| Previous changeset 7:f5e44aad6498 (2015-10-01) Next changeset 9:d004ca37843e (2016-10-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144 |
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modified:
COPYING prokka.xml readme.rst |
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added:
test-data/out.err test-data/out.faa test-data/out.ffn test-data/out.fna test-data/out.fsa test-data/out.gbk test-data/out.gff test-data/out.sqn test-data/out.tbl test-data/out.txt test-data/phiX174.fasta |
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removed:
tool_dependencies.xml |
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| diff -r f5e44aad6498 -r 392255fa7ab9 COPYING --- a/COPYING Thu Oct 01 14:14:06 2015 -0400 +++ b/COPYING Fri Oct 28 13:03:19 2016 -0400 |
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| @@ -1,9 +1,9 @@ -Copyright © 2015 The Genome Analysis Centre http://www.tgac.ac.uk/ +Copyright © 2013 Lionel Guy Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/ -Copyright © 2013 Lionel Guy +Copyright © 2015-2016 Earlham Institute http://earlham.ac.uk/ Created by: Paolo Uva <paolo.uva@crs4.it> -Nicola Soranzo <nicola.soranzo@tgac.ac.uk> +Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Lionel Guy <lionel.guy@icm.uu.se> Philip Mabon <philipmabon@gmail.com> |
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| diff -r f5e44aad6498 -r 392255fa7ab9 prokka.xml --- a/prokka.xml Thu Oct 01 14:14:06 2015 -0400 +++ b/prokka.xml Fri Oct 28 13:03:19 2016 -0400 |
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| b'@@ -1,162 +1,204 @@\n-<tool id="prokka" name="Prokka" version="1.11.0">\n- <description>prokaryotic genome annotation</description>\n- <requirements>\n- <requirement type="package" version="2.2.31">blast+</requirement>\n- <requirement type="package" version="3.1b2">hmmer</requirement>\n- <requirement type="package" version="1.2.36">aragorn</requirement>\n- <requirement type="package" version="2.60">prodigal</requirement>\n- <requirement type="package" version="24.3">tbl2asn</requirement>\n- <requirement type="package" version="20131122">gnu_parallel</requirement>\n- <requirement type="package" version="0.7">barrnap</requirement>\n- <requirement type="package" version="1.1">infernal</requirement>\n- <requirement type="package" version="0.1.6">minced</requirement>\n- <requirement type="package" version="1.11">prokka</requirement>\n- </requirements>\n- <version_command>prokka --version</version_command>\n- <command>\n- prokka\n- --cpus \\${GALAXY_SLOTS:-8}\n- --quiet ## to avoid non-error messages written to stderr\n- --outdir outdir --prefix prokka ## used in outputs section\n- #if $locustag\n- --locustag "$locustag"\n- #end if\n- #if str($increment)\n- --increment $increment\n- #end if\n- --gffver $gffver\n- #if $compliant.compliant_select == "no"\n- #if $compliant.addgenes\n+<tool id="prokka" name="Prokka" version="1.11.1">\n+ <description>prokaryotic genome annotation</description>\n+ <requirements>\n+ <requirement type="package" version="1.11">prokka</requirement>\n+ </requirements>\n+ <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <version_command>prokka --version</version_command>\n+ <command><![CDATA[\n+prokka\n+--cpus \\${GALAXY_SLOTS:-8}\n+--quiet ## to avoid non-error messages written to stderr\n+--outdir outdir --prefix prokka ## used in outputs section\n+#if $locustag\n+ --locustag \'$locustag\'\n+#end if\n+#if str($increment)\n+ --increment $increment\n+#end if\n+--gffver $gffver\n+#if $compliant.compliant_select == "no"\n+ #if $compliant.addgenes\n --addgenes\n- #end if\n- #if str($compliant.mincontig)\n- --mincontig $compliant.mincontig\n- #end if\n- #else\n- --compliant\n- #end if\n- #if $centre\n- --centre "$centre"\n #end if\n- #if $genus\n- --genus "$genus"\n- #end if\n- #if $species\n- --species "$species"\n- #end if\n- #if $strain\n- --strain "$strain"\n- #end if\n- #if $plasmid\n- --plasmid "$plasmid"\n- #end if\n- --kingdom $kingdom.kingdom_select\n- #if str($kingdom.gcode)\n- --gcode $kingdom.gcode\n- #end if\n- #if $usegenus\n- --usegenus\n- #end if\n- #if $proteins\n- --proteins $proteins\n- #end if\n- #if $metagenome\n- --metagenome\n- #end if\n- #if $fast\n- --fast\n- #end if\n- #if str($evalue)\n- --evalue $evalue\n- #end if\n- #if $rfam\n- --rfam\n- #end if\n- #if $norrna\n- --norrna\n- #end if\n- #if $notrna\n- --notrna\n+ #if str($compliant.mincontig)\n+ --mincontig $compliant.mincontig\n #end if\n- $input\n- </command>\n- <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n- <inputs>\n- <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />\n- <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />\n- <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)">\n- <validator type="in_range" min="1" />\n- </param>\n- <param name="gffver" type="select" label="GFF version (--gffver)">\n- <option value="3">3</option>\n- <option value="2">2</option>\n- <option value="1">1</option>\n- </p'..b'ng}: gbk" from_work_dir="outdir/prokka.gbk">\n+ <filter>\'gbk\' in outputs</filter>\n+ </data>\n+ <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">\n+ <filter>\'fna\' in outputs</filter>\n+ </data>\n+ <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">\n+ <filter>\'faa\' in outputs</filter>\n+ </data>\n+ <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">\n+ <filter>\'ffn\' in outputs</filter>\n+ </data>\n+ <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">\n+ <filter>\'sqn\' in outputs</filter>\n+ </data>\n+ <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">\n+ <filter>\'fsa\' in outputs</filter>\n+ </data>\n+ <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">\n+ <filter>\'tbl\' in outputs</filter>\n+ </data>\n+ <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">\n+ <filter>\'err\' in outputs</filter>\n+ </data>\n+ <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">\n+ <filter>\'txt\' in outputs</filter>\n+ </data>\n+ <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input" ftype="fasta" value="phiX174.fasta" />\n+ <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" />\n+ <output name="out_gff" file="out.gff" />\n+ <output name="out_gbk" file="out.gbk" lines_diff="14" />\n+ <output name="out_fna" file="out.fna" />\n+ <output name="out_faa" file="out.faa" />\n+ <output name="out_ffn" file="out.ffn" />\n+ <output name="out_sqn" file="out.sqn" lines_diff="84" />\n+ <output name="out_fsa" file="out.fsa" />\n+ <output name="out_tbl" file="out.tbl" />\n+ <output name="out.err" file="out.err" />\n+ <output name="out_txt" file="out.txt" />\n+ <output name="out_log">\n+ <assert_contents>\n+ <has_text text="Type \'prokka --citation\' for more details." />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n **What it does**\n \n Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.\n@@ -192,17 +234,18 @@\n \n **License and citation**\n \n-This Galaxy tool is Copyright \xc2\xa9 2013-2014 `CRS4 Srl.`_, \xc2\xa9 2013 Lionel Guy and is released under the `MIT license`_.\n+This Galaxy tool is Copyright \xc2\xa9 2013 Lionel Guy, \xc2\xa9 2013-2014 `CRS4 Srl.`_, \xc2\xa9 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.\n \n .. _CRS4 Srl.: http://www.crs4.it/\n-.. _MIT license: http://opensource.org/licenses/MIT\n+.. _Earlham Institute: http://earlham.ac.uk/\n+.. _MIT license: https://opensource.org/licenses/MIT\n \n You can use this tool only if you agree to the license terms of: `Prokka`_.\n \n .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml\n- </help>\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btu135</citation>\n- <citation type="doi">10.1093/bioinformatics/btu153</citation>\n- </citations>\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btu135</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu153</citation>\n+ </citations>\n </tool>\n' |
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| diff -r f5e44aad6498 -r 392255fa7ab9 readme.rst --- a/readme.rst Thu Oct 01 14:14:06 2015 -0400 +++ b/readme.rst Fri Oct 28 13:03:19 2016 -0400 |
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| @@ -17,13 +17,6 @@ .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/ .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/ -Configuration -------------- - -prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). - -If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool. - Version history --------------- @@ -41,8 +34,3 @@ - prokka 1.1.0: Merge the wrappers by CRS4 and Lionel Guy. Add COPYING file with MIT license. Make all params optional. Add 'gffver' param. Correctly quote text params in command. Use float type for 'evalue' param. Describe output files in help. Upgrade BLAST+ dependency to v. 2.2.28. Depend on package_aragorn_1_2_36 instead of trna_prediction. Depend on package_prodigal_2_60 instead of prodigal. Depend on package_barrnap_0_2 instead of barrnap. Add PROKKA_SITE_OPTIONS to env.sh and remove 'cpus' param. - prokka 0.2: Added this readme file. Support Prokka 1.7. Add dependencies management. - prokka 0.1: Initial release in the Tool Shed, supports Prokka 1.6. - -Development ------------ - -Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome! |
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| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.err --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.err Fri Oct 28 13:03:19 2016 -0400 |
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| @@ -0,0 +1,46 @@ +>PROKKA_00001 hypothetical protein +ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC +ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC +AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT +GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC +GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC +GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG +TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA +AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA +>PROKKA_00002 hypothetical protein +ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT +ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA +>PROKKA_00003 hypothetical protein +ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT +TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT +GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT +TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC +TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG +TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG +CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT +CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG +TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT +CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG +CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG +TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT +CGCGATTCAATCATGACTTCGTGA +>PROKKA_00004 hypothetical protein +TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT +TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA +ACAATACTGTAG +>PROKKA_00005 hypothetical protein +ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT +TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG +GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT +GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT +AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG +ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA +AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA +AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA +GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT +AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT +ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT +GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC +GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA |
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| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.faa Fri Oct 28 13:03:19 2016 -0400 |
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| @@ -0,0 +1,20 @@ +>PROKKA_00001 hypothetical protein +MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVY +GTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAEL +FAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM +>PROKKA_00002 hypothetical protein +MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF +>PROKKA_00003 hypothetical protein +MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAY +ANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQ +FSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVL +YGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDL +QERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS +>PROKKA_00004 hypothetical protein +MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL +>PROKKA_00005 hypothetical protein +MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNAWERAG +ADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQ +NEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKV +SAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASGVVDIFHGIDKAVADTWNNFWKD +GKADGIGSNLSRK |
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| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.ffn Fri Oct 28 13:03:19 2016 -0400 |
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| @@ -0,0 +1,46 @@ +>PROKKA_00001 hypothetical protein +ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC +ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC +AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT +GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC +GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC +GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG +TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA +AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA +>PROKKA_00002 hypothetical protein +ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT +ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA +>PROKKA_00003 hypothetical protein +ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT +TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT +GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT +TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC +TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG +TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG +CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT +CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG +TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT +CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG +CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG +TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT +CGCGATTCAATCATGACTTCGTGA +>PROKKA_00004 hypothetical protein +TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT +TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA +ACAATACTGTAG +>PROKKA_00005 hypothetical protein +ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT +TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG +GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT +GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT +AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG +ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA +AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA +AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA +GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT +AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT +ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT +GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC +GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA |
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| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.fna Fri Oct 28 13:03:19 2016 -0400 |
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| @@ -0,0 +1,99 @@ +>contig1 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA +AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC +TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT +GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG +TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT +CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +>contig2 +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA +TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG +GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC +CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA +TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT +CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT +ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT +GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC +CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG +GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA +TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC +AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA +TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +>contig3 +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA +AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA +TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT +TGTTTCAGGGTTATTTGAATATCTATAACA +>contig4 +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC +AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC +TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA +TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC +AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC +GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG +ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC +CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA +TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG +TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT +ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG +AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT +GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG +AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG +AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA +TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC +ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT +TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC +TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +>contig5 +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT +TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT +TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA +CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT +TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT +TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC +GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT +TTTGTTTCTG +>contig6 +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG +CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG +GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG +CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC +TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA +AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG +CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA +CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA +AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT +CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG +TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA +AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA +CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA +AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC +ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG +GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC +GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG +TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT +GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT +GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT +TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA +CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT +TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG +CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT +TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA +GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC +CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG +TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA +AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +>contig7 +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT +GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC +GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT +TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG +CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA |
| b |
| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.fsa Fri Oct 28 13:03:19 2016 -0400 |
| [ |
| @@ -0,0 +1,99 @@ +>contig1 [gcode=11] [organism=Genus species] [strain=strain] +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA +AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC +TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT +GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG +TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT +CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +>contig2 [gcode=11] [organism=Genus species] [strain=strain] +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA +TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG +GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC +CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA +TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT +CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT +ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT +GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC +CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG +GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA +TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC +AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA +TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +>contig3 [gcode=11] [organism=Genus species] [strain=strain] +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA +AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA +TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT +TGTTTCAGGGTTATTTGAATATCTATAACA +>contig4 [gcode=11] [organism=Genus species] [strain=strain] +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC +AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC +TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA +TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC +AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC +GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG +ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC +CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA +TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG +TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT +ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG +AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT +GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG +AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG +AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA +TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC +ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT +TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC +TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +>contig5 [gcode=11] [organism=Genus species] [strain=strain] +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT +TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT +TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA +CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT +TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT +TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC +GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT +TTTGTTTCTG +>contig6 [gcode=11] [organism=Genus species] [strain=strain] +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG +CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG +GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG +CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC +TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA +AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG +CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA +CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA +AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT +CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG +TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA +AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA +CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA +AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC +ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG +GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC +GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG +TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT +GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT +GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT +TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA +CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT +TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG +CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT +TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA +GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC +CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG +TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA +AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +>contig7 [gcode=11] [organism=Genus species] [strain=strain] +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT +GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC +GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT +TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG +CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA |
| b |
| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.gbk Fri Oct 28 13:03:19 2016 -0400 |
| b |
| b'@@ -0,0 +1,250 @@\n+LOCUS contig1 350 bp DNA linear 11-OCT-2016\n+DEFINITION Genus species strain strain.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com.\n+FEATURES Location/Qualifiers\n+ source 1..350\n+ /organism="Genus species"\n+ /mol_type="genomic DNA"\n+ /strain="strain"\n+ORIGIN \n+ 1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa\n+ 61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac\n+ 121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt\n+ 181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag\n+ 241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt\n+ 301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc\n+//\n+LOCUS contig2 840 bp DNA linear 11-OCT-2016\n+DEFINITION Genus species strain strain.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com.\n+FEATURES Location/Qualifiers\n+ source 1..840\n+ /organism="Genus species"\n+ /mol_type="genomic DNA"\n+ /strain="strain"\n+ CDS 40..498\n+ /locus_tag="PROKKA_00001"\n+ /inference="ab initio prediction:Prodigal:2.60"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="hypothetical protein"\n+ /translation="MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWI\n+ ATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAE\n+ FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM"\n+ CDS 498..614\n+ /locus_tag="PROKKA_00002"\n+ /inference="ab initio prediction:Prodigal:2.60"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="hypothetical protein"\n+ /translation="MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF"\n+ORIGIN \n+ 1 tgagtccgat gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa\n+ 61 tccgtacgtt tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg\n+ 121 gatttaaccg aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac\n+ 181 cgctctcgtg ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga\n+ 241 taccctcgct ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat\n+ 301 cccgtcaaca ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt\n+ 361 attaatggcg tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta\n+ 421 cgcgcaggaa acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt\n+ 481 gcggaaggag tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc\n+ 541 cgcagccgtt gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg\n+ 601 gtcaacaatt ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata\n+ 661 ttcaaactgg cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc\n+ 721 agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga\n+ 781 tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta\n+//\n+LOCUS contig3 210 bp DNA linear 11-OCT-2016\n+DEFINITION Genus species strain strain.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com.\n+FEATURES Location/Qualifiers\n+ source 1..210\n+ /organism="Genus species"\n+ /mol_type="genomic DNA"\n+ '..b'nference="ab initio prediction:Prodigal:2.60"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="hypothetical protein"\n+ /translation="MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRD\n+ YLAAAFPELNAWERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIA\n+ GIQSATSRQNTKDQVYAQNEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQ\n+ AQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASG\n+ VVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK"\n+ORIGIN \n+ 1 gtgctatggc taaagctggt aaaggacttc ttgaaggtac gttgcaggct ggcacttctg\n+ 61 ccgtttctga taagttgctt gatttggttg gacttggtgg caagtctgcc gctgataaag\n+ 121 gaaaggatac tcgtgattat cttgctgctg catttcctga gcttaatgct tgggagcgtg\n+ 181 ctggtgctga tgcttcctct gctggtatgg ttgacgccgg atttgagaat caaaaagagc\n+ 241 ttactaaaat gcaactggac aatcagaaag agattgccga gatgcaaaat gagactcaaa\n+ 301 aagagattgc tggcattcag tcggcgactt cacgccagaa tacgaaagac caggtatatg\n+ 361 cacaaaatga gatgcttgct tatcaacaga aggagtctac tgctcgcgtt gcgtctatta\n+ 421 tggaaaacac caatctttcc aagcaacagc aggtttccga gattatgcgc caaatgctta\n+ 481 ctcaagctca aacggctggt cagtatttta ccaatgacca aatcaaagaa atgactcgca\n+ 541 aggttagtgc tgaggttgac ttagttcatc agcaaacgca gaatcagcgg tatggctctt\n+ 601 ctcatattgg cgctactgca aaggatattt ctaatgtcgt cactgatgct gcttctggtg\n+ 661 tggttgatat ttttcatggt attgataaag ctgttgccga tacttggaac aatttctgga\n+ 721 aagacggtaa agctgatggt attggctcta atttgtctag gaaataaccg tcaggattga\n+ 781 caccctccca attgtatgtt ttcatgcctc caaatcttgg aggctttttt atggttcgtt\n+ 841 cttattaccc ttctgaatgt cacgctgatt attttgactt tgagcgtatc gaggctctta\n+ 901 aacctgctat tgaggcttgt ggcatttcta ctctttctca atccccaatg cttggcttcc\n+ 961 ataagcagat ggataaccgc atcaagctct tggaagagat tctgtctttt cgtatgcagg\n+ 1021 gcgttgagtt cgataatggt gatatgtatg ttgacggcca taaggctgct tctgacgttc\n+ 1081 gtgatgagtt tgtatctgtt actgagaagt taatggatga attggcacaa tgctacaatg\n+ 1141 tgctccccca acttgatatt aataacacta tagaccaccg ccccgaaggg gacgaaaaat\n+ 1201 ggtttttaga gaacgagaag acggttacgc agttttgccg caagctggct gctgaacgcc\n+ 1261 ctcttaagga tattcgcgat gagtataatt accccaaaaa gaaaggtatt aaggatgagt\n+ 1321 gttcaagatt gctggaggcc tccactatga aatcgcgtag aggctttgct attcagcgtt\n+ 1381 tgatgaatgc aatgcgacag gctcatgctg atggttggtt tatcgttttt gacactctca\n+ 1441 cgttggctga cgaccgatta gaggcgtttt atgataatcc caatgctttg cgtgactatt\n+ 1501 ttcgtgatat tggtcgtatg gttcttgctg ccgagggtcg caaggctaat gattcacacg\n+ 1561 ccgactgcta tcagtatttt tgtgtgcctg agtatggtac agctaatggc cgtcttcatt\n+ 1621 tccatgcggt gcactttatg cggacacttc ctacaggtag cgttgaccct aattttggtc\n+ 1681 gtcgggtacg caatcgccgc cagttaaata gcttgcaaaa tacgtggcct tatggttaca\n+ 1741 gtatgcccat cgcagttcgc tacacgcagg acgctttttc acgttctggt tggttgtggc\n+ 1801 ctgttgatgc taaaggtgag ccgcttaaag ctaccagtta tatggctgtt ggtttctatg\n+ 1861 tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta\n+ 1921 aagaatggaa caactcacta aaaaccaagc tgtcgctact\n+//\n+LOCUS contig7 276 bp DNA linear 11-OCT-2016\n+DEFINITION Genus species strain strain.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com.\n+FEATURES Location/Qualifiers\n+ source 1..276\n+ /organism="Genus species"\n+ /mol_type="genomic DNA"\n+ /strain="strain"\n+ORIGIN \n+ 1 tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa tgctcacaat\n+ 61 gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg acgcgacgcc\n+ 121 gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc tgggaaaagt\n+ 181 tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca aatttatgcg\n+ 241 cgcttcgata aaaatgattg gcgtatccaa cctgca\n+//\n' |
| b |
| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.gff Fri Oct 28 13:03:19 2016 -0400 |
| b |
| @@ -0,0 +1,113 @@ +##gff-version 3 +##sequence-region contig1 1 350 +##sequence-region contig2 1 840 +##sequence-region contig3 1 210 +##sequence-region contig4 1 1260 +##sequence-region contig5 1 490 +##sequence-region contig6 1 1960 +##sequence-region contig7 1 276 +contig2 Prodigal:2.60 CDS 40 498 . + 0 ID=PROKKA_00001;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00001;product=hypothetical protein +contig2 Prodigal:2.60 CDS 498 614 . + 0 ID=PROKKA_00002;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00002;product=hypothetical protein +contig4 Prodigal:2.60 CDS 21 884 . + 0 ID=PROKKA_00003;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00003;product=hypothetical protein +contig5 Prodigal:2.60 CDS 275 406 . + 0 ID=PROKKA_00004;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00004;product=hypothetical protein +contig6 Prodigal:2.60 CDS 6 767 . + 0 ID=PROKKA_00005;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00005;product=hypothetical protein +##FASTA +>contig1 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA +AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC +TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT +GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG +TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT +CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +>contig2 +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA +TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG +GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC +CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA +TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT +CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT +ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT +GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC +CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG +GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA +TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC +AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA +TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +>contig3 +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA +AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA +TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT +TGTTTCAGGGTTATTTGAATATCTATAACA +>contig4 +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC +AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC +TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA +TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC +AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC +GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG +ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC +CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA +TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG +TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT +ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG +AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT +GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG +AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG +AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA +TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC +ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT +TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC +TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +>contig5 +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT +TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT +TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA +CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT +TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT +TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC +GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT +TTTGTTTCTG +>contig6 +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG +CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG +GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG +CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC +TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA +AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG +CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA +CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA +AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT +CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG +TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA +AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA +CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA +AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC +ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG +GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC +GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG +TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT +GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT +GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT +TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA +CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT +TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG +CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT +TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA +GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC +CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG +TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA +AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +>contig7 +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT +GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC +GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT +TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG +CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA |
| b |
| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.sqn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.sqn Fri Oct 28 13:03:19 2016 -0400 |
| [ |
| b'@@ -0,0 +1,836 @@\n+Seq-entry ::= set {\n+ class genbank ,\n+ seq-set {\n+ seq {\n+ id {\n+ local\n+ str "contig1" } ,\n+ descr {\n+ source {\n+ org {\n+ taxname "Genus species" ,\n+ orgname {\n+ mod {\n+ {\n+ subtype strain ,\n+ subname "strain" } } ,\n+ gcode 11 } } } ,\n+ molinfo {\n+ biomol genomic } ,\n+ comment "Annotated using prokka 1.11 from\n+ http://www.vicbioinformatics.com" ,\n+ user {\n+ type\n+ str "NcbiCleanup" ,\n+ data {\n+ {\n+ label\n+ str "method" ,\n+ data\n+ str "SeriousSeqEntryCleanup" } ,\n+ {\n+ label\n+ str "version" ,\n+ data\n+ int 8 } ,\n+ {\n+ label\n+ str "month" ,\n+ data\n+ int 10 } ,\n+ {\n+ label\n+ str "day" ,\n+ data\n+ int 11 } ,\n+ {\n+ label\n+ str "year" ,\n+ data\n+ int 2016 } } } ,\n+ create-date\n+ std {\n+ year 2016 ,\n+ month 10 ,\n+ day 11 } } ,\n+ inst {\n+ repr raw ,\n+ mol dna ,\n+ length 350 ,\n+ seq-data\n+ iupacna "GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGA\n+AAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAG\n+AAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAA\n+AACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACA\n+TTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC" } } ,\n+ set {\n+ class nuc-prot ,\n+ descr {\n+ source {\n+ org {\n+ taxname "Genus species" ,\n+ orgname {\n+ mod {\n+ {\n+ subtype strain ,\n+ subname "strain" } } ,\n+ gcode 11 } } } ,\n+ comment "Annotated using prokka 1.11 from\n+ http://www.vicbioinformatics.com" ,\n+ user {\n+ type\n+ str "NcbiCleanup" ,\n+ data {\n+ {\n+ label\n+ str "method" ,\n+ data\n+ str "SeriousSeqEntryCleanup" } ,\n+ {\n+ label\n+ str "version" ,\n+ data\n+ int 8 } ,\n+ {\n+ label\n+ str "month" ,\n+ data\n+ int 10 } ,\n+ {\n+ label\n+ str "day" ,\n+ data\n+ int 11 } ,\n+ {\n+ label\n+ str "year" ,\n+ data\n+ int 2016 } } } ,\n+ create-date\n+ std {\n+ year 2016 ,\n+ month 10 ,\n+ day 11 } } ,\n+ seq-set {\n+ seq {\n+ id {\n+ local\n+ str "contig2" } ,\n+ descr {\n+ molinfo {\n+ biomol genomic } } ,\n+ inst {\n+ repr raw ,\n+ mol dna ,\n+ length 840 ,\n+ seq-data\n+ iupacna "TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTG\n+AACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAG\n+ATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT\n+GCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTT\n+ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATG\n+GCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTA\n+CTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGG\n+CGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGG\n+TCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTG'..b'AAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATG\n+GAACAACTCACTAAAAACCAAGCTGTCGCTACT" } } ,\n+ seq {\n+ id {\n+ local\n+ str "contig6_1" } ,\n+ descr {\n+ title "hypothetical protein PROKKA_00005 [Genus species]" ,\n+ molinfo {\n+ biomol peptide ,\n+ tech concept-trans } } ,\n+ inst {\n+ repr raw ,\n+ mol aa ,\n+ length 253 ,\n+ seq-data\n+ ncbieaa "MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNA\n+WERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQNEMLAYQQKESTA\n+RVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNV\n+VTDAASGVVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK" } ,\n+ annot {\n+ {\n+ data\n+ ftable {\n+ {\n+ id\n+ local\n+ id 10 ,\n+ data\n+ prot {\n+ name {\n+ "hypothetical protein" } } ,\n+ location\n+ int {\n+ from 0 ,\n+ to 252 ,\n+ id\n+ local\n+ str "contig6_1" } } } } } } } ,\n+ annot {\n+ {\n+ data\n+ ftable {\n+ {\n+ id\n+ local\n+ id 9 ,\n+ data\n+ cdregion {\n+ frame one ,\n+ code {\n+ id 11 } } ,\n+ product\n+ whole\n+ local\n+ str "contig6_1" ,\n+ location\n+ int {\n+ from 5 ,\n+ to 766 ,\n+ strand plus ,\n+ id\n+ local\n+ str "contig6" } ,\n+ qual {\n+ {\n+ qual "inference" ,\n+ val "ab initio prediction:Prodigal:2.60" } } ,\n+ xref {\n+ {\n+ data\n+ gene {\n+ locus-tag "PROKKA_00005" } } } } } } } } ,\n+ seq {\n+ id {\n+ local\n+ str "contig7" } ,\n+ descr {\n+ source {\n+ org {\n+ taxname "Genus species" ,\n+ orgname {\n+ mod {\n+ {\n+ subtype strain ,\n+ subname "strain" } } ,\n+ gcode 11 } } } ,\n+ molinfo {\n+ biomol genomic } ,\n+ comment "Annotated using prokka 1.11 from\n+ http://www.vicbioinformatics.com" ,\n+ user {\n+ type\n+ str "NcbiCleanup" ,\n+ data {\n+ {\n+ label\n+ str "method" ,\n+ data\n+ str "SeriousSeqEntryCleanup" } ,\n+ {\n+ label\n+ str "version" ,\n+ data\n+ int 8 } ,\n+ {\n+ label\n+ str "month" ,\n+ data\n+ int 10 } ,\n+ {\n+ label\n+ str "day" ,\n+ data\n+ int 11 } ,\n+ {\n+ label\n+ str "year" ,\n+ data\n+ int 2016 } } } ,\n+ create-date\n+ std {\n+ year 2016 ,\n+ month 10 ,\n+ day 11 } } ,\n+ inst {\n+ repr raw ,\n+ mol dna ,\n+ length 276 ,\n+ seq-data\n+ iupacna "TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAA\n+TGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGA\n+AGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGA\n+CGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA" } } } }\n' |
| b |
| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.tbl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.tbl Fri Oct 28 13:03:19 2016 -0400 |
| b |
| @@ -0,0 +1,27 @@ +>Feature contig1 +>Feature contig2 +40 498 CDS + inference ab initio prediction:Prodigal:2.60 + locus_tag PROKKA_00001 + product hypothetical protein +498 614 CDS + inference ab initio prediction:Prodigal:2.60 + locus_tag PROKKA_00002 + product hypothetical protein +>Feature contig3 +>Feature contig4 +21 884 CDS + inference ab initio prediction:Prodigal:2.60 + locus_tag PROKKA_00003 + product hypothetical protein +>Feature contig5 +275 406 CDS + inference ab initio prediction:Prodigal:2.60 + locus_tag PROKKA_00004 + product hypothetical protein +>Feature contig6 +6 767 CDS + inference ab initio prediction:Prodigal:2.60 + locus_tag PROKKA_00005 + product hypothetical protein +>Feature contig7 |
| b |
| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.txt Fri Oct 28 13:03:19 2016 -0400 |
| b |
| @@ -0,0 +1,4 @@ +organism: Genus species strain +contigs: 7 +bases: 5386 +CDS: 5 |
| b |
| diff -r f5e44aad6498 -r 392255fa7ab9 test-data/phiX174.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Fri Oct 28 13:03:19 2016 -0400 |
| b |
| @@ -0,0 +1,85 @@ +>contig1 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +>contig2 +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +>contig3 +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +>contig4 +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +>contig5 +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +>contig6 +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +>contig7 +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + |
| b |
| diff -r f5e44aad6498 -r 392255fa7ab9 tool_dependencies.xml --- a/tool_dependencies.xml Thu Oct 01 14:14:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,52 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="blast+" version="2.2.31"> - <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="hmmer" version="3.1b2"> - <repository changeset_revision="040ca41b61c1" name="package_hmmer_3_1b2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="aragorn" version="1.2.36"> - <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="prodigal" version="2.60"> - <repository changeset_revision="9ec3f1e9198e" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="tbl2asn" version="24.3"> - <repository changeset_revision="41764d6a6a3c" name="package_tbl2asn_24_3" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="gnu_parallel" version="20131122"> - <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <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> - <package name="infernal" version="1.1"> - <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="minced" version="0.1.6"> - <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="prokka" version="1.11"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.11.tar.gz</action> - <action type="shell_command">bin/prokka --setupdb</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Warning: Prokka includes custom databases and is thus about a 360 MB download! - -Dependencies of Prokka which needs to be installed separately: -- Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds; -- Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) >= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ). - </readme> - </package> -</tool_dependency> |