| Previous changeset 0:a8ac09e937f3 (2015-08-03) Next changeset 2:3699b6b771e0 (2016-03-29) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty |
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modified:
sortmerna.xml test-data/sortmerna_wrapper_accept1.fastq test-data/sortmerna_wrapper_other1.fastq tool-data/rRNA_databases.loc.sample tool_dependencies.xml |
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added:
test-data/read_small.fasta test-data/read_small.fastq test-data/ref_small.fasta test-data/sortmerna_wrapper_accept2.fasta test-data/sortmerna_wrapper_other2.fasta test-data/sortmerna_wrapper_sam1.sam test-data/sortmerna_wrapper_sam2.sam |
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removed:
sortmerna.py test-data/merged-paired-reads_output.fastq test-data/sortmerna_wrapper_in1.fastq tool-data/rRNA_databases.loc |
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| diff -r a8ac09e937f3 -r b482293b2987 sortmerna.py --- a/sortmerna.py Mon Aug 03 08:18:26 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,72 +0,0 @@ -#!/usr/bin/env python - -""" -Runs SortMeRNA -""" - -import subprocess -import optparse -import shlex - - -def main(): - """Parse the command line, exectutes SortMeRNA and buildtrie if neeeded.""" - #TODO: Put all SortMeRNA options in the command-line parser - parser = optparse.OptionParser() - parser.add_option('--sortmerna', dest='sortmerna_cmd', help='') - parser.add_option('--buildtrie', dest='buildtrie', - default=False, action='store_true', help='') - (options, args) = parser.parse_args() - if not args: - raise Exception('Please provide at least one database') - - if options.buildtrie: - buildtrie = 'buildtrie' - for database in args: - run_buildtrie([buildtrie, '--db', database]) - - if options.sortmerna_cmd: - sortmerna = 'sortmerna' - run_sortmerna([sortmerna] + - shlex.split(options.sortmerna_cmd) + - ['-m', '262144', '-n', str(len(args)), '--db'] + - args) - - -def run_buildtrie(cmd): - """Run the BuildTrie program.""" - try: - stdout_arg = subprocess.PIPE - stderr_arg = subprocess.PIPE - child_process = subprocess.Popen(args=" ".join(cmd), shell=True, - stdin=None, stdout=stdout_arg, - stderr=stderr_arg) - stdout_str, stderr_str = child_process.communicate() - return_code = child_process.returncode - if return_code is not 0: - raise Exception(stderr_str) - - except Exception, error: - raise Exception('Error while running Buildtrie:\n' + - '\n'.join([str(error), stdout_str, stderr_str])) - - -def run_sortmerna(cmd): - """Run the SortMeRNA program.""" - try: - stdout_arg = subprocess.PIPE - stderr_arg = subprocess.PIPE - child_process = subprocess.Popen(args=" ".join(cmd), shell=True, - stdin=None, stdout=stdout_arg, - stderr=stderr_arg) - stdout_str, stderr_str = child_process.communicate() - return_code = child_process.returncode - if return_code is not 0: - raise Exception(stderr_str) - except Exception, error: - raise Exception('Error while running SortMeRNA:\n' + - '\n'.join([str(error), stdout_str, stderr_str])) - - -if __name__ == "__main__": - main() |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 sortmerna.xml --- a/sortmerna.xml Mon Aug 03 08:18:26 2015 -0400 +++ b/sortmerna.xml Wed Aug 05 02:50:43 2015 -0400 |
| [ |
| b'@@ -1,7 +1,7 @@\n-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="1.9.0">\n+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.0.0">\n <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>\n <requirements>\n- <requirement type=\'package\' version="1.9">sortmerna</requirement>\n+ <requirement type=\'package\' version="2.0">sortmerna</requirement>\n </requirements>\n <stdio>\n <regex match="This program builds a Burst trie on an input rRNA database"\n@@ -18,145 +18,167 @@\n sortmerna --version 2>&1|grep \'SortMeRNA version\'\n ]]>\n </version_command>\n- <command interpreter="python">\n+ <command>\n <![CDATA[\n- sortmerna.py\n- --sortmerna "\n- $strand_search\n- #if str( $read_family.read_family_selector ) == \'other\':\n- --I $input_reads -r $read_family.ratio_parameter\n- #else:\n- $read_family.read_family_selector $input_reads\n- #end if\n-\n- #if str( $sequencing_type.sequencing_type_selector ) == \'paired\':\n- $sequencing_type.paired_type\n+ #set $ref = \'\'\n+ #set $sep=\'\'\n+ #if str( $databases_type.databases_selector ) == \'history\':\n+ #for $db in $databases_type.database_name\n+ #set $ref += $sep + str($db) + \',\' + $os.path.splitext($os.path.basename(str($db)))[0]\n+ #set $sep = \':\'\n+ #end for\n+ indexdb_rna --ref $ref\n+ &&\n+ #else:\n+ ## databases path is not directly accessible, must match by hand with LOC file contents\n+ #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])\n+ #for $db in $databases_type.input_databases.value\n+ #set $ref += $sep + $data_table[$db] + \',\' + $os.path.splitext($data_table[$db])[0]\n+ #set $sep = \':\'\n+ #end for\n+ #end if\n+ sortmerna --ref $ref --reads $input_reads --aligned aligned\n+ #if str( $sequencing_type.sequencing_type_selector ) == \'paired\'\n+ $sequencing_type.paired_type\n+ #end if\n+ $strand_search\n+ $aligned_fastx.aligned_fastx_selector\n+ #if $aligned_fastx.aligned_fastx_selector == \'--fastx\'\n+ #if $aligned_fastx.other\n+ --other other_file\n #end if\n-\n- #if $outputs_selected:\n- #if \'accept\' in $outputs_selected.value:\n- --accept accept_file\n- #end if\n- #if \'other\' in $outputs_selected.value:\n- --other other_file\n- #end if\n- #end if\n-\n- $log\n- -a \\${GALAXY_SLOTS:-4}\n- "\n- #if str( $databases_type.databases_selector ) == \'history\':\n- --buildtrie\n- #for $db in $databases_type.input_databases\n- $db.database_name\n- #end for\n- #else:\n- ## databases path is not directly accessible, must match by hand with LOC file contents\n- ${\' \'.join([dict([(x[0], x[2]) for x in $databases_type.input_databases.input.options.tool_data_table.data])[y]\n- for y in $databases_type.input_databases.value])}\n- #end if\n+ #end if\n+ $aligned_sam.aligned_sam_selector\n+ #if $aligned_sam.aligned_sam_selector == \'--sam\'\n+ $aligned_sam.sq\n+ #end if\n+ $aligned_blast\n+ $log\n+ -a \\${GALAXY_SLOTS:-1}\n ]]>\n </command>\n <inputs>\n- <conditional name="read_family">\n- <param name="read_family_selector" type="select" format="text" label="Sequencing technology of querying sequences (reads)"\n- help="The Illumina platform is more common for large scale metatranscriptomic projects requiring a high throughput.">\n- <option value="--I">Illumina Solexa</option>\n- <option value="--454">454 Roche</option>\n- <option value="other">Other</option>\n+ <param format="fasta,fastq" name="input_reads" type="data" label="Querying sequences" help="In FASTA or FASTQ form'..b'lsevalue="" label="Generate statistics file"\n+ help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">\n+ </param>\n </inputs>\n <outputs>\n- <data format_source="input_reads" name="output_accept" from_work_dir="accept_file.dat"\n- label="Matching reads on ${on_string} (${input_reads.datatype.file_ext})">\n- <filter>outputs_selected and \'accept\' in outputs_selected</filter>\n+ <data format_source="input_reads" name="output_fastx" from_work_dir="aligned.dat"\n+ label="Aligned reads on ${on_string} (${input_reads.datatype.file_ext})">\n+ <filter>aligned_fastx[\'aligned_fastx_selector\']</filter>\n </data>\n <data format_source="input_reads" name="output_other" from_work_dir="other_file.dat"\n- label="Reads not found on ${on_string} (${input_reads.datatype.file_ext})">\n- <filter>outputs_selected and \'other\' in outputs_selected</filter>\n+ label="Rejected reads on ${on_string} (${input_reads.datatype.file_ext})">\n+ <filter>aligned_fastx[\'aligned_fastx_selector\'] and aligned_fastx[\'other\']</filter>\n+ </data>\n+ <data format="sam" name="output_sam" from_work_dir="aligned.sam"\n+ label="Alignments on ${on_string} (SAM)">\n+ <filter>aligned_sam[\'aligned_sam_selector\']</filter>\n </data>\n- <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="log_file.log">\n+ <data format="tabular" name="output_blast" from_work_dir="aligned.blast"\n+ label="Alignments on ${on_string} (BLAST)">\n+ <filter>aligned_blast</filter>\n+ <change_format>\n+ <when input="aligned_blast" value="--blast 0" format="txt" />\n+ </change_format>\n+ </data>\n+ <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">\n <filter>log</filter>\n </data>\n </outputs>\n <tests>\n <test>\n- <param name="read_family_selector" value="I" />\n- <param name="input_reads" value="sortmerna_wrapper_in1.fastq" />\n+ <param name="input_reads" value="read_small.fastq" />\n <param name="sequencing_type_selector" value="not_paired" />\n <param name="strand_search" value="" />\n- <param name="databases_selector" value="cached" />\n- <param name="input_databases" value="rfam-5.8s,rfam-5s" />\n- <param name="outputs_selected" value="accept,other" />\n+ <param name="databases_selector" value="history" />\n+ <param name="database_name" value="ref_small.fasta" />\n+ <param name="other" value="True" />\n <param name="log" value="" />\n- <param name="options_type_selector" value="less" />\n- <output name="output_accept" file="sortmerna_wrapper_accept1.fastq" />\n+ <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />\n <output name="output_other" file="sortmerna_wrapper_other1.fastq" />\n+ <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />\n+ </test>\n+ <test>\n+ <param name="input_reads" value="read_small.fasta" />\n+ <param name="sequencing_type_selector" value="not_paired" />\n+ <param name="strand_search" value="" />\n+ <param name="databases_selector" value="history" />\n+ <param name="database_name" value="ref_small.fasta" />\n+ <param name="other" value="True" />\n+ <param name="log" value="" />\n+ <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />\n+ <output name="output_other" file="sortmerna_wrapper_other2.fasta" />\n+ <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />\n </test>\n </tests>\n <help>\n' |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/merged-paired-reads_output.fastq --- a/test-data/merged-paired-reads_output.fastq Mon Aug 03 08:18:26 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,50 +0,0 @@ -@PHOSPHORE_0118:4:1101:5073:2473#ATCACG/1 -CTCGCGCCACTGGCTGGCTCTCCCCTCTCTCTCTCTCTCTCCCCTCTCTCTCCCCGAGTACACCCGCGCGGGC -+PHOSPHORE_0118:4:1101:5073:2473#ATCACG/1 -___cccccggggghhhhf_YbcgecZYa^Y^ceXccacXIXaafX`_]VMHVbdhSTFKU_Z]b]WFW_aZ__ -@PHOSPHORE_0118:4:1101:1143:2236#ATCACG/1 -CGCGCGCACCATGCCCGTGCTCGACTGCTCGCCGCCCGCGCCGCGCCACGCCTCGCCGTTCACCTTGACCTCCACGCGCAGGCC -+PHOSPHORE_0118:4:1101:1143:2236#ATCACG/1 -__beeeecggcgfhhhhhhhhhhfhhhhhhhhhhhgececcccccccacaccccaccccac`bbbcbbbcbbc[`_a[aLT[aa -@PHOSPHORE_0118:4:1101:17780:2432#ATCACG/1 -GCGGTCTGGAACCACCTGATCCCATCCCGAACTCAGCCGTGAAACAGACCAGCGCCGATGGTAGTGTGGCTTCTGCCCGT -+PHOSPHORE_0118:4:1101:17780:2432#ATCACG/1 -bbbeeeeegggggiiiiiiihiiihiiiiiiihiidhhigfhihiihgiiiiiggeccaccbbb_b`baccab`]_ba[T -@PHOSPHORE_0118:4:1101:1397:2156#ATCACG/1 -ATGCGCTTGAGGTAGCCAAGGGCACGCAGTTCACACCGTATGGCGGCGATGCGAGGCGGCGGCAGGAGG -+PHOSPHORE_0118:4:1101:1397:2156#ATCACG/1 -bbbeeeeegggggiiiiiiiiihfhiheghihgihiiihiiiiihifc^acac^_cEHVZaccaac^__ -@PHOSPHORE_0118:4:1101:7859:3729#ATCACG/1 -GCATCGCCGCCCTCGCCCTCGCCCCCGCCGCCCTCGCCCT -+PHOSPHORE_0118:4:1101:7859:3729#ATCACG/1 -___c`cc`Yeee[ePY_`UY^_eGL_F_`dUU\F\^Q\a_ -@PHOSPHORE_0118:4:1101:1633:2146#ATCACG/1 -TGACCAATGTTCTTCATAACGTCCCCGATAGACATGCCAACATTCGGTCCGTTGCGAAGATAGTCATCGCCGTCATAGTC -+PHOSPHORE_0118:4:1101:1633:2146#ATCACG/1 -_bbecdecgggggihhiiiihghhhiihiichdfghiffghfghiifiifhhhiiggaaaddddbdd`bccaQ\a`bc_b -@PHOSPHORE_0118:4:1101:7007:4197#ATCACG/1 -CCCCACTCACCACGCACGGCACCGCACGGCACTCTCACGGTTTCTCTCTCTCTCTCCCATCCTTCTCACTCCTTTCTCTCTCTCCCTATCTCTCTCTCTC -+PHOSPHORE_0118:4:1101:7007:4197#ATCACG/1 -bbbeeeeeggggghiiiiihfhifhhiihiagfhiiiiig^dceeeedcddddcccccRZ``bbcbcbbR_bb`b`bb`bbb`bbcbR]b_]]`bb_b_b -@PHOSPHORE_0118:4:1101:1719:2154#ATCACG/1 -GCATGCCAAACGTGGAGGCGGTGGGCGCGACGCCGGTGGGGAACTTGGACTTGTACATGGCCGGCCGCTGCGTCACCATCGA -+PHOSPHORE_0118:4:1101:1719:2154#ATCACG/1 -bbbeeeeeggggegifhiiii^fgh\edgffeeccc\acccWV_ccccbccccbbdccccccccaaacaZ]acaa^bccccb -@PHOSPHORE_0118:4:1101:7113:4916#ATCACG/1 -AGCCTGACGATAACCTACTTTCACACTGGTTGCAGCACTATCATCGGCGCAAAGTCGTTTCACGGTCCTGTTCGGGATGGGAAGGGGTGGGACCGACTTGC -+PHOSPHORE_0118:4:1101:7113:4916#ATCACG/1 -bbbeeeeegggggiiiiiiiiiihiiiiigiiiiiiiiiiiiiiiiiiiihiiggggeeeeddccccccccccccccccccbbccccHXaacccc]acacb -@PHOSPHORE_0118:4:1101:1730:2193#ATCACG/1 -GTTCGATTAGTCTTTCGCCCCTATACCCAAATTTGACGATCGATTTGCACGTCAGAATCGCTAC -+PHOSPHORE_0118:4:1101:1730:2193#ATCACG/1 -baaeeeeeggggghhifhiiihfgbghhhiihihfhihfhihdfghhiiifhiihdbfgddged -@PHOSPHORE_0118:4:1101:11597:5204#ATCACG/1 -GCCGAAGAAGGACGTGGGAATCTGCGATAAGCCTGGTGGAGTCGATAACCGGACGTTGAGACCAGGATTTCCGAATGGGGAAACCCCGCACGACGTGTCGT -+PHOSPHORE_0118:4:1101:11597:5204#ATCACG/1 -bbbeeeeegggggifgiiiiiiiiiihiihiiiiiicfhgheghiiihihggcecccccccccccccccccccccccccccaacccaccc__[_a[a^[_Q - -@PHOSPHORE_0118:4:1101:13427:6518#ATCACG/1 -GCGCTCGAGGAGGACGTGGCGCCCGAGGCTGCCGAGGCTG -+PHOSPHORE_0118:4:1101:13427:6518#ATCACG/1 -Z__cccc`ecg^_fe^[^^^Y_ffc]_`[eZ_c_W\]]b` - |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/read_small.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read_small.fasta Wed Aug 05 02:50:43 2015 -0400 |
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| @@ -0,0 +1,2 @@ +>read1 +GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC |
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| diff -r a8ac09e937f3 -r b482293b2987 test-data/read_small.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read_small.fastq Wed Aug 05 02:50:43 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +@read1 +GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC ++read1 +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/ref_small.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref_small.fasta Wed Aug 05 02:50:43 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>EncFa169 count=1; cluster_weight=27830; cluster=EncFa169; cluster_score=1.000000; cluster_center=True; +AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGCTTCTTTCCTCCCGAGTGCTTGCACTCAATTGGAAAGAGGAGTGGCGGACGGGTGAGTAACACGTGGGTAACCTACCCATCAGAGGGGGATAACACTTGGAAACAGGTGCTAATACCGCATAACAGTTTATGCCGCATGGCATAAGAGTGAAAGGCGCTTTCGGGTGTCGCTGATGGATGGACCCGCGGTGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCCACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACAAGGACGTTAGTAACTGAACGTCCCCTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTGGAGGGTTTCCGCCCTTCAGTGCTGCAGCAAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTTTGACCACTCTAGAGATAGAGCTTTCCCTTCGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTGTTAGTTGCCATCATTTAGTTGGGCACTCTAGCGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGGAAGTACAACGAGTCGCTAGACCGCGAGGTCATGCAAATCTCTTAAAGCTTCTCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGTGAGGTAACCTTTTTGGAGCCAGCCGCCTAAGGTGGGATAGATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCT |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/sortmerna_wrapper_accept1.fastq --- a/test-data/sortmerna_wrapper_accept1.fastq Mon Aug 03 08:18:26 2015 -0400 +++ b/test-data/sortmerna_wrapper_accept1.fastq Wed Aug 05 02:50:43 2015 -0400 |
| [ |
| @@ -1,28 +1,4 @@ -@PHOSPHORE_0118:4:1101:5073:2473#ATCACG/1 -CTCGCGCCACTGGCTGGCTCTCCCCTCTCTCTCTCTCTCTCCCCTCTCTCTCCCCGAGTACACCCGCGCGGGC -+PHOSPHORE_0118:4:1101:5073:2473#ATCACG/1 -___cccccggggghhhhf_YbcgecZYa^Y^ceXccacXIXaafX`_]VMHVbdhSTFKU_Z]b]WFW_aZ__ -@PHOSPHORE_0118:4:1101:17780:2432#ATCACG/1 -GCGGTCTGGAACCACCTGATCCCATCCCGAACTCAGCCGTGAAACAGACCAGCGCCGATGGTAGTGTGGCTTCTGCCCGT -+PHOSPHORE_0118:4:1101:17780:2432#ATCACG/1 -bbbeeeeegggggiiiiiiihiiihiiiiiiihiidhhigfhihiihgiiiiiggeccaccbbb_b`baccab`]_ba[T -@PHOSPHORE_0118:4:1101:7859:3729#ATCACG/1 -GCATCGCCGCCCTCGCCCTCGCCCCCGCCGCCCTCGCCCT -+PHOSPHORE_0118:4:1101:7859:3729#ATCACG/1 -___c`cc`Yeee[ePY_`UY^_eGL_F_`dUU\F\^Q\a_ -@PHOSPHORE_0118:4:1101:7007:4197#ATCACG/1 -CCCCACTCACCACGCACGGCACCGCACGGCACTCTCACGGTTTCTCTCTCTCTCTCCCATCCTTCTCACTCCTTTCTCTCTCTCCCTATCTCTCTCTCTC -+PHOSPHORE_0118:4:1101:7007:4197#ATCACG/1 -bbbeeeeeggggghiiiiihfhifhhiihiagfhiiiiig^dceeeedcddddcccccRZ``bbcbcbbR_bb`b`bb`bbb`bbcbR]b_]]`bb_b_b -@PHOSPHORE_0118:4:1101:7113:4916#ATCACG/1 -AGCCTGACGATAACCTACTTTCACACTGGTTGCAGCACTATCATCGGCGCAAAGTCGTTTCACGGTCCTGTTCGGGATGGGAAGGGGTGGGACCGACTTGC -+PHOSPHORE_0118:4:1101:7113:4916#ATCACG/1 -bbbeeeeegggggiiiiiiiiiihiiiiigiiiiiiiiiiiiiiiiiiiihiiggggeeeeddccccccccccccccccccbbccccHXaacccc]acacb -@PHOSPHORE_0118:4:1101:11597:5204#ATCACG/1 -GCCGAAGAAGGACGTGGGAATCTGCGATAAGCCTGGTGGAGTCGATAACCGGACGTTGAGACCAGGATTTCCGAATGGGGAAACCCCGCACGACGTGTCGT -+PHOSPHORE_0118:4:1101:11597:5204#ATCACG/1 -bbbeeeeegggggifgiiiiiiiiiihiihiiiiiicfhgheghiiihihggcecccccccccccccccccccccccccccaacccaccc__[_a[a^[_Q -@PHOSPHORE_0118:4:1101:13427:6518#ATCACG/1 -GCGCTCGAGGAGGACGTGGCGCCCGAGGCTGCCGAGGCTG -+PHOSPHORE_0118:4:1101:13427:6518#ATCACG/1 -Z__cccc`ecg^_fe^[^^^Y_ffc]_`[eZ_c_W\]]b` +@read1 +GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC ++read1 +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/sortmerna_wrapper_accept2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sortmerna_wrapper_accept2.fasta Wed Aug 05 02:50:43 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>read1 +GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/sortmerna_wrapper_in1.fastq --- a/test-data/sortmerna_wrapper_in1.fastq Mon Aug 03 08:18:26 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,48 +0,0 @@ -@PHOSPHORE_0118:4:1101:1143:2236#ATCACG/1 -CGCGCGCACCATGCCCGTGCTCGACTGCTCGCCGCCCGCGCCGCGCCACGCCTCGCCGTTCACCTTGACCTCCACGCGCAGGCC -+PHOSPHORE_0118:4:1101:1143:2236#ATCACG/1 -__beeeecggcgfhhhhhhhhhhfhhhhhhhhhhhgececcccccccacaccccaccccac`bbbcbbbcbbc[`_a[aLT[aa -@PHOSPHORE_0118:4:1101:1397:2156#ATCACG/1 -ATGCGCTTGAGGTAGCCAAGGGCACGCAGTTCACACCGTATGGCGGCGATGCGAGGCGGCGGCAGGAGG -+PHOSPHORE_0118:4:1101:1397:2156#ATCACG/1 -bbbeeeeegggggiiiiiiiiihfhiheghihgihiiihiiiiihifc^acac^_cEHVZaccaac^__ -@PHOSPHORE_0118:4:1101:5073:2473#ATCACG/1 -CTCGCGCCACTGGCTGGCTCTCCCCTCTCTCTCTCTCTCTCCCCTCTCTCTCCCCGAGTACACCCGCGCGGGC -+PHOSPHORE_0118:4:1101:5073:2473#ATCACG/1 -___cccccggggghhhhf_YbcgecZYa^Y^ceXccacXIXaafX`_]VMHVbdhSTFKU_Z]b]WFW_aZ__ -@PHOSPHORE_0118:4:1101:17780:2432#ATCACG/1 -GCGGTCTGGAACCACCTGATCCCATCCCGAACTCAGCCGTGAAACAGACCAGCGCCGATGGTAGTGTGGCTTCTGCCCGT -+PHOSPHORE_0118:4:1101:17780:2432#ATCACG/1 -bbbeeeeegggggiiiiiiihiiihiiiiiiihiidhhigfhihiihgiiiiiggeccaccbbb_b`baccab`]_ba[T -@PHOSPHORE_0118:4:1101:7859:3729#ATCACG/1 -GCATCGCCGCCCTCGCCCTCGCCCCCGCCGCCCTCGCCCT -+PHOSPHORE_0118:4:1101:7859:3729#ATCACG/1 -___c`cc`Yeee[ePY_`UY^_eGL_F_`dUU\F\^Q\a_ -@PHOSPHORE_0118:4:1101:1633:2146#ATCACG/1 -TGACCAATGTTCTTCATAACGTCCCCGATAGACATGCCAACATTCGGTCCGTTGCGAAGATAGTCATCGCCGTCATAGTC -+PHOSPHORE_0118:4:1101:1633:2146#ATCACG/1 -_bbecdecgggggihhiiiihghhhiihiichdfghiffghfghiifiifhhhiiggaaaddddbdd`bccaQ\a`bc_b -@PHOSPHORE_0118:4:1101:1719:2154#ATCACG/1 -GCATGCCAAACGTGGAGGCGGTGGGCGCGACGCCGGTGGGGAACTTGGACTTGTACATGGCCGGCCGCTGCGTCACCATCGA -+PHOSPHORE_0118:4:1101:1719:2154#ATCACG/1 -bbbeeeeeggggegifhiiii^fgh\edgffeeccc\acccWV_ccccbccccbbdccccccccaaacaZ]acaa^bccccb -@PHOSPHORE_0118:4:1101:7007:4197#ATCACG/1 -CCCCACTCACCACGCACGGCACCGCACGGCACTCTCACGGTTTCTCTCTCTCTCTCCCATCCTTCTCACTCCTTTCTCTCTCTCCCTATCTCTCTCTCTC -+PHOSPHORE_0118:4:1101:7007:4197#ATCACG/1 -bbbeeeeeggggghiiiiihfhifhhiihiagfhiiiiig^dceeeedcddddcccccRZ``bbcbcbbR_bb`b`bb`bbb`bbcbR]b_]]`bb_b_b -@PHOSPHORE_0118:4:1101:7113:4916#ATCACG/1 -AGCCTGACGATAACCTACTTTCACACTGGTTGCAGCACTATCATCGGCGCAAAGTCGTTTCACGGTCCTGTTCGGGATGGGAAGGGGTGGGACCGACTTGC -+PHOSPHORE_0118:4:1101:7113:4916#ATCACG/1 -bbbeeeeegggggiiiiiiiiiihiiiiigiiiiiiiiiiiiiiiiiiiihiiggggeeeeddccccccccccccccccccbbccccHXaacccc]acacb -@PHOSPHORE_0118:4:1101:11597:5204#ATCACG/1 -GCCGAAGAAGGACGTGGGAATCTGCGATAAGCCTGGTGGAGTCGATAACCGGACGTTGAGACCAGGATTTCCGAATGGGGAAACCCCGCACGACGTGTCGT -+PHOSPHORE_0118:4:1101:11597:5204#ATCACG/1 -bbbeeeeegggggifgiiiiiiiiiihiihiiiiiicfhgheghiiihihggcecccccccccccccccccccccccccccaacccaccc__[_a[a^[_Q -@PHOSPHORE_0118:4:1101:1730:2193#ATCACG/1 -GTTCGATTAGTCTTTCGCCCCTATACCCAAATTTGACGATCGATTTGCACGTCAGAATCGCTAC -+PHOSPHORE_0118:4:1101:1730:2193#ATCACG/1 -baaeeeeeggggghhifhiiihfgbghhhiihihfhihfhihdfghhiiifhiihdbfgddged -@PHOSPHORE_0118:4:1101:13427:6518#ATCACG/1 -GCGCTCGAGGAGGACGTGGCGCCCGAGGCTGCCGAGGCTG -+PHOSPHORE_0118:4:1101:13427:6518#ATCACG/1 -Z__cccc`ecg^_fe^[^^^Y_ffc]_`[eZ_c_W\]]b` |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/sortmerna_wrapper_other1.fastq --- a/test-data/sortmerna_wrapper_other1.fastq Mon Aug 03 08:18:26 2015 -0400 +++ b/test-data/sortmerna_wrapper_other1.fastq Wed Aug 05 02:50:43 2015 -0400 |
| [ |
| @@ -1,20 +0,0 @@ -@PHOSPHORE_0118:4:1101:1143:2236#ATCACG/1 -CGCGCGCACCATGCCCGTGCTCGACTGCTCGCCGCCCGCGCCGCGCCACGCCTCGCCGTTCACCTTGACCTCCACGCGCAGGCC -+PHOSPHORE_0118:4:1101:1143:2236#ATCACG/1 -__beeeecggcgfhhhhhhhhhhfhhhhhhhhhhhgececcccccccacaccccaccccac`bbbcbbbcbbc[`_a[aLT[aa -@PHOSPHORE_0118:4:1101:1397:2156#ATCACG/1 -ATGCGCTTGAGGTAGCCAAGGGCACGCAGTTCACACCGTATGGCGGCGATGCGAGGCGGCGGCAGGAGG -+PHOSPHORE_0118:4:1101:1397:2156#ATCACG/1 -bbbeeeeegggggiiiiiiiiihfhiheghihgihiiihiiiiihifc^acac^_cEHVZaccaac^__ -@PHOSPHORE_0118:4:1101:1633:2146#ATCACG/1 -TGACCAATGTTCTTCATAACGTCCCCGATAGACATGCCAACATTCGGTCCGTTGCGAAGATAGTCATCGCCGTCATAGTC -+PHOSPHORE_0118:4:1101:1633:2146#ATCACG/1 -_bbecdecgggggihhiiiihghhhiihiichdfghiffghfghiifiifhhhiiggaaaddddbdd`bccaQ\a`bc_b -@PHOSPHORE_0118:4:1101:1719:2154#ATCACG/1 -GCATGCCAAACGTGGAGGCGGTGGGCGCGACGCCGGTGGGGAACTTGGACTTGTACATGGCCGGCCGCTGCGTCACCATCGA -+PHOSPHORE_0118:4:1101:1719:2154#ATCACG/1 -bbbeeeeeggggegifhiiii^fgh\edgffeeccc\acccWV_ccccbccccbbdccccccccaaacaZ]acaa^bccccb -@PHOSPHORE_0118:4:1101:1730:2193#ATCACG/1 -GTTCGATTAGTCTTTCGCCCCTATACCCAAATTTGACGATCGATTTGCACGTCAGAATCGCTAC -+PHOSPHORE_0118:4:1101:1730:2193#ATCACG/1 -baaeeeeeggggghhifhiiihfgbghhhiihihfhihfhihdfghhiiifhiihdbfgddged |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/sortmerna_wrapper_sam1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sortmerna_wrapper_sam1.sam Wed Aug 05 02:50:43 2015 -0400 |
| b |
| @@ -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 |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 test-data/sortmerna_wrapper_sam2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sortmerna_wrapper_sam2.sam Wed Aug 05 02:50:43 2015 -0400 |
| b |
| @@ -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 |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 tool-data/rRNA_databases.loc --- a/tool-data/rRNA_databases.loc Mon Aug 03 08:18:26 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -rfam-5.8s Database Rfam 5.8s $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta -rfam-5s Database Rfam 5s $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta -silva-arc-16s Database Silva-Arc 16s $SORTMERNADIR/rRNA_databases/silva-arc-16s-database-id95.fasta -silva-arc-23s Database Silva-Arc 23s $SORTMERNADIR/rRNA_databases/silva-arc-23s-database-id98.fasta -silva-bac-16s Database Silva-Bac 16s $SORTMERNADIR/rRNA_databases/silva-bac-16s-database-id85.fasta -silva-bac-23s Database Silva-Bac 23s $SORTMERNADIR/rRNA_databases/silva-bac-23s-database-id98.fasta -silva-euk-18s Databse Silva-Euk 18s $SORTMERNADIR/rRNA_databases/silva-euk-18s-database-id95.fasta -silva-euk-28s Database Silva-Euk 28s $SORTMERNADIR/rRNA_databases/silva-euk-28s-database-id98.fasta |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 tool-data/rRNA_databases.loc.sample --- a/tool-data/rRNA_databases.loc.sample Mon Aug 03 08:18:26 2015 -0400 +++ b/tool-data/rRNA_databases.loc.sample Wed Aug 05 02:50:43 2015 -0400 |
| b |
| @@ -1,26 +1,30 @@ #This is a sample file distributed with Galaxy that is used to define a -#list of public ribosomal databases, using three columns tab separated -#(longer whitespace are TAB characters): +#list of public ribosomal databases for SortMeRNA, using the following format +#(white space characters are TAB characters): # -#<unique_id> <database_caption> <base_name_path> +#<unique_id> <database_caption> <fasta_file_path> # -#It is important that the actual database name does not have a space in it, -#and that the first tab that appears in the line is right before the 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: # -#So, for example, if your database is rfam-5.8s and the path to your base name -#is /data/rRNA_databases/rfam-5.8s, 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 # -#rfam-5.8s Rfam 5.8S eukarya /data/rRNA_databases/rfam-5.8s +#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: # -#Since SortMeRNA comes bundled with eight ribosomal databases, which are ready -#for use after the tool installation, this sample file is in fact an actual file -#to save the user the trouble of setting it. +# indexdb_rna --ref /data/rRNA_databases/rfam-5.8s-id98.fasta,/data/rRNA_databases/rfam-5.8s-id98 # -rfam-5.8s Rfam 5.8S eukarya $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta -rfam-5s Rfam 5S archaea/bacteria $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta -silva-arc-16s SILVA 16S archaea $SORTMERNADIR/rRNA_databases/silva-arc-16s-database-id95.fasta -silva-arc-23s SILVA 16S bacteria $SORTMERNADIR/rRNA_databases/silva-arc-23s-database-id98.fasta -silva-bac-16s SILVA 16S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-16s-database-id85.fasta -silva-bac-23s SILVA 23S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-23s-database-id98.fasta -silva-euk-18s SILVA 18S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-18s-database-id95.fasta -silva-euk-28s SILVA 28S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-28s-database-id98.fasta +#Since SortMeRNA comes bundled with eight ribosomal databases, you can use them +#by creating the actual index files as explained above and uncommenting the +#following lines. +#rfam-5.8s-id98 Rfam 5.8S eukarya $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta +#rfam-5s-id98 Rfam 5S archaea/bacteria $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta +#silva-arc-16s-id95 SILVA v.119 16S archaea $SORTMERNADIR/rRNA_databases/silva-arc-16s-id95.fasta +#silva-arc-23s-id98 SILVA v.119 23S archaea $SORTMERNADIR/rRNA_databases/silva-arc-23s-id98.fasta +#silva-bac-16s-id90 SILVA v.119 16S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-16s-id90.fasta +#silva-bac-23s-id98 SILVA v.119 23S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-23s-id98.fasta +#silva-euk-18s-id95 SILVA v.119 18S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-18s-id95.fasta +#silva-euk-28s-id98 SILVA v.119 28S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta |
| b |
| diff -r a8ac09e937f3 -r b482293b2987 tool_dependencies.xml --- a/tool_dependencies.xml Mon Aug 03 08:18:26 2015 -0400 +++ b/tool_dependencies.xml Wed Aug 05 02:50:43 2015 -0400 |
| b |
| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="sortmerna" version="1.9"> + <package name="sortmerna" version="2.0"> <install version="1.0"> <actions> - <action type="download_by_url">http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-1.9.tar.gz</action> + <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> <action type="autoconf"/> <action type="set_environment"> <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable> |