# HG changeset patch
# User iuc
# Date 1506678686 14400
# Node ID 6fcbee531de602bbf3b13e9aa61980e0be3d83b0
# Parent  2f581f956e1c131c406a3af9897662d96561352c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67

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
@@ -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[
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
@@ -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
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
@@ -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
+###
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
@@ -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
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
@@ -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