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Bumped barrnap to 0.9
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@Slugger70
Slugger70 committed May 4, 2018
1 parent 6a36234 commit 2aeb301
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Showing 6 changed files with 53 additions and 29 deletions.
18 changes: 16 additions & 2 deletions tools/barrnap/barrnap.xml
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<tool id="barrnap" name="barrnap" version="1.2.0">
<tool id="barrnap" name="barrnap" version="0.9.1">
<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[
Expand All @@ -14,6 +14,9 @@
#if $incseq
--incseq
#end if
#if $outseq
--outseq '$fasta_out'
#end if
--kingdom $kingdom
'$fasta_file'
> '$gff'
Expand All @@ -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>
Expand All @@ -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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44 changes: 22 additions & 22 deletions tools/barrnap/test-data/test_1.gff
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##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
6 changes: 3 additions & 3 deletions tools/barrnap/test-data/test_2.gff
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##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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4 changes: 2 additions & 2 deletions tools/barrnap/test-data/test_3.gff
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##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
6 changes: 6 additions & 0 deletions tools/barrnap/test-data/test_4.fna
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>16S_rRNA::P.marinus:353313-354793(+)
ACGGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAACCTTCGGGTTAGTGGCGGACGGGTGAGTAACGCGTGGGAATCTGCCCTCAGGAGGGGGATAACGGTTGGAAACGACCGCTAATACCCCATATGCCGAGAGGTGAAATGAATTTCGCCTGAGGATGAGCCCGCGTCTGATTAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCTTCGATCAGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGGGATGAAGGCCTCTGGGCTGTAAACCTCTTTTCTCAAGGAAGAAGATATGACGGTACTTGAGGAATAAGCCACGGCTAATTCCGTGCCAGCAGCCGCGGTAATACGGGAGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGTCCGCAGGCGGCCTTTCAAGTCTGCTGTAAAAACGTGGAGCTTAACTCCATCATCGCAGTGGAAACTGAAGGGCTCGAGTGTGGTAGGGGCAGAGGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAAGAACACCAGTGGCGAAGGCGCTCTGCTGGGCCATAACTGACGCTCATGGACGAAAGCCAGGGGAGCGAAAGGGATTAGATACCCCTGTAGTCCTGGCCGTAAACGATGAACACTAGGTGTCGGGGGAATCGACCCCTTCGGTGTCGTAGCTAACGCGTTAAGTGTTCCGCCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCAGGATTTGACATCCTGCGAACCTCTTAGAAATTTGAGGGTGCCTTCGGGAACGCAGTGACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCACGTTTTTAGTTGCCAGCATTTAGTTGGGCACTCTAGAAAGACCGCCGGTGATAAACCGGAGGAAGGTGTGGATGACGTCAAGTCATCATGCCCCTTACATCCTGGGCTACACACGTACTACAATGCTACGGACAAAGGGCAGCAAACTCGCGAGAGCAAGCAAATCCCATAAACCGTGGCTCAGTTCAGATCGTAGGCTGCAACTCGCCTACGTGAAGCAGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGAAGTTGGCCACGCCCGAAGTCGTTACTCCAACCCTTGTGGAGGAGGACGCCGAAGGTGGGGCTGATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCT
>23S_rRNA::P.marinus:355463-358334(+)
TCAAGCTACAAAGGGCTCACGGTGGATACCTTGGCACACAGAGGCGATGAAGGACGTGGTTACCTGCGATAAGTCTCGGGGAGCTGGAAGCACGCTTTGATCCGGGAATTTCCGAATGGGGCAACCCTTAATACGGCCAGCTGAATATATAGGCTGGAACGAGCCAACCCAGCGAACTGAAACATCTTAGTAGCTGGAGGAAAGGAAAGTAAAAACGACTCCCTAAGTAGCGGCGAGCGAACGGGGACAAGCCCAAACCGATAGTTTCGACTGTCGGGGTTGTGGGACAGCAACGTGGACCAATGAACCTAGAAGAAGCGTTTGAATGGCGCGCCATAGAGGGTGAAAGCCCCGTAATCGAAAGGAGAGTTGGCCTAGCTGTATCCCGAGTAACACGGAGCACGTGGAATTCCGTGTGAATCTACGAGGACCACCTCGTAAGGCTAAGTACTCCTGTGTGACCGATAGCGAAACAGTACCGCGAGGGAAAGGTGAAAAGAACCCCGGGAGGGGAGTGAAATAGAACATGAAACCGTGAGCTTACAAGCAATGGGAGCCCGACTAATCGGGTGACCGTGTGCCTGTTGAAGAATGAGCCGGCGACTTATAGGCACTGGCGGGTTAAACCGGGAATGGTGGAGCCATAGCGAAAGCGAGTCTTAATAGGGCGTTTGTCAGTGTTTATAGACCCGAACCCTGGTGATCTAACCATGGCCAGGATGAAGCTTGGGTGATACCAAGTGGAGGTCCGAACCGACTGATGTTGAAAAATCAGCGGATGAGCTGTGGTTAGGGGTGAAATGCCAATCGAACCAGGAGCTAGCTGGTTCTCCCCGAAATACGTTGAGGCGTAGCGTCTAGTGCTCCAGCAGGGGGGTAAAGCCACCATTTCGGTGCGGGCTGCGAAAGCGGTACCAAATCGATATGAACTCTGAATACCCTGTGTGTAACTAGGCAGTCAGACTGTGGGGGATAAGCTCCACACTCGAAAGGGAAACAGCCCAGACCGCCAGCTAAGGTCCCAAAATCAGTACTAAGTGATAAAGGAGGTGGGATTGCTTAGACAACCAGGAGGTTTGCTTAGAAGCAGCCATCCTCAAAGGAGTGCGTAATAGCTCACTGGTCGAGCGATCCTGCGCCGAAAATGAACGGGGCTAAGTGCTGTACCGAAGCTGCGGATTTACTTGTAAATGGTAGGGGAGCGTTCTATGTGGGGTGAAGCGTTAGCGTAAGCGGGCGTGGACTGCATTGAAGTGAGAATGTCGGCTTGAGTAGCGAAAACATGGGTGAGAATCCCATGCCCCGAAACCCTAAGGGTTCCTCCGGCAGGCTCGTCCGCGGAGGGTTAGTCTGGACCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGATAACAGGTCAACATTCCTGTACCGGTTATGTTTTGGGAAGGGGGACGGAGAAGGCTAGCCAATCCAGATGTTGGTTACTGGTTCAAGCGTTCAAGGCTATGAGGAACGGAGAAAACGTTCTGAGCTAAGGCGTGAGTACGAGTTGCTACGGCAACGAAGTTGGTGATGTCATGCTTCCAAGAAAAGCCCTATACCCGTTAAGGCATAACTGCCTGTACCCGAAACCGACACAGGTGGGGTGGTAGAGAATACCGAGGGGCGCGAGATAACTCTCTCTAAGGAACTCGGCAAAATGGCCCCGTAACTTCGGGAGAAGGGGTGCCAGCGAGAGCTGGCCGCAGTGAAGAGGCCCAAGCGACTGTTTACCAAAAACACAGGTCTCCGCTAAGTCGCAAGACGATGTATGGGGGCTGACGCCTGCCCAGTGCCGGAAGGTTAAGGAAGCCGGTTAGCGTAAGCAAAGCTGGCGACTGAAGCCCCGGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCGCTGTCTCGGAGAGAGGCTCGGCGAAATAGAATTGTCTGTGAAGATGCGGACTACGTACACCCGGACAGAAAGACCCTATGAAGCTTTACTGTAGGTTGATATTGGTCTCGGGCTCTGAATGCGCAGGATAGGTGGGAGACTATGAAGTAGTGCTTGTGGGTGCTATTGAGTCAATGGTGAGATACCACTCTTTCAGAGCTAGGGTTCTAACGCTTACCCGTTATCCGGGAAGCGGACAGTATCTGCTGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGTACAAAGGTTCCCTCAGGCTGGTTGGAAATCAGTCGCTGAGTGCAAAAGCAGAAGGGAGCTTGACTGTGAGACCTACAAGTCGAACAGGGACGAAAGTCGGTTTTAGTGATCCGACGGTTCTGAGTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGCTGATCTCCCCCAAGAGTTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCAACCTGGGGCTGAAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCATATCCGGTGTACGCGCAGGAATATTGAGAGGATTTCTCCCTAGTACGAGAGGACCGGGAGGAACGCACCTCTGGTGTGCCAGTTATCGTGCCAACGGTAAACGCTGGGTAGCCATGTGCGGAGTGGATAACCGCTGAAAGCATCTAAGTGGGAAGCCCACCTCAAGATGAGTATTCCCATGGCATAAGCCAGTAAGGTCACGGGAAGAACACCCGTTGATAGGCTCTACGTGGAAGCTTGGTAACAAGTGCAGCGGAGGAGTACTAATAGACCGAGGGCTTGACCT
>5S_rRNA::P.marinus:358432-358536(+)
TGGTGTTCATCGCGATGTGGACCCACTCCGATCCATCCCGAACTCGGTTGTGAAACGCATCAGCGGCGACGATATTTGGGGGGAAGCCCCCTGAGAAAATAGCT
4 changes: 4 additions & 0 deletions tools/barrnap/test-data/test_4.gff
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##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

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