 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<tables> - <!-- Locations of public ribosomal databases --> - <table name="rRNA_databases" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/rRNA_databases.loc" /> - </table> -</tables>
--- a/sortmerna/tool_dependencies.xml Tue Aug 04 15:13:04 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="sortmerna" version="2.0"> - <install version="1.0"> - <actions> - <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> - <action type="autoconf"/> - <action type="set_environment"> - <environment_variable name="SORTMERNADIR" action="set_to">$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>
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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 $SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Aug 04 15:14:58 2015 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of public ribosomal databases --> + <table name="rRNA_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/rRNA_databases.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Aug 04 15:14:58 2015 -0400 @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="sortmerna" version="2.0"> + <install version="1.0"> + <actions> + <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> + <action type="autoconf"/> + <action type="set_environment"> + <environment_variable name="SORTMERNADIR" action="set_to">$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>