| Previous changeset 2:2f581f956e1c (2016-11-04) Next changeset 4:0834c823d4b9 (2018-02-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67 |
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modified:
quast.xml |
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added:
test-data/NC000913.3_1-6650.fasta test-data/NC000913.3_1-6650.gff test-data/Quast_report_withref.tsv test-data/Quast_report_withref_withgenes.tsv |
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| diff -r 2f581f956e1c -r 6fcbee531de6 quast.xml --- a/quast.xml Fri Nov 04 05:06:15 2016 -0400 +++ b/quast.xml Fri Sep 29 05:51:26 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="quast" name="Quast" version="4.1.1" > +<tool id="quast" name="Quast" version="4.5" > <description>Genome assembly Quality</description> <requirements> - <requirement type="package" version="4.1">quast</requirement> + <requirement type="package" version="4.5">quast</requirement> </requirements> <stdio> <regex match="ERROR! exception caught!" @@ -13,6 +13,7 @@ <![CDATA[ #import re quast + --threads \${GALAXY_SLOTS:-4} -o outputdir #if $gene_selection == "eukaryote": --eukaryote @@ -34,7 +35,7 @@ --min-contig $min_contig -l #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ]) - + $names --contig-thresholds $threshold_contig #for $k in $files: @@ -48,7 +49,7 @@ mv outputdir/report.tsv '$quast_tsv' && mv outputdir/report.tex '$quast_tex' && mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' && - mv outputdir/report.html '$report_html' + mv outputdir/report.html '$report_html' ]]> </command> <inputs> @@ -91,6 +92,21 @@ <param name="gene_selection" value="prokaryotes"/> <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/> </test> + <test> + <param name="input" value="contigs_1.fasta"/> + <param name="input.type_file" value="contig"/> + <param name="input_ref" value="NC000913.3_1-6650.fasta"/> + <param name="gene_selection" value="prokaryotes"/> + <output name="quast_tsv" file="Quast_report_withref.tsv" lines_diff="4"/> + </test> + <test> + <param name="input" value="contigs_1.fasta"/> + <param name="input.type_file" value="contig"/> + <param name="input_ref" value="NC000913.3_1-6650.fasta"/> + <param name="annot" value="NC000913.3_1-6650.gff"/> + <param name="gene_selection" value="prokaryotes"/> + <output name="quast_tsv" file="Quast_report_withref_withgenes.tsv" lines_diff="4"/> + </test> </tests> <help> <![CDATA[ |
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| diff -r 2f581f956e1c -r 6fcbee531de6 test-data/NC000913.3_1-6650.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC000913.3_1-6650.fasta Fri Sep 29 05:51:26 2017 -0400 |
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| @@ -0,0 +1,112 @@ +>NC_000913.3:1-6650 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC +TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG +TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC +ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT +AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT +ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC +AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG +GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA +CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT +AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA +ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC +GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT +GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC +TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC +GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG +ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC +ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT +CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC +ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG +GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG +ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG +CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG +CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC +TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC +GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG +ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG +TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA +AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT +CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC +AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC +CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG +CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC +TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC +GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA +TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC +GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG +GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT +GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG +TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC +TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT +ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG +TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG +CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT +GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC +GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT +TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA +CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA +GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGA +AAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT +GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAT +GGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTT +TCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG +GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC +CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCT +GGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA +AGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCA +GGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT +CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTA +CCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGT +ACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC +GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC +GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGC +GAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGT +GCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCT +GGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA +AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGA +TACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT +CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAA +TATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC +GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACAT +CAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGA +GACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGG +TCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA +CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC +GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTT +CCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCAC +GCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT +AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCAC +CGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCT +GCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGA +TTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT +CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATG +ACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGA +ATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATA +AAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT +CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGAT +AGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTG +GTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC +GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA +TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTG +GCGCGTCTTATCAGGCCTACGTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGG +CAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAAACTTAACGCTGCTCGTAGCG +TTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT +AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAG +ACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG +GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTC +ATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT +GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACG +GATCCCCATTTCCAGACGATAAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAA +GCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAATCGTCTTCGCTGAAGGTTTC +GGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC +CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC +GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAA +CTGCTGGGAATTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTG +GTAATCAAGCGTTTTCGCAGGTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATT +TATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA +AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC +AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA |
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| diff -r 2f581f956e1c -r 6fcbee531de6 test-data/NC000913.3_1-6650.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC000913.3_1-6650.gff Fri Sep 29 05:51:26 2017 -0400 |
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| @@ -0,0 +1,22 @@ +##gff-version 3 +#!gff-spec-version 1.21 +#!processor NCBI annotwriter +#!genome-build ASM584v2 +#!genome-build-accession NCBI_Assembly:GCF_000005845.2 +##sequence-region NC_000913.3 1 4641652 +##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145 +NC_000913.3 RefSeq region 1 4641652 . + . ID=id0;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655 +NC_000913.3 RefSeq gene 190 255 . + . ID=gene0;Dbxref=EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001,JW4367;locus_tag=b0001 +NC_000913.3 RefSeq CDS 190 255 . + 0 ID=cds0;Parent=gene0;Dbxref=ASAP:ABE-0000006,UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;Ontology_term=GO:0009088;gbkey=CDS;gene=thrL;go_process=threonine biosynthetic process|0009088||;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11 +NC_000913.3 RefSeq gene 337 2799 . + . ID=gene1;Dbxref=EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,JW0001,thrA1,thrA2,thrD;locus_tag=b0002 +NC_000913.3 RefSeq CDS 337 2799 . + 0 ID=cds1;Parent=gene1;Dbxref=ASAP:ABE-0000008,UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;Note=bifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal);Ontology_term=GO:0005737,GO:0009088,GO:0009086,GO:0009090;experiment=N-terminus verified by Edman degradation: PMID 354697%2C4562989;gbkey=CDS;gene=thrA;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||,methionine biosynthetic process|0009086||,homoserine biosynthetic process|0009090||;product=Bifunctional aspartokinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11 +NC_000913.3 RefSeq gene 2801 3733 . + . ID=gene2;Dbxref=EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003,JW0002;locus_tag=b0003 +NC_000913.3 RefSeq CDS 2801 3733 . + 0 ID=cds2;Parent=gene2;Dbxref=ASAP:ABE-0000010,UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;Ontology_term=GO:0005737,GO:0009088;gbkey=CDS;gene=thrB;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11 +NC_000913.3 RefSeq gene 3734 5020 . + . ID=gene3;Dbxref=EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004,JW0003;locus_tag=b0004 +NC_000913.3 RefSeq CDS 3734 5020 . + 0 ID=cds3;Parent=gene3;Dbxref=ASAP:ABE-0000012,UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;Ontology_term=GO:0005737,GO:0009088;experiment=N-terminus verified by Edman degradation: PMID 9298646%2C9600841%2C9740056;gbkey=CDS;gene=thrC;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=L-threonine synthase;protein_id=NP_414545.1;transl_table=11 +NC_000913.3 RefSeq gene 5234 5530 . + . ID=gene4;Dbxref=EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005,JW0004;locus_tag=b0005 +NC_000913.3 RefSeq CDS 5234 5530 . + 0 ID=cds4;Parent=gene4;Dbxref=ASAP:ABE-0000015,UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;product=DUF2502 family putative periplasmic protein;protein_id=NP_414546.1;transl_table=11 +NC_000913.3 RefSeq repeat_region 5565 5669 . + . ID=id1;Note=RIP1 (repetitive extragenic palindromic) element%3B contains 2 REP sequences and 1 IHF site;gbkey=repeat_region +NC_000913.3 RefSeq gene 5683 6459 . - . ID=gene5;Dbxref=EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006,JW0005;locus_tag=b0006 +NC_000913.3 RefSeq CDS 5683 6459 . - 0 ID=cds5;Parent=gene5;Dbxref=ASAP:ABE-0000018,UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;product=peroxide resistance protein%2C lowers intracellular iron;protein_id=NP_414547.1;transl_table=11 +### |
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| diff -r 2f581f956e1c -r 6fcbee531de6 test-data/Quast_report_withref.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Quast_report_withref.tsv Fri Sep 29 05:51:26 2017 -0400 |
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| @@ -0,0 +1,37 @@ +Assembly contigs_1_fasta +# contigs (>= 0 bp) 3 +# contigs (>= 1000 bp) 3 +Total length (>= 0 bp) 6710 +Total length (>= 1000 bp) 6710 +# contigs 3 +Largest contig 3980 +Total length 6710 +Reference length 6650 +GC (%) 51.28 +Reference GC (%) 52.00 +N50 3980 +NG50 3980 +N75 1610 +NG75 1610 +L50 1 +LG50 1 +L75 2 +LG75 2 +# misassemblies 0 +# misassembled contigs 0 +Misassembled contigs length 0 +# local misassemblies 0 +# unaligned mis. contigs 0 +# unaligned contigs 0 + 1 part +Unaligned length 1950 +Genome fraction (%) 71.579 +Duplication ratio 1.000 +# N's per 100 kbp 0.00 +# mismatches per 100 kbp 0.00 +# indels per 100 kbp 0.00 +Largest alignment 2030 +Total aligned length 4760 +NA50 1610 +NGA50 1610 +LA50 2 +LGA50 2 |
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| diff -r 2f581f956e1c -r 6fcbee531de6 test-data/Quast_report_withref_withgenes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Quast_report_withref_withgenes.tsv Fri Sep 29 05:51:26 2017 -0400 |
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| @@ -0,0 +1,38 @@ +Assembly contigs_1_fasta +# contigs (>= 0 bp) 3 +# contigs (>= 1000 bp) 3 +Total length (>= 0 bp) 6710 +Total length (>= 1000 bp) 6710 +# contigs 3 +Largest contig 3980 +Total length 6710 +Reference length 6650 +GC (%) 51.28 +Reference GC (%) 52.00 +N50 3980 +NG50 3980 +N75 1610 +NG75 1610 +L50 1 +LG50 1 +L75 2 +LG75 2 +# misassemblies 0 +# misassembled contigs 0 +Misassembled contigs length 0 +# local misassemblies 0 +# unaligned mis. contigs 0 +# unaligned contigs 0 + 1 part +Unaligned length 1950 +Genome fraction (%) 71.579 +Duplication ratio 1.000 +# N's per 100 kbp 0.00 +# mismatches per 100 kbp 0.00 +# indels per 100 kbp 0.00 +# genes 3 + 3 part +Largest alignment 2030 +Total aligned length 4760 +NA50 1610 +NGA50 1610 +LA50 2 +LGA50 2 |