| Previous changeset 0:8fd427007e93 (2017-08-28) Next changeset 2:fe48aa4ccd5e (2022-06-23) |
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Commit message:
planemo upload commit 19a431ffca44dd1fd61ba2b66e5fc5ca96364f81 |
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modified:
barrnap.xml test-data/test_1.gff test-data/test_2.gff test-data/test_3.gff |
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added:
test-data/test_4.fna test-data/test_4.gff |
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| diff -r 8fd427007e93 -r 7355bbf5e05f barrnap.xml --- a/barrnap.xml Mon Aug 28 14:14:41 2017 -0400 +++ b/barrnap.xml Sun Jun 10 03:26:56 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="barrnap" name="barrnap" version="1.2.0"> +<tool id="barrnap" name="barrnap" version="1.2.1"> <description>Locate ribosomal RNA's in a fasta file. (GFF output)</description> <requirements> - <requirement type="package" version="0.8">barrnap</requirement> + <requirement type="package" version="0.9">barrnap</requirement> </requirements> <version_command>barrnap --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -14,6 +14,9 @@ #if $incseq --incseq #end if + #if $outseq + --outseq '$fasta_out' + #end if --kingdom $kingdom '$fasta_file' > '$gff' @@ -32,10 +35,14 @@ <param name="lencutoff" type="float" value="0.8" label="Length cutoff" help="Proportional length threshold to tag a find as pseudo" /> <param name="evalue" type="float" value="1e-06" label="e-value" help="Similarity e-value cutoff" /> <param name="incseq" type="boolean" label="Include Sequences in GFF" help="Include the fasta sequences in the GFF output file" /> + <param name="outseq" type="boolean" label="Save rRNA hit seqs as FASTA" help="Produce an output file of the rRNA sequences found in FASTA format." /> </inputs> <outputs> <data name="gff" format="gff3" label="${tool.name} on ${on_string}: rRNA GFF"/> + <data name="fasta_out" format="fasta" label="${tool.name} on ${on_string}: rRNA Sequences"> + <filter>outseq</filter> + </data> </outputs> <tests> @@ -56,6 +63,13 @@ <param name="evalue" value="0.00000001" /> <output name="gff" value="test_3.gff" ftype="gff3" /> </test> + <test><!-- Test 4 --> + <param name="fasta_file" value="small.fna" ftype="fasta" /> + <param name="outseq" value="true" /> + <param name="kingdom" value="bac" /> + <output name="gff" value="test_4.gff" ftype="gff3" /> + <output name="fasta_out" value="test_4.fna" ftype="fasta" /> + </test> </tests> <help> |
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| diff -r 8fd427007e93 -r 7355bbf5e05f test-data/test_1.gff --- a/test-data/test_1.gff Mon Aug 28 14:14:41 2017 -0400 +++ b/test-data/test_1.gff Sun Jun 10 03:26:56 2018 -0400 |
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| @@ -1,23 +1,23 @@ ##gff-version 3 -E.coli barrnap:0.8 rRNA 223774 225311 0 + . Name=16S_rRNA;product=16S ribosomal RNA -E.coli barrnap:0.8 rRNA 225761 228661 0 + . Name=23S_rRNA;product=23S ribosomal RNA -E.coli barrnap:0.8 rRNA 228760 228870 1.9e-11 + . Name=5S_rRNA;product=5S ribosomal RNA -E.coli barrnap:0.8 rRNA 2724096 2724206 1.9e-11 - . Name=5S_rRNA;product=5S ribosomal RNA -E.coli barrnap:0.8 rRNA 2724304 2727204 0 - . Name=23S_rRNA;product=23S ribosomal RNA -E.coli barrnap:0.8 rRNA 2727639 2729176 0 - . Name=16S_rRNA;product=16S ribosomal RNA -E.coli barrnap:0.8 rRNA 3421450 3421560 4.4e-11 - . Name=5S_rRNA;product=5S ribosomal RNA -E.coli barrnap:0.8 rRNA 3421695 3421805 1.9e-11 - . Name=5S_rRNA;product=5S ribosomal RNA -E.coli barrnap:0.8 rRNA 3421903 3424803 0 - . Name=23S_rRNA;product=23S ribosomal RNA -E.coli barrnap:0.8 rRNA 3425244 3426781 0 - . Name=16S_rRNA;product=16S ribosomal RNA -E.coli barrnap:0.8 rRNA 3939834 3941371 0 + . Name=16S_rRNA;product=16S ribosomal RNA -E.coli barrnap:0.8 rRNA 3941729 3944629 0 + . Name=23S_rRNA;product=23S ribosomal RNA -E.coli barrnap:0.8 rRNA 3944727 3944837 1.9e-11 + . Name=5S_rRNA;product=5S ribosomal RNA -E.coli barrnap:0.8 rRNA 4033557 4035094 0 + . Name=16S_rRNA;product=16S ribosomal RNA -E.coli barrnap:0.8 rRNA 4035544 4038445 0 + . Name=23S_rRNA;product=23S ribosomal RNA -E.coli barrnap:0.8 rRNA 4038544 4038654 2.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA -E.coli barrnap:0.8 rRNA 4164685 4166222 0 + . Name=16S_rRNA;product=16S ribosomal RNA -E.coli barrnap:0.8 rRNA 4166666 4169566 0 + . Name=23S_rRNA;product=23S ribosomal RNA -E.coli barrnap:0.8 rRNA 4169664 4169774 6.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA -E.coli barrnap:0.8 rRNA 4206173 4207710 0 + . Name=16S_rRNA;product=16S ribosomal RNA -E.coli barrnap:0.8 rRNA 4208068 4210968 0 + . Name=23S_rRNA;product=23S ribosomal RNA -E.coli barrnap:0.8 rRNA 4211067 4211177 6.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.9 rRNA 223774 225311 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.9 rRNA 225761 228661 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.9 rRNA 228760 228870 1.9e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.9 rRNA 2724096 2724206 1.9e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.9 rRNA 2724304 2727204 0 - . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.9 rRNA 2727639 2729176 0 - . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.9 rRNA 3421450 3421560 4.4e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.9 rRNA 3421695 3421805 1.9e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.9 rRNA 3421903 3424803 0 - . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.9 rRNA 3425244 3426781 0 - . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.9 rRNA 3939834 3941371 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.9 rRNA 3941729 3944629 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.9 rRNA 3944727 3944837 1.9e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.9 rRNA 4033557 4035094 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.9 rRNA 4035544 4038445 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.9 rRNA 4038544 4038654 2.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.9 rRNA 4164685 4166222 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.9 rRNA 4166666 4169566 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.9 rRNA 4169664 4169774 6.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.9 rRNA 4206173 4207710 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.9 rRNA 4208068 4210968 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.9 rRNA 4211067 4211177 6.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA |
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| diff -r 8fd427007e93 -r 7355bbf5e05f test-data/test_2.gff --- a/test-data/test_2.gff Mon Aug 28 14:14:41 2017 -0400 +++ b/test-data/test_2.gff Sun Jun 10 03:26:56 2018 -0400 |
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| @@ -1,7 +1,7 @@ ##gff-version 3 -P.marinus barrnap:0.8 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA -P.marinus barrnap:0.8 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA -P.marinus barrnap:0.8 rRNA 358433 358536 9.6e-07 + . Name=5S_rRNA;product=5S ribosomal RNA +P.marinus barrnap:0.9 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA +P.marinus barrnap:0.9 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA +P.marinus barrnap:0.9 rRNA 358433 358536 9.6e-07 + . Name=5S_rRNA;product=5S ribosomal RNA ##FASTA >P.marinus Prochlorococcus marinus subsp. marinus str. CCMP1375 chromosome, complete genome AAAGCTAGATGGCAGAAAGGTTTTTGAATAATTTCCACAGATTCCACAAGACCTACTACTACTGTATTAA |
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| diff -r 8fd427007e93 -r 7355bbf5e05f test-data/test_3.gff --- a/test-data/test_3.gff Mon Aug 28 14:14:41 2017 -0400 +++ b/test-data/test_3.gff Sun Jun 10 03:26:56 2018 -0400 |
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| @@ -1,3 +1,3 @@ ##gff-version 3 -P.marinus barrnap:0.8 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA -P.marinus barrnap:0.8 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA +P.marinus barrnap:0.9 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA +P.marinus barrnap:0.9 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA |
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| diff -r 8fd427007e93 -r 7355bbf5e05f test-data/test_4.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_4.fna Sun Jun 10 03:26:56 2018 -0400 |
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| @@ -0,0 +1,6 @@ +>16S_rRNA::P.marinus:353313-354793(+) +ACGGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAACCTTCGGGTTAGTGGCGGACGGGTGAGTAACGCGTGGGAATCTGCCCTCAGGAGGGGGATAACGGTTGGAAACGACCGCTAATACCCCATATGCCGAGAGGTGAAATGAATTTCGCCTGAGGATGAGCCCGCGTCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCTTCGATCAGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGGGATGAAGGCCTCTGGGCTGTAAACCTCTTTTCTCAAGGAAGAAGATATGACGGTACTTGAGGAATAAGCCACGGCTAATTCCGTGCCAGCAGCCGCGGTAATACGGGAGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGTCCGCAGGCGGCCTTTCAAGTCTGCTGTAAAAACGTGGAGCTTAACTCCATCATCGCAGTGGAAACTGAAGGGCTCGAGTGTGGTAGGGGCAGAGGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAAGAACACCAGTGGCGAAGGCGCTCTGCTGGGCCATAACTGACGCTCATGGACGAAAGCCAGGGGAGCGAAAGGGATTAGATACCCCTGTAGTCCTGGCCGTAAACGATGAACACTAGGTGTCGGGGGAATCGACCCCTTCGGTGTCGTAGCTAACGCGTTAAGTGTTCCGCCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCAGGATTTGACATCCTGCGAACCTCTTAGAAATTTGAGGGTGCCTTCGGGAACGCAGTGACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCACGTTTTTAGTTGCCAGCATTTAGTTGGGCACTCTAGAAAGACCGCCGGTGATAAACCGGAGGAAGGTGTGGATGACGTCAAGTCATCATGCCCCTTACATCCTGGGCTACACACGTACTACAATGCTACGGACAAAGGGCAGCAAACTCGCGAGAGCAAGCAAATCCCATAAACCGTGGCTCAGTTCAGATCGTAGGCTGCAACTCGCCTACGTGAAGCAGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGAAGTTGGCCACGCCCGAAGTCGTTACTCCAACCCTTGTGGAGGAGGACGCCGAAGGTGGGGCTGATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCT +>23S_rRNA::P.marinus:355463-358334(+) +TCAAGCTACAAAGGGCTCACGGTGGATACCTTGGCACACAGAGGCGATGAAGGACGTGGTTACCTGCGATAAGTCTCGGGGAGCTGGAAGCACGCTTTGATCCGGGAATTTCCGAATGGGGCAACCCTTAATACGGCCAGCTGAATATATAGGCTGGAACGAGCCAACCCAGCGAACTGAAACATCTTAGTAGCTGGAGGAAAGGAAAGTAAAAACGACTCCCTAAGTAGCGGCGAGCGAACGGGGACAAGCCCAAACCGATAGTTTCGACTGTCGGGGTTGTGGGACAGCAACGTGGACCAATGAACCTAGAAGAAGCGTTTGAATGGCGCGCCATAGAGGGTGAAAGCCCCGTAATCGAAAGGAGAGTTGGCCTAGCTGTATCCCGAGTAACACGGAGCACGTGGAATTCCGTGTGAATCTACGAGGACCACCTCGTAAGGCTAAGTACTCCTGTGTGACCGATAGCGAAACAGTACCGCGAGGGAAAGGTGAAAAGAACCCCGGGAGGGGAGTGAAATAGAACATGAAACCGTGAGCTTACAAGCAATGGGAGCCCGACTAATCGGGTGACCGTGTGCCTGTTGAAGAATGAGCCGGCGACTTATAGGCACTGGCGGGTTAAACCGGGAATGGTGGAGCCATAGCGAAAGCGAGTCTTAATAGGGCGTTTGTCAGTGTTTATAGACCCGAACCCTGGTGATCTAACCATGGCCAGGATGAAGCTTGGGTGATACCAAGTGGAGGTCCGAACCGACTGATGTTGAAAAATCAGCGGATGAGCTGTGGTTAGGGGTGAAATGCCAATCGAACCAGGAGCTAGCTGGTTCTCCCCGAAATACGTTGAGGCGTAGCGTCTAGTGCTCCAGCAGGGGGGTAAAGCCACCATTTCGGTGCGGGCTGCGAAAGCGGTACCAAATCGATATGAACTCTGAATACCCTGTGTGTAACTAGGCAGTCAGACTGTGGGGGATAAGCTCCACACTCGAAAGGGAAACAGCCCAGACCGCCAGCTAAGGTCCCAAAATCAGTACTAAGTGATAAAGGAGGTGGGATTGCTTAGACAACCAGGAGGTTTGCTTAGAAGCAGCCATCCTCAAAGGAGTGCGTAATAGCTCACTGGTCGAGCGATCCTGCGCCGAAAATGAACGGGGCTAAGTGCTGTACCGAAGCTGCGGATTTACTTGTAAATGGTAGGGGAGCGTTCTATGTGGGGTGAAGCGTTAGCGTAAGCGGGCGTGGACTGCATTGAAGTGAGAATGTCGGCTTGAGTAGCGAAAACATGGGTGAGAATCCCATGCCCCGAAACCCTAAGGGTTCCTCCGGCAGGCTCGTCCGCGGAGGGTTAGTCTGGACCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGATAACAGGTCAACATTCCTGTACCGGTTATGTTTTGGGAAGGGGGACGGAGAAGGCTAGCCAATCCAGATGTTGGTTACTGGTTCAAGCGTTCAAGGCTATGAGGAACGGAGAAAACGTTCTGAGCTAAGGCGTGAGTACGAGTTGCTACGGCAACGAAGTTGGTGATGTCATGCTTCCAAGAAAAGCCCTATACCCGTTAAGGCATAACTGCCTGTACCCGAAACCGACACAGGTGGGGTGGTAGAGAATACCGAGGGGCGCGAGATAACTCTCTCTAAGGAACTCGGCAAAATGGCCCCGTAACTTCGGGAGAAGGGGTGCCAGCGAGAGCTGGCCGCAGTGAAGAGGCCCAAGCGACTGTTTACCAAAAACACAGGTCTCCGCTAAGTCGCAAGACGATGTATGGGGGCTGACGCCTGCCCAGTGCCGGAAGGTTAAGGAAGCCGGTTAGCGTAAGCAAAGCTGGCGACTGAAGCCCCGGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCGCTGTCTCGGAGAGAGGCTCGGCGAAATAGAATTGTCTGTGAAGATGCGGACTACGTACACCCGGACAGAAAGACCCTATGAAGCTTTACTGTAGGTTGATATTGGTCTCGGGCTCTGAATGCGCAGGATAGGTGGGAGACTATGAAGTAGTGCTTGTGGGTGCTATTGAGTCAATGGTGAGATACCACTCTTTCAGAGCTAGGGTTCTAACGCTTACCCGTTATCCGGGAAGCGGACAGTATCTGCTGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGTACAAAGGTTCCCTCAGGCTGGTTGGAAATCAGTCGCTGAGTGCAAAAGCAGAAGGGAGCTTGACTGTGAGACCTACAAGTCGAACAGGGACGAAAGTCGGTTTTAGTGATCCGACGGTTCTGAGTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGCTGATCTCCCCCAAGAGTTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCAACCTGGGGCTGAAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCATATCCGGTGTACGCGCAGGAATATTGAGAGGATTTCTCCCTAGTACGAGAGGACCGGGAGGAACGCACCTCTGGTGTGCCAGTTATCGTGCCAACGGTAAACGCTGGGTAGCCATGTGCGGAGTGGATAACCGCTGAAAGCATCTAAGTGGGAAGCCCACCTCAAGATGAGTATTCCCATGGCATAAGCCAGTAAGGTCACGGGAAGAACACCCGTTGATAGGCTCTACGTGGAAGCTTGGTAACAAGTGCAGCGGAGGAGTACTAATAGACCGAGGGCTTGACCT +>5S_rRNA::P.marinus:358432-358536(+) +TGGTGTTCATCGCGATGTGGACCCACTCCGATCCATCCCGAACTCGGTTGTGAAACGCATCAGCGGCGACGATATTTGGGGGGAAGCCCCCTGAGAAAATAGCT |
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| diff -r 8fd427007e93 -r 7355bbf5e05f test-data/test_4.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_4.gff Sun Jun 10 03:26:56 2018 -0400 |
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| @@ -0,0 +1,4 @@ +##gff-version 3 +P.marinus barrnap:0.9 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA +P.marinus barrnap:0.9 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA +P.marinus barrnap:0.9 rRNA 358433 358536 9.6e-07 + . Name=5S_rRNA;product=5S ribosomal RNA |