# HG changeset patch
# User iuc
# Date 1528615616 14400
# Node ID 7355bbf5e05fba0383e6e22b022583d40c7c322c
# Parent  8fd427007e93049ea773085c37c465ca6756d7a5
planemo upload commit 19a431ffca44dd1fd61ba2b66e5fc5ca96364f81

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
@@ -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>
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
@@ -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
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
@@ -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
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
@@ -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
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
@@ -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
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
@@ -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