Galaxy |

Changeset 0:9c1ee25aa943 (2020-10-07)

Next changeset 1:7c2f5268d01c (2020-10-09)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty commit 56a2d363e48230451517156ba39057c8741e81f7"

added:
novoplasty.xml
test-data/chloroplast.fasta
test-data/combined.fasta
test-data/combined.fasta.gz
test-data/forward.fasta.gz
test-data/reference.fasta
test-data/reference.fasta.gz
test-data/reverse.fasta.gz
test-data/seed.fasta

diff -r 000000000000 -r 9c1ee25aa943 novoplasty.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/novoplasty.xml Wed Oct 07 09:22:21 2020 +0000

[

b'@@ -0,0 +1,687 @@\n+<?xml version="1.0"?>\n+<tool id="novoplasty" name="NOVOplasty" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">\n+ <description>de novo assembler for short circular genomes</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">4.0</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="content" token_min="" token_max="">\n+ <param name="genome_range_min" type="text" value="@MIN@" label="Set lower limit for the expected genome size range" help="(Genome Range)"/>\n+ <param name="genome_range_max" type="text" value="@MAX@" label="Set upper limit for the expected genome size range" help="(Genome Range)"/>\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">novoplasty</requirement>\n+ </requirements>\n+ <version_command><![CDATA[NOVOPlasty.pl 2>&1 | grep \'Version\' | awk -F\' \' \'{print $2}\']]></version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+## initialize\n+## samples require extension .fasta or .fasta.gz\n+#if $reads_cond.reads_sel == \'combined\' \n+ ln -s \'$reads_cond.combined_reads\' \'combined.${reads_cond.combined_reads.datatype.file_ext}\' &&\n+#else if $reads_cond.reads_sel == \'separate\'\n+ ln -s \'$reads_cond.forward_reads\' \'forward.${reads_cond.forward_reads.datatype.file_ext}\' &&\n+ ln -s \'$reads_cond.reverse_reads\' \'reverse.${reads_cond.reverse_reads.datatype.file_ext}\' &&\n+#end if\n+\n+## run\n+NOVOPlasty.pl -c \'$config\'\n+\n+## postprocessing\n+&& cp \'$config\' \'config.txt\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="config"><![CDATA[\n+Project:\n+-----------------------\n+Project name = result\n+Type = ${type_cond.type_sel}\n+Genome Range = ${type_cond.genome_range_min}-${type_cond.genome_range_max}\n+K-mer = ${kmer}\n+Max memory = \n+Extended log = 1\n+Save assembled reads = ${save_assembled_reads}\n+Seed Input = ${seed_input}\n+Extend seed directly = ${extend_seed_directly}\n+Reference sequence = #if $reference then $reference else \'\'#\n+Variance detection = #if $platform_cond.platform_sel == \'illumina\' and $platform_cond.mode_cond.mode_sel == \'variance\' then \'yes\' else \'\'#\n+Heteroplasmy = \n+MAF = #if $platform_cond.platform_sel == \'illumina\' and $platform_cond.mode_cond.mode_sel == \'heteroplasmy\' then $platform_cond.mode_cond.maf else \'\'#\n+HP exclude list = \n+Chloroplast sequence = #if $type_cond.type_sel == \'mito_plant\' and $type_cond.chloroplast_sequence then $type_cond.chloroplast_sequence else \'\'#\n+\n+Dataset 1:\n+-----------------------\n+Read Length = ${read_length}\n+Insert size = ${insert_size}\n+Platform = ${$platform_cond.platform_sel}\n+Single/Paired = ${single_paired}\n+Combined reads = #if $reads_cond.reads_sel == \'combined\' then \'combined.\'+$reads_cond.combined_reads.datatype.file_ext else \'\'#\n+Forward reads = #if $reads_cond.reads_sel == \'separate\' then \'forward.\'+$reads_cond.forward_reads.datatype.file_ext else \'\'#\n+Reverse reads = #if $reads_cond.reads_sel == \'separate\' then \'reverse.\'+$reads_cond.reverse_reads.datatype.file_ext else \'\'#\n+\n+Optional:\n+-----------------------\n+Insert size auto = ${insert_size_auto}\n+Use Quality Scores = ${use_quality_scores}\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="reads_cond">\n+ <param name="reads_sel" type="select" label="Select read file type" help="(Combined reads/Forward reads/Reverse reads)">\n+ <option value="combined">Combined reads</option>\n+ <option value="separate">Separate reads</option>\n+ </param>\n+ <when value="combined">\n+ <param name="combined_reads" type="data" format="fasta,fasta.gz" label="Select file with combined reads" help="(Combined reads)"/>\n+ </whe'..b'plant"/>\n+ <param name="chloroplast_sequence" value="chloroplast.fasta"/>\n+ </conditional>\n+ \n+ <output name="out_c">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ct">\n+ <assert_contents>\n+ <has_n_lines n="2"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ar1">\n+ <assert_contents>\n+ <has_n_lines n="10"/>\n+ <has_line line=">20/1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ar2">\n+ <assert_contents>\n+ <has_n_lines n="10"/>\n+ <has_line line=">20/2"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_ua">\n+ <assert_contents>\n+ <has_text_matching expression=">Contig01.+"/>\n+ <has_n_lines n="110"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+*NOVOPlasty* is a de novo assembler and heteroplasmy/variance caller for short circular genomes.\n+\n+**Input**\n+\n+- suitable seed: There are different types of seed possible: A single read from the dataset that originates from the organelle genome. A organelle sequence derived from the same or a related species. A complete organelle sequence of a more distant species (recommended when there is no close related sequence available)\n+- input reads: Either two separate files(forward and reverse) or a merged fastq/fasta file. Multiple libraries as input is not yet supported. There is also an Ion Torrent option, but it does not produce the best results.\n+- reference: The assembly will still be de novo, but references of the same genus can be used as a guide to resolve duplicated regions in the plant mitochondria or the inverted repeat in the chloroplast. \n+\n+**Output**\n+\n+*Assembly*\n+\n+- Contigs: This file contains all the assembled contigs.\n+- Circularized assembly: When NOVOPlasty is able to circularize one contig, without any additional contigs being produced, it will just output this circularized fasta file.\n+- Uncircularized assembly\n+- Merged contigs: When there are multiple contigs, NOVOPlasty will try to combine all contigs in to a complete circular genome, all the different possibilities can be found in this file.\n+- Contigs Tmp: If non of the above files are outputted or are empty, you can retrieve some contigs from this file.\n+\n+*Variance*\n+\n+- Variance: When the variance detection option is selected, an additional VCF file will be outputted.\n+\n+*Heteroplasmy*\n+\n+- Heteroplasmy: This VCF file contains all the detected heteroplasmy positions.\n+- Heteroplasmy assemblies: NOVOPlasty will assemble around each position of the above VCF output. The resulting assemblies will be outputted in this fasta file.\n+- Linkage table heteroplasmy: This file contains all the polymorphisms that are fully/partially/not linked with each detected heteroplasmic position.\n+- Possible NUMTs / Possible NUMTs assemblies / Linkage table NUMTs: These are the same files as the above three, but then for all the polymorphisms that were identified as NUMT origin.\n+- Circos mutations / Circos links: These files can be used to draw figures with Circos.\n+\n+*Others*\n+\n+- Log: This is a basic log file with the information that shows up on your terminal.\n+- Extended log: An elaborate log file.\n+- Config file\n+\n+.. class:: infomark\n+\n+**References**\n+\n+More information are available on `github <https://github.com/ndierckx/NOVOPlasty/>`_.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/nar/gkw955</citation>\n+ <citation type="doi">10.1093/nargab/lqz011</citation>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r 9c1ee25aa943 test-data/chloroplast.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chloroplast.fasta Wed Oct 07 09:22:21 2020 +0000

b'@@ -0,0 +1,110 @@\n+>Contig01+seed\n+TTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCA\n+TGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCT\n+ACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCAT\n+ACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTT\n+CGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAAT\n+CACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGG\n+CTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTT\n+TGTAGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAA\n+CACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTAT\n+TACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGG\n+ATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTATGATAATCATATCTACCAAATGCCCCTCATTTACATAAATATTATACTAGCATTTACCATCTCACTTCTAGGAATACTAGTATATCG\n+CTCACACCTCATATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGT\n+GGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAAC\n+ACAACCACCCACAGCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTBTTCCCCAACCTTTTCCTCCGACCCCCTAACAWCCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACA\n+ATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAACCACACTT\n+ATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTGATTTACACTCACAACACCCTAGGCTCACTAAACATT\n+CTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCT\n+GGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCTCCATCTGC\n+CTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGACTTACATCCTCATTACTA\n+TTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTG\n+GGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATA\n+AAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGC\n+TTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA\n+TAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCA\n+CAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATATTCATCCCTGTAGCATTGTTCGTTACATGGTCAATCA\n+TAGAATTCTCACTGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATAT\n+CCTTCTTGCTCA'..b'ACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATAATCATAAT\n+GGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAGA\n+CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCTACCGTACAACCCTAACAT\n+AACCATTCTTAATTTAACTATTTATATTATCCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTWCTWCTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC\n+CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCAC\n+CTCAAKCAMACTACTCCCCATATCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT\n+TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGG\n+GACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC\n+TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGAACACTATACCTATTATT\n+CGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC\n+CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGC\n+AGGAACAGGTTGAACAGTCTACCCTCCCTTAGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA\n+ACCCCCTGCCATAMCCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCC\n+CGCCGGAGGAGGAGACCCCATTCTATATCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG\n+TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGTATTTAG\n+CTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA\n+CGTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTATCATATTCATCGGCGTAAA\n+TCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACGCCACATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT\n+TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCC\n+CCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC\n+GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATA\n+GAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC\n+GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCAC\n+TCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCKCTACACGACCGGGKGTATACTACKGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA\n+GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATG\n+CCCCAACTAAATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTCCTTATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCMCTCACMAAAGCCCATAAAAATAAAAAATTATAACAAMCCCTGA\n+GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTA\n'

diff -r 000000000000 -r 9c1ee25aa943 test-data/combined.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combined.fasta Wed Oct 07 09:22:21 2020 +0000

b'@@ -0,0 +1,4000 @@\n+>26632/1\n+GAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGT\n+>23828/1\n+TTCTAAACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCCCTATAGT\n+>15693/1\n+ACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAGACGTAAGCCTTCTCCTC\n+>38326/1\n+TTGTTAGCGGTAACTAAGATTAGTATGGTAATTAGGAAGATGAGTAGATATTTGAAGAACTGATTAATGTTTGGGTCTGAGTTTATATATCACAGTGAGAATTCTATGATTGACCATGTAACGAACAATGCTACAGGGATGAATATTATGG\n+>6198/1\n+CGCAGTGCGCCGATCAGGGCGTAGTTTGAGTTTGATGCTCACCCTGATCAGAGGATTGAGTAAACGGCTAGGCTAGAGGTGGCTAGAATAAATAGGAGGCCTAGGTTGAGGTTGACCAGGGGGTTGGGTATGGGGAGGGGGGTTCATAGTA\n+>34901/1\n+ACACTTACCATGTTACGACTTGTCTCCTCTATATAAATGCGTAGGGGTTTTAGTTAAATGTCCTTTGAAGTATACTTGAGGAGGGTGACGGGCGGTGTGTACGCGCTTCAGGGCCCTGTTCAACTAAGCACTCTACTCTCAGTTTACTGCT\n+>27087/1\n+GTGGTAGTTTGTGTTTAATATTTTTAGTTGGGTGATAAGGAATAGTGTAAGGAGTATGGGGGTAATTATGGTGGGCCATACGGTAGTATTTAGTTGGGGCATTTCACTGTAAAGAGGTGTTGGTTCTCTTAATCTTTAACTTAAAAGGTTA\n+>37932/1\n+ACGGTAGAACTGCTATTATTCATCCTATGTGGGTAATTGAGGAGTATGCTAAGATTTTGCGTAGCTGGGTTTGGTTTAATCCACCTCAACTGCCTGCTATGATGGATAAGATTGAGAGAGTGAGGAGAAGGCTTACGTCTAGTGAGGGAGG\n+>3649/1\n+CCCGGTAATGATGTCGGGGTTGAGGGATAGGAGGAGAATGGGGGATAGGTGTATGAACATGAGGGTGTTTTCTCGTGTGAATGAGGGTTTTATGTTGTTAATGTGGTGGGTGAGTGAGCCCCATTGTGTTGTGGTAAATATGTAGAGGGAG\n+>38422/1\n+ATTTAACCTAAATTTCTATAAGATTATTAGTATAAAAGGGGAGATAGGTAGGAGTAGCGTGGTAAGGGCGATGAGTGTGGGGAGGAATGGGGTGGGTTTTGTATGTTCAAACTGTCATTTTATTTTTACGTTGTTAGATATGGGGAGTAGT\n+>2555/1\n+AGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCC\n+>24632/1\n+CTGGATTACTCCGGTCTGAACTCAGATCACGTAGGACTTTAATCGTTGGACAAACGAACCTTTAATAGCGGCTGCACCATCGGGATGTCCTGATCCAACATCGAGGTCGTAAACCCTATTGTTGATATGGACTCTAGAATAGGATTGCGCT\n+>30339/1\n+CTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGA\n+>19131/1\n+CAGTGTATTGCTTTGAGGAGGTAAGCTACATAAACTGTGGGGGGTGTCATTGGGGTTTGGTTGGTTCGGGGTAGGGGGTTAGCAGCGGTGGGGGTGTGCTGGGGAGGAGGGGCGGGGGTTGTATTGGTGCGATTAGGAGTATGGGAGTGGG\n+>20344/1\n+GGATTAGGATTGTTGTGAAGTATAGTACGGATGCTACTTGTCCAATGATGGTAAAAGGGTAGCTTACTGGTTGTCCTCCGATTCAGGTTAGAATGAGGAGGTCTGCGGCTAGGAGTCAATAAAGTGATTGGCTTAGTGGGCGAAATATTAT\n+>34256/1\n+CAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATGGTATTAGCAAACTCATCACTAGACATCGTACTCCAC\n+>18611/1\n+CCAATGATGGTAAAAGGGTAGCTTACTGGTTGTCCTCCGATTCAGGTTAGAATGAGGAGGTCTGAGGCGAGTAGTCAATAAAGTGATTGGCTTAGTGGGCGAAATATTAGGCGTTGTTGTTGGGATATATGGAGGATGGGGATTATTGCTA\n+>10644/1\n+TTTATGGCCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTAGCTACCCCCAAGTGTTATGGGCCCGGAGCGAGGAGAGTAGCACTCTTGTGCGGGATATTGATTTCACGGAGGATGGTGGTCAAGGGACCCCTATCTGAGGGGGG\n+>4829/1\n+AGGAGTAGCGTGGTAAGGGCGATGAGTGTGGGGAGGAATGGGGTGGGTTTTGTATGTTCAAACTGTCATTTTATTTTTACGTTGTTAGATATGGGGAGTAGTGTGATTGAGGTGGAGTAGATTAGGCGTAGGTAGAAGTAGAGGTTAAGGA\n+>8675/1\n+CGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGTGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACC\n+>36324/1\n+CAAATAATAAGAAGGTAATAGCGACTAAGAAGAATTTTATGGAGAAAGGGACGCGGGCGGGGGATATAGGGTCGAAGCCGCACTCGTAAGGGGGGGATTTTTCTATGTAGCCGGTGAGGTGTGGTGGTCAGAGTGTAGTAATTATTCGTAG\n+>29376/1\n+GGTGTTCTTGTGTTGTGATAAGGGTGGAGAGGTTAAAGGAGCCACTTATTAGTAATGTTGATAGTAGAATGATGGCTAGGGTGACTTCATATGAGATTGTTTGGGCTACTGCTCGCAGTGCGCCGATCAGGGCGTAGTTTGAGTTTGATGC\n+>21169/1\n+GAAGTAGGCCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGATCACGTAGGACTTTAATCGTTGAACAAACGAACCTTTAATAGCGGCTGCACCATCGGGATG\n+>4484/1\n+GTTTGCTGAAGATGGCGGTATATAGGCTGAGCAAGAGGTGGTGAGGTTGATCGGGGTTTATCGATTACAGAACAGGCTCCTCTAGAGGGATATGAAGCACCGCCAGGTCCTTTGAGTTTTAAGCTGTGGCTCGTAGTGTTCTGGCGAGCAG\n+>15371/1\n+GTAGGGCTCATGGTAGGGGTAAAAGGAGGGCAATTTCTAGATCAAATAATAAGAAGGTAATAG'..b'CTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTCGTCAA\n+>1380/2\n+ACAGAGAATAGTTTAAATTAGAATCTTAGCTTTGGGTGCTAATGGTGGAGTTAAAGACTTTTTCTCTGATTTGTCCTTGGAAAAAGGTTTTCATCTTCGGTTTACAAGACTGGTGTATTAGTTTATACTACAAGGACAGGCCCATTTGAGT\n+>25566/2\n+CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCC\n+>33609/2\n+CTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGACTAACAGTTAAATTTACAAGGGGATTTAGAGGGTTCTGTGGGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCTATCACCAGGCTCGGTAGGTTT\n+>12075/2\n+GAGTCCGTAAAGAGGTATCTTTACTATAAAAGCTATTGTGTAAGCTAGTCATATTAAGTTGTTGGCTCAGGAGTTTGATAGTTCTTGGGCAGTGAGAGTGAGTAGTAGAATGTTTAGTGAGCCTAGGGTGTTGTGAGTGTAAATCAGTGCG\n+>27791/2\n+AAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCA\n+>20823/2\n+CATTTCGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGG\n+>34233/2\n+TTCCTTTTACTTTTTTTAACCTTTCCTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTTTTAATCTGACGCAGGCTTATGCGGAGGAGAAT\n+>29087/2\n+GCTGCGAACAGAGTGGTGATAGCGCCTAAGCATAGTGTTAGAGTTTGGATTAGTGGGCTATTTTCTGCTAGGGGGTGGAAGCGGATGAGTAAGAAGATTCCTGCTACAACTATAGTGCTTGAGTGGAGTAGGGCTGAGACTGGGGTGGGGC\n+>35527/2\n+TTATTTTAAGTTTGTTGGCTAGGTAGTTGAGGTCTAGGGCTGTTAGAAGTCCTAGGAAAGTGACAGCGAGGGCTGTGAGTTTTAGGTATAGGGGGACTGTTGTTTGGAAGGGGGATGCGGGGGAAATGTTGTTAGTAATGAGAAATCCTGC\n+>37541/2\n+ATTATGCCTCATAGGGATAGTACAAGGAAGGGGTAGGCTATGTGTTTTGTCAGGGGGTTGAGAATGAGTGTGAGGCGTATTATACCATAGCCGCCTAGTTTTAAGAGTACTGCGGCAAGTACTATTGACCCAGCGATGGGGGATTCGACAT\n+>2616/2\n+TTTTGTTGATTTAACTGTTGAGGTTTAGGGCTAAGCATAGTGGGGTATCTAATCCCAGTTTGGGTCTTAGCTATTGTGTGTTCAGATATGTTAAAGCCACTTTCGTAGTCTATTTTGTGTCAACTGGAGTTTTTTACAACTCAGGTGAGTT\n+>9388/2\n+AAAGGCTAGGACCAAACCTATTTGTTTATGGGGTGATGTGAGCCCGTCTAAACATTTTCAGTGTATTGCTTTGAGGAGGTAAGCTACATAAACTGTGGGGGGTGTCTTTGGGGTTTGGTTGGTTCGGGGGATGGGGTTAGCAGCGGTGGGT\n+>26293/2\n+CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAGCTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCA\n+>16422/2\n+AAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTAGAACTTGCCGAAGGGGAGACCGAACTAGTCTCAGGCTTCAACATCGAATACGCAGCAGGCCC\n+>899/2\n+CCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA\n+>6693/2\n+TCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAAT\n+>25132/2\n+TTAGTATTAGGAGGGGGGTTGTTAGGGGGTCGGAGGAAAAGGTTGGGGAACAGCTAAATAGGTTGTTGTTGATTTGGTTAAAAAATAGTAGAGGGATGATGCTAATAATTAGGCTGTGGGTGGTTGTGTTGATTCAAATTATGTGTTTTTT\n+>32821/2\n+CATGATTGTGAGGGGTAGGAGTCAGGTAGTTAGTATTAGGAGGGGGGTTGTTAGGGGGTCGGAGGAAAAGGTTGGGGAACAGCTAAATAGGTTGTTGTTGATGTGGTTAAAAAATAGTAGAGGGATGATGCTAATAATTAGGCTGTGGGTG\n+>2847/2\n+GACCTTAGCTCTCACCATCGCTATTCTACTATGAACCCCCCTCCCCATACCCAACACCCTTGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAACCGTTTACTCAATCCTCTGATCAGGGTGATCATCAAACTCA\n+>29886/2\n+CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTGACCCTATAGCACCCCC\n+>36323/2\n+CTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAAC\n+>37437/2\n+CAAAAAAAGGGAAACAATGTATTAGAGAGTTTGTATCTGAACCATTTTGCAACAGTCAACAGAGACCTGAGTTGTAAAAAACTCCAGTTGATACAAAATAAACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAA\n+>21905/2\n+TATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCC\n+>5042/2\n+GTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAA\n'

diff -r 000000000000 -r 9c1ee25aa943 test-data/combined.fasta.gz

Binary file test-data/combined.fasta.gz has changed

diff -r 000000000000 -r 9c1ee25aa943 test-data/forward.fasta.gz

Binary file test-data/forward.fasta.gz has changed

diff -r 000000000000 -r 9c1ee25aa943 test-data/reference.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fasta Wed Oct 07 09:22:21 2020 +0000

diff -r 000000000000 -r 9c1ee25aa943 test-data/reference.fasta.gz

Binary file test-data/reference.fasta.gz has changed

diff -r 000000000000 -r 9c1ee25aa943 test-data/reverse.fasta.gz

Binary file test-data/reverse.fasta.gz has changed

diff -r 000000000000 -r 9c1ee25aa943 test-data/seed.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seed.fasta Wed Oct 07 09:22:21 2020 +0000