| Previous changeset 1:a41418a3bd38 (2013-09-03) |
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Commit message:
Barrnap version 0.7 |
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modified:
tool_dependencies.xml |
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added:
barrnap.xml test-data/bacteria.fna test-data/bacteria.gff |
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removed:
barrnap_wrapper.xml |
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| diff -r a41418a3bd38 -r 0b8af9f63afc barrnap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/barrnap.xml Sat Jul 04 10:33:34 2015 -0400 |
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| @@ -0,0 +1,96 @@ +<tool id="barrnap" name="barrnap" version="1.1.0"> + <description>Locate bacterial ribosomal RNA's in a fasta file. (GFF output)</description> + <requirements> + <requirement type="package" version="0.7">barrnap</requirement> + </requirements> + + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + + <command><![CDATA[ + barrnap + --quiet + --threads \${GALAXY_SLOTS:-1} + --reject $reject + --lencutoff $lencutoff + --evalue $evalue + #if $incseq + --incseq + #end if + --kingdom $kingdom + $fasta_file + > $gff + ]]> + </command> + + <inputs> + <param name="fasta_file" type="data" format="fasta" label="Fasta file" help="Fasta file to look for rRNA's in" /> + <param name="kingdom" type="select" label="Kingdom"> + <option value="bac">Bacteria</option> + <option value="euk">Eukaryote</option> + <option value="mito">Mitochondria</option> + <option value="arc">Archaea</option> + </param> + <param name="reject" type="float" value="0.5" label="Reject length threshold" help="Proportional length threshold to reject prediction" /> + <param name="lencutoff" type="float" value="0.8" label="Length cutoff" help="Proportional length threshold to tag a find as pseudo" /> + <param name="evalue" type="float" value="1e-06" label="e-value" help="Similarity e-value cutoff" /> + <param name="incseq" type="boolean" label="Include Sequences in GFF" help="Include the fasta sequences in the GFF output file" /> + </inputs> + + <outputs> + <data name="gff" format="gff3" lavel="${tool.name} on ${on_string}: rRNA GFF"/> + </outputs> + + <tests> + <test> + <param name="fasta_file" value="bacteria.fna" ftype="fasta" /> + <param name="kingdom" value="bac" /> + <output name="gff" value="bacteria.gff" ftype="gff3" /> + </test> + </tests> + +<help> + +**barrnap** +:: +barrnap_ predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequences. Barrnap now supports Archaea, Eukaryota and Mitochondria. It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1-dev for HMM searching in DNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. +This tool is designed to be a substitute for RNAmmer. It was motivated by my desire to remove Prokka's dependency on RNAmmer which is encumbered by an free-for-academic sign-up license, and by the needed legacy HMMER 2.x which conflicts with HMMER 3.x that most people are using now. + +RNAmmer is more sophisticated than Barrnap, and more accurate. because it uses HMMER 2.x in glocal alignment mode, whereas HMMER 3.x currently only supports local alignment (Sean Eddy expects glocal to be supported in 2014). In practice, Barrnap will find all the typical 5/16/23S genes in bacteria, but may get the end points out by a few bases and will probably miss wierd rRNAs. The HMM models it uses are derived from RFAM, Silva, and GreenGenes. + +The name Barrnap is derived from BActerial Ribosomal RNA Predictor. It was spawned at CodeFest 2013 in Berlin, Germany by Torsten Seemann and Tim Booth. + +.. _barrnap: http://www.vicbioinformatics.com/software.barrnap.shtml + +**Inputs/Parameters** +:: +**Fasta file** +The fasta file whose contents you want to search for ribosomal RNA's. +:: +**Kingdom** +Select the Kingdom of the organism: Bacteria, Eukarote, Mitochondria or Archaea. +:: +**Length cutoff** +Proportional length threshold to tag a possible rRNA as pseudo. +:: +**Reject length threshold** +Proportional length threshold to reject prediction +:: +**E-value** +Similarity cutoff e-value. +</help> +<citations> + <citation type="bibtex">@UNPUBLISHED{Seemann2013, + author = "Torsten Seemann", + title = "barrnap 0.7 : rapid ribosomal RNA prediction", + year = "2013", + note = "https://github.com/Victorian-Bioinformatics-Consortium/barrnap"} + </citation> +</citations> +</tool> |
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| diff -r a41418a3bd38 -r 0b8af9f63afc barrnap_wrapper.xml --- a/barrnap_wrapper.xml Tue Sep 03 00:25:08 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,55 +0,0 @@ -<tool id="barrnap" name="barrnap" version="1.0.0"> - <description>Locate bacterial ribosomal RNA's in a fasta file. (GFF output)</description> - <requirements> - <requirement type="package" version="0.1">package_barrnap_0_1</requirement> - </requirements> - <command> - barrnap - --lencutoff $lencutoff - --evalue $evalue - $fasta_file - > $gff - 2> $stderr - </command> - - <inputs> - <param name="fasta_file" type="data" format="fasta" label="Fasta file" help="Fasta file to look for rRNA's in" /> - <param name="lencutoff" type="float" value="0.8" label="Length cutoff" help="Proportional length threshold to tag a find as pseudo" /> - <param name="evalue" type="float" value="1e-06" label="e-value" help="Similarity e-value cutoff" /> - </inputs> - - <outputs> - <data name="stderr" format="tabular" label="${tool.name} on ${on_string}: STDERR"/> - <data name="gff" format="gff3" lavel="${tool.name} on ${on_string}: rRNA GFF"/> - </outputs> - - <help> -**barrnap** -:: -barrnap_ predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequences. It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1-dev for HMM searching in DNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. -This tool is designed to be a substitute for RNAmmer for bacteria. It was motivated by my desire to remove Prokka's dependency on RNAmmer which is encumbered by an free-for-academic sign-up license, and by the needed legacy HMMER 2.x which conflicts with HMMER 3.x that most people are using now. - -RNAmmer is more sophisticated than Barrnap, and more accurate. because it uses HMMER 2.x in glocal alignment mode, whereas HMMER 3.x currently only supports local alignment (Sean Eddy expects glocal to be supported in 2014). In practice, Barrnap will find all the typical 5/16/23S genes in bacteria, but may get the end points out by a few bases and will probably miss wierd rRNAs. The HMM models it uses are derived from RFAM, Silva, and GreenGenes. - -Barrnap is for bacteria (prokaryota) only. If you want to find rRNA genes in Archaea or Eukaryota then you should continue to use RNAmmer. - -The name Barrnap is derived from BActerial Ribosomal RNA Predictor. It was spawned at CodeFest 2013 in Berlin, Germany by Torsten Seemann and Tim Booth. - -.. _barrnap: http://www.vicbioinformatics.com/software.barrnap.shtml - ------- - -**Inputs/Parameters** -:: -**Fasta file** -The fasta file whose contents you want to search for ribosomal RNA's. -:: -**Length cutoff** -:: -Proportional length threshold to tag a possible rRNA as pseudo. -:: -**E-value** -Similarity cutoff e-value. - - </help> -</tool> |
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| diff -r a41418a3bd38 -r 0b8af9f63afc test-data/bacteria.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bacteria.fna Sat Jul 04 10:33:34 2015 -0400 |
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| b'@@ -0,0 +1,66284 @@\n+>E.coli Escherichia coli str. K-12 substr. MG1655, complete genome\n+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC\n+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA\n+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC\n+ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG\n+CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA\n+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC\n+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG\n+AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT\n+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT\n+GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC\n+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT\n+TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT\n+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG\n+CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC\n+TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT\n+CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG\n+CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATAC\n+CGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC\n+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGG\n+CGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGA\n+ATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTC\n+TACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGG\n+TAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATAT\n+CAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG\n+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG\n+GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA\n+TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG\n+GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA\n+AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC\n+CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC\n+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG\n+GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT\n+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG\n+CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA\n+AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT\n+GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC\n+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG\n+ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA\n+AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC\n+AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC\n+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG\n+TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA\n+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG\n+CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT\n+CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC\n+GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC\n+GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC\n+AAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC\n+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTC\n+ATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCT\n+ACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAG\n+CGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCC\n+GACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGG\n+GCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC\n+GCAAGCCGTAACCCAGGGGTTG'..b'GGTTAACGTTGCTGCTGAACCGGCGTTAC\n+TGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCT\n+AAGCGCCGAAGTGGATCAGGAACACGTCACGCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTAC\n+GCGCTTTCACGTATTTTTGAACGCTTTTACTCTTTGCCTCGTGCAAATGGGCAAAAAAGCAGCGGTCTGG\n+GGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGG\n+TGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCCACATAGTCTTCG\n+TATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGT\n+TTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGATTCGGCAGGTGATTGTCGAACGTGCTGATTA\n+CCGTAGCGATGTGGAAGATGCGATTCGCCAAAGTACCAGCGGGCCGCAAAAACTCGTTGGGCCGCTCATC\n+GCTATTCCTGTGACCGAGCTTTATACGGTGCAGGAAGAGGATAAAACCGTGGAGCGGAAACGAAGTTTTA\n+TCCATTTTTGGTTACCTGAGTCATTGATGGTTGATGGCAATCAGAACGTGGAAGAACGCAAGATAGGGAT\n+TTATACCGGTCAGGTCTGGCACAGTGATTTAACGTTAAAAGCCGATTTCGATGTTTCGCGTCTTAGCGAA\n+CTCAACGCGCCAAATATCACCTTAGGCAAGCCATTTATTGTGATTAGCGTCGGGGATGCGCGTGGTATTG\n+GTGTGGTGAAAGCGCCTGAAGTTAACGGAACGGCGCTGACCATTGAACCCGGCACCGGGTTAGAGCAAGG\n+CGGGCAGGGCGTGCATATCCCTTTACCTGAAGGGGACTGGCGGAAGCAGAACCTGAAGCTGAATATGGCC\n+CTGAATTTAAGCGGTACCGGCGATCTTTCTGTGGTGCCTGGCGGGCGTAATAGCGAAATGACCTTAACCA\n+GCAACTGGCCGCATCCCAGTTTTTTAGGTGATTTTCTACCAGCCAAACGGGAAGTTAGCGAGTCAGGTTT\n+TCAGGCGCACTGGCAAAGCAGCTGGTTTGCTAATAATCTCGGTGAGCGTTTTGCTTCAGGCAATGATACC\n+GGCTGGGAAAACTTCCCGGCGTTTAGCGTCGCAGTAACGACGCCAGCCGATCAATACCAATTAACTGACC\n+GGGCGACTAAGTACGCCATTCTGCTGATTGCACTGACTTTTATGGCGTTCTTTGTTTTTGAAACGCTCAC\n+CGCGCAACGTTTACACCCAATGCAATATTTGCTGGTGGGGCTTTCATTGGTGATGTTTTATTTGCTCTTG\n+CTGGCGCTTTCTGAACATACCGGTTTTACCGTGGCATGGATAATCGCCAGTCTGATTGGGGCGATAATGA\n+ACGGTATTTATTTGCAAGCGGTATTGAAAGGTTGGTGCAACAGCATGTTGTTTACCCTCGCGCTGTTGTT\n+GCTGGATGGTGTGATGTGGGGACTGCTCAACTCTGCCGATAGCGCGCTGTTGTTGGGAACCAGTGTGCTG\n+GTGGTGGCGCTGGCCGGCATGATGTTTGTGACCCGTAATATCGACTGGTATGCGTTTTCACTGCCGAAAA\n+TGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAAC\n+GGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGA\n+TAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAGATTCGAAATGTTTACGAATAC\n+GGCGGATCGTCACGTCTACAGTACGGTCGTGCGGTTTCAGCTCACGGCCGGTCATTTTCTTCAGCAGTTC\n+AGCACGGGACTGAATTTTGCCTGGGTTTTCACAGAAGTGAAGCATGGCGCGGAACTCGCTGCGCGGCAGC\n+TTGTACTGCTCGCCATCAGGGCCGATCAACGAACGGCTGTTGATGTCCAGTTCCCAACCATTGAACTTGT\n+AGCTTTCAACGCTACGACGTTCTTCGCTGACAGTACCCAGATTCATGGTACGGGACAGTAGGTTGCGTGC\n+ACGAATCGTCAGTTCACGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGA\n+ATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCAC\n+GCGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGA\n+GAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTT\n+TTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCT\n+AAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAAC\n+ATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACAT\n+CATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCAAAAACGGCTGTCATCCTAACCATT\n+TTAACAGCAACATAACAGGCTAAGAGGGGCCGGACACCCAATAAAACTACGCTTCGTTGACATATATCAA\n+GTTCAATTGTAGCACGTTAACAGTTTGATGAAATCATCGTATCTAAATGCTAGCTTTCGTCACATTATTT\n+TAATAATCCAACTAGTTGCATCATACAACTAATAAACGTGGTGAATCCAATTGTCGAGATTTATTTTTTA\n+TAAAATTATCCTAAGTAAACAGAAGGATATGTAGCATTTTTTAACAACTCAACCGTTAGTACAGTCAGGA\n+AATAGTTTAGCCTTTTTTAAGCTAAGTAAAGGGCTTTTTCTGCGACTTACGTTAAGAATTTGTAAATTCG\n+CACCGCGTAATAAGTTGACAGTGATCACCCGGTTCGCGGTTATTTGATCAAGAAGAGTGGCAATATGCGT\n+ATAACGATTATTCTGGTCGCACCCGCCAGAGCAGAAAATATTGGGGCAGCGGCGCGGGCAATGAAAACGA\n+TGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACA\n+TGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAATCGTTACACGATGTCGAT\n+TTCACTGTCGCCACCACTGCGCGCAGTCGGGCGAAATATCATTACTACGCCACGCCAGTTGAACTGGTGC\n+CGCTGTTAGAGGAAAAATCTTCATGGATGAGCCATGCCGCGCTGGTGTTTGGTCGCGAAGATTCCGGGTT\n+GACTAACGAAGAGTTAGCGTTGGCTGACGTTCTTACTGGTGTGCCGATGGTGGCGGATTATCCTTCGCTC\n+AATCTGGGGCAGGCGGTGATGGTCTATTGCTATCAATTAGCAACATTAATACAACAACCGGCGAAAAGTG\n+ATGCAACGGCAGACCAACATCAACTGCAAGCTTTACGCGAACGAGCCATGACATTGCTGACGACTCTGGC\n+AGTGGCAGATGACATAAAACTGGTCGACTGGTTACAACAACGCCTGGGGCTTTTAGAGCAACGAGACACG\n+GCAATGTTGCACCGTTTGCTGCATGATATTGAAAAAAATATCACCAAATAAAAAACGCCTTAGTAAGTAT\n+TTTTC\n+\n' 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| diff -r a41418a3bd38 -r 0b8af9f63afc test-data/bacteria.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bacteria.gff Sat Jul 04 10:33:34 2015 -0400 |
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| @@ -0,0 +1,23 @@ +##gff-version 3 +E.coli barrnap:0.7 rRNA 223774 225311 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.7 rRNA 225761 228661 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.7 rRNA 228760 228870 1.9e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.7 rRNA 2724096 2724206 1.9e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.7 rRNA 2724304 2727204 0 - . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.7 rRNA 2727639 2729177 0 - . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.7 rRNA 3421450 3421560 4.3e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.7 rRNA 3421695 3421805 1.9e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.7 rRNA 3421903 3424803 0 - . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.7 rRNA 3425244 3426782 0 - . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.7 rRNA 3939834 3941371 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.7 rRNA 3941729 3944629 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.7 rRNA 3944727 3944837 1.9e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.7 rRNA 4033557 4035094 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.7 rRNA 4035544 4038445 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.7 rRNA 4038544 4038654 2.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.7 rRNA 4164685 4166222 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.7 rRNA 4166666 4169566 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.7 rRNA 4169664 4169774 6.3e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.7 rRNA 4206173 4207710 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.7 rRNA 4208068 4210968 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.7 rRNA 4211067 4211177 6.3e-11 + . Name=5S_rRNA;product=5S ribosomal RNA |
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| diff -r a41418a3bd38 -r 0b8af9f63afc tool_dependencies.xml --- a/tool_dependencies.xml Tue Sep 03 00:25:08 2013 -0400 +++ b/tool_dependencies.xml Sat Jul 04 10:33:34 2015 -0400 |
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| @@ -1,18 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="package_barrnap_0_1" version="0.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://www.vicbioinformatics.com/barrnap-0.1.tar.gz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - <action type="shell_command">chmod ugo+x $INSTALL_DIR/bin/barrnap</action> - </actions> - </install> + <package name="barrnap" version="0.7"> + <repository changeset_revision="c46ab932a19b" name="package_barrnap_0_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |