| Previous changeset 5:81df4950d65b (2018-12-04) Next changeset 7:59db8ea8c845 (2019-07-24) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b |
|
modified:
quast.xml test-data/test2_report.pdf |
|
added:
test-data/contigs3.fasta test-data/contigs3.fasta.textClipping test-data/test1.tabular test-data/test1_kmers.tabular test-data/test1_mis_ass.tabular test-data/test1_unalign.tabular test-data/test2.tabular test-data/test3.tabular |
|
removed:
test-data/test1_output.tsv test-data/test2_output.tsv |
| b |
| diff -r 81df4950d65b -r f30d03867854 quast.xml --- a/quast.xml Tue Dec 04 06:49:05 2018 -0500 +++ b/quast.xml Wed Mar 06 14:09:08 2019 -0500 |
| [ |
| b'@@ -1,102 +1,406 @@\n-<tool id="quast" name="Quast" version="5.0.2" >\n+<tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy0" >\n <description>Genome assembly Quality</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">5.0.2</token>\n+ <xml name="gene_thresholds">\n+ <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/>\n+ </xml>\n+ </macros>\n <requirements>\n- <requirement type="package" version="5.0.2">quast</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">quast</requirement>\n </requirements>\n <command detect_errors="exit_code">\n <![CDATA[\n #import re\n-quast\n---threads \\${GALAXY_SLOTS:-4}\n--o outputdir\n-#if $gene_selection == "eukaryote":\n- --eukaryote\n-#else if $gene_selection == "metagenes":\n- --meta\n+\n+#if str($in.custom) == \'false\'\n+ #set $labels = \',\'.join( [re.sub(\'[^\\w\\-_]\', \'_\', str($x.element_identifier)) for $x in $in.inputs ])\n+#else\n+ #set $labels = []\n+ #for $x in $in.inputs\n+ #if str($x.labels) != \'\'\n+ #silent $labels.append(re.sub(\'[^\\w\\-_]\', \'_\', str($x.labels)))\n+ #else\n+ #silent $labels.append(re.sub(\'[^\\w\\-_]\', \'_\', str($x.input.element_identifier)))\n+ #end if\n+ #end for\n+ #set $labels = \',\'.join($labels)\n+#end if\n+\n+#if $assembly.type == \'metagenome\' and $assembly.ref.origin == \'list\'\n+ #set $temp_ref_list_fp = \'temp_ref_list_fp\'\n+ #set $temp_ref_list_f = open($temp_ref_list_fp, \'w\')\n+ #silent $temp_ref_list_f.write(\'\\n\'.join([x.strip() for x in $assembly.ref.references_list.split(\',\')]))\n+ #silent $temp_ref_list_f.close()\n #end if\n-$large\n-#if $input_ref:\n- -R \'$input_ref\'\n- #if $input_operon:\n- -O \'$input_operon\'\n+\n+#if $assembly.type == \'genome\'\n+quast\n+#else\n+metaquast\n+#end if\n+ -o outputdir\n+\n+#if $assembly.type == \'genome\'\n+ #if $assembly.ref.use_ref == \'true\'\n+ -r \'$assembly.ref.r\'\n+ #if $assembly.ref.features\n+ --features \'$assembly.ref.features\'\n+ #end if\n+ #if $assembly.ref.operons\n+ --operons \'$assembly.ref.operons\'\n+ #end if\n+ #else if $assembly.ref.est_ref_size\n+ --est-ref-size $assembly.ref.est_ref_size\n #end if\n- #if $annot:\n- -g \'$annot\'\n+ $assembly.orga_type\n+#else\n+ #if $assembly.ref.origin == \'history\'\n+ -r \'$assembly.ref.r\'\n+ #else if $assembly.ref.origin == \'list\'\n+ --references-list \'$temp_ref_list_fp\'\n+ #else if $assembly.ref.origin == \'silva\'\n+ --test-no-ref\n+ --max-ref-num \'$assembly.ref.max_ref_num\'\n #end if\n #end if\n-#if $input_size:\n- --est-ref-size $input_size\n+ --min-contig $min_contig\n+ --threads \\${GALAXY_SLOTS:-4}\n+ $split_scaffolds\n+ --labels $labels\n+ $large\n+ $k_mer.k_mer_stats\n+#if str($k_mer.k_mer_stats) != \'\'\n+ --k-mer-size $k_mer.k_mer_size\n #end if\n---min-contig $min_contig\n--l\n-#set names = \',\'.join( [re.sub(\'[^\\w\\-_]\', \'_\', str($x.element_identifier)) for $x in $input ])\n+ $circos\n+#if str($genes.gene_finding.tool) != \'none\'\n+ $genes.gene_finding.tool\n+ #if $genes.gene_finding.tool == \'--gene_finding\' or $genes.gene_finding.tool == \'--glimmer\'\n+ #set $gene_threshold = \',\'.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(\',\')])\n+ --gene-thresholds \'$gene_threshold\'\n+ #end if\n+#end if\n+ $genes.rna_finding\n+ $genes.conserved_genes_finding\n+ $al.use_all_alignments\n+ --min-alignment $al.min_alignment\n+ --min-identity $al.min_identity\n+ --ambiguity-usage \'$al.ambiguity_usage\'\n+ $al.fragmented\n+ #set $contig_thresholds = \',\'.join([x.strip() for x in str($contig_thresholds).split(\',\')])\n+ --contig-thresholds \'$contig_thresholds\'\n+ $strict_NA\n+ --extensive-mis-size $extensive_mis_size\n+ --scaffold-gap-max-size $scaffold_gap_max_size\n+ --unaligned-part-'..b'onditional name="k_mer">\n+ <param name="k_mer_stats" value=""/>\n+ </conditional>\n+ <param name="circos" value="false"/>\n+ <section name="genes">\n+ <conditional name="gene_finding">\n+ <param name="tool" value="none"/>\n+ </conditional>\n+ <param name="rna_finding" value="false"/>\n+ <param name="conserved_genes_finding" value="false"/>\n+ </section>\n+ <section name="al">\n+ <param name="use_all_alignments" value="false"/>\n+ <param name="min_alignment" value="65"/>\n+ <param name="min_identity" value="95.0"/>\n+ <param name="ambiguity_usage" value="one"/>\n+ <param name="ambiguity_score" value="0.99"/>\n+ <param name="fragmented" value="false"/>\n+ <param name="fragmented_max_indent" value="50"/>\n+ <param name="upper_bound_assembly" value="false"/>\n+ <param name="upper_bound_min_con" value="2"/>\n+ </section>\n+ <param name="contig_thresholds" value="0,1000, 500"/>\n+ <param name="strict_NA" value="false"/>\n+ <param name="extensive_mis_size" value="1000"/>\n+ <param name="scaffold_gap_max_size" value="1000"/>\n+ <param name="unaligned_part_size" value="500"/>\n+ <param name="skip_unaligned_mis_contigs" value="-"/>\n+ <output name="quast_tabular" file="test2.tabular"/>\n+ <output name="report_html" file="test2_report.html" compare="sim_size"/>\n <output name="report_pdf" file="test2_report.pdf" compare="sim_size"/>\n </test>\n+ <test>\n+ <!-- Test with metagenomics -->\n+ <conditional name="in">\n+ <param name="custom" value="false"/>\n+ <param name="inputs" value="contigs3.fasta"/>\n+ </conditional>\n+ <conditional name="assembly">\n+ <param name="type" value="metagenome"/>\n+ <conditional name="ref">\n+ <param name="origin" value="none"/>\n+ </conditional>\n+ </conditional>\n+ <param name="min_contig" value="500"/>\n+ <param name="split_scaffolds" value="false"/>\n+ <param name="large" value="false"/>\n+ <conditional name="k_mer">\n+ <param name="k_mer_stats" value=""/>\n+ </conditional>\n+ <param name="circos" value="false"/>\n+ <section name="genes">\n+ <conditional name="gene_finding">\n+ <param name="tool" value="--mgm"/>\n+ </conditional>\n+ <param name="rna_finding" value="false"/>\n+ <param name="conserved_genes_finding" value="false"/>\n+ </section>\n+ <section name="al">\n+ <param name="use_all_alignments" value="false"/>\n+ <param name="min_alignment" value="65"/>\n+ <param name="min_identity" value="95.0"/>\n+ <param name="ambiguity_usage" value="one"/>\n+ <param name="ambiguity_score" value="0.99"/>\n+ <param name="fragmented" value="false"/>\n+ <param name="fragmented_max_indent" value="50"/>\n+ <param name="upper_bound_assembly" value="false"/>\n+ <param name="upper_bound_min_con" value="2"/>\n+ </section>\n+ <param name="contig_thresholds" value="0,1000, 500"/>\n+ <param name="strict_NA" value="false"/>\n+ <param name="extensive_mis_size" value="1000"/>\n+ <param name="scaffold_gap_max_size" value="1000"/>\n+ <param name="unaligned_part_size" value="500"/>\n+ <param name="skip_unaligned_mis_contigs" value="-"/>\n+ <output name="quast_tabular" file="test3.tabular"/>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n' |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/contigs3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs3.fasta Wed Mar 06 14:09:08 2019 -0500 |
| b |
| b'@@ -0,0 +1,20000 @@\n+>NODE_1_length_78752_cov_2.35353\n+AGGTTGCCGGCAAGTCGGGCTAGTCGTTCCAGCCAGCGGTAGAAACCCGGCTCAAACTCT\n+GCTCTCGAAGGTACGGCTACCTGTATTCTTCTCAATGTATTCAACGGCTGTCTGATGCGT\n+GCCATGATAATCTGGCGGCTCAATCCGTTGAAAAGACTCTGGTGGAATTCTCCCCAGAAC\n+TTCGGCGAAACCTCAGGATGCATGTGCATTCCGATGATAATCTCAGAACATTGGAACTCG\n+TTGAAGGCATGCTTGATGCCGTTGGCGATGTTGGCGGCAATACGAACCTGGGTCTGCGTC\n+ATCACATCGGTGGCAGCAGCCAGCTGACTGCAATGTTCCAGAATCCGTCTTCCCTGTTCC\n+TGGTTGTATCGCATGTCCTTGTCTTCATATACCACATTCAGGCAGATGAGTCCCCTGTTC\n+AGTTTCTGGTTTCTCACCAGAAACGCCAGACTCATCAGGTTGTCGGCATATTCAGGATAT\n+TTCACCGGAACCAGAATCTTCTCATCGCTCACTTTCTTGTCGTCTTCCGCATCAGGCAGT\n+TCCTTGTCTCTCAGGATAATCTTCTGCGAAGACCGGTCGGTAAGGATGGATGAGATGATG\n+CAGGTAATCAGAATCATCATAACCACACCATTGAGCATATCATCGTTGACGAGGTAAGTG\n+CCCGGTGCTACGAGCAGATGCATACCCACCATCACCATGGCGATACTTCCGGCAGCATGA\n+GCCGAAGTGAGTCCGAACATCATGTGACCCGAAGAAAGTGGCAATCGAAAACCCAGACAG\n+GCGATATAGGCTGCGATGGCTTTGCCCAGGGTTCCGAAGAAGGCGATACAGAATACGACC\n+CATAGAATATGACTGCCCTGAAACAGCAGATTGATATTGATTAGCATGCCCACACCTATC\n+AGGAAATAAGGAATGAAGAGGGCATTGCCGATAAATTCGAGGCGGTTCATCAGTGGCGAA\n+ACATGCGGAATATATCTGTTTAATATCAGACCGGCGAAGAAAGCACCGAAAACGCCCTCG\n+ATGCCCACTATCTGGGAAAGTGCCGCACTCATAAAGAGCATCGAAAGTACGAAGATAAAC\n+TGCATCACCGCATCGCTGTATCTTCGCAAGAACCATCTTGTAAGTCGGGGAATCAGCATG\n+ATCATCACGCCACAATAGACAGCAAACTTGAGGGTGAAGAATACCCAGAACAGTACGCCG\n+TCATGCTTGCTGAACGATGCTACCAGTCCGGCAAGCATAATCAGGGCTATGAGCAGCGAA\n+ATCATGCTCGACCCCACACTTAGCGTAACGCTCGGTTTCTGTTGCAGTCCGTATCTCGAA\n+ACGATAGGATAGGCAATCAGCGTATTGGATGCCATGATGCAGCTCAGCAGGAAGGAAGCC\n+TTGGCAGAGTAGTGGAGCAGCCAGATGCTCATGCCATAGGTGAGGAAGAACGGTATAAAA\n+CAGGTGAGCAGGCCATAGATAAGCAGTCGCGACTTGTTCTTTTTCATGCCTTCCATATCC\n+ATCTCCAGTGCAGCGAGGAACATGATGTAATAGAGTCCCACCTTTCCGAAGAGCTCAAAC\n+GAAGAGTCGCGCTCCAGGATATTCAGTCCGTATTTGCCTATGAGCACACCTGCCAGCACC\n+ATTCCGATGATGTGCGGGATACGGAGTTTACCCATGATGATAGGGGCAAAGAGGATGATG\n+AGGAGCACTACGAAGAATATCAACGTAGGGTCTGTGATAGGGAAGTATTGAGCGATATGG\n+AACATAGGCTTTCTTCTTTTTTGTTATACTTAAAGAGGGATTTCTGCATCAGCATTCATC\n+CCTCCCTTTCTGTTTTTGACTGCAAAAGTACGAATAAATCTTGAAAGCACAAAGTTTTTC\n+TGCCCTTATCCTACAATCATGGTGATATTTTTGCATGTTCACTATTGTTTCTATCTTTTC\n+AAATCCCTATCCACCATGGCACAGACACAGGAATCAGACCATACGTTTTCTGCCGTCTCA\n+ATCATGTCGATGATAGTATAGATTGGCAGGATGATGCCCATGATGCCGATAGGAGCATTG\n+ATACCGGACATCAGAGATAGGGTAAGGAAATAACATCCCATCGGTACTCCTGCATTACCC\n+ACTGCTGAGATAACTGAAATGAAGAGCCAGAGAATCATCGTAGTCCAAGGTAAAGGCATT\n+CCTCCATTCTGCATCAGGAATAAGGAGGTTACGAGGATAAACGCAGCGCAACCATTCATG\n+TTGATGGTAGTACAGATAGGTAATACAAAGCGGGAAACCTGATTGGAAACTCCCAGTCTG\n+TCTTCTGCTGTCTGCATCGTTACCGGCAACGTAGCAGCAGAACTTTTTGTAAACAGAGCC\n+ATTAATACTGCCGGCATCATCTTGCCCAGTGTACGCACAGGATTCAAGCCTCTTGCCAAG\n+AGGAAGAGCGGAAGGATGATGAAGAATTGAATGACATTACCTCCCAGGATAACAGCTACG\n+TACTTTCCTAGAGAAGCCATCACGATACCCGCAGAGAACTGGGCTGAGAGTTGTGCTGCA\n+AAGGCAACGATACCCAGAGGCAGAGCCCAGATTAATCCATGAATCAGCATGAAAAGCAGA\n+TCCTGCAGACCAAACAATCCCTTCATCACGACTTCTTTCTTATCGCTTGATGGCATCTTG\n+GCTAAAGCAATACCTGCTGCTGCCGCCAAAATCAATATAGAGAGTACATTTCCTTCGGCA\n+AACGGCTTGATGATGTTGTTGGGTATTACCCCAAGAATATGGTCATAATAGCTGGTTTCT\n+CCCAGCTTTTGGGGAACATCCGCCATACCGCTCTGTACCAAGGCTGTAGGTAAATTGCCT\n+GGAGCAACGATGTTGTAGAGCACCAGTCCCACTGCTGCAGCTGCTATCGTTGTGAGCAGG\n+GTGTAGGTGATGGCGTGGCGGAATATCTTACCGGTATCTGCCTGGTTGCCCAAGGATGCC\n+AGGGTTGTGATAACAGCCAAGGCTATGGTTGGTACTGCCAGAAGCTGGAATAAGCGGGTA\n+TAGACCGTGGCTATGAAGTTCATCAGACTATCCAGCCAGCTGATGCCGAATATCCCCAAG\n+ACGGCGCCTACTATCAAAGCACCAATCCATAGTACCAGCTGCCGGGTTTGCTTATTCTTC\n+ACTCCTTTTTGCTTACTGCAGCCAGCATTGCTATCCGGCTGTCTATTTCCAATATTATTC\n+ATTGTTTCTACCATGATTTTAAACTATTATTTTCAAAAGGCAAAGGTATTATTTTTTTTC\n+CTTGTCAACAATCCCACAAATATGGTATTTTGCAATCTCGTTATTTTTTTCGGGCTATTC\n+CTTTGCTTGTATCATTATTTTTTGTAACTTTGCCGAAAGAAAATTAAAACGGCAGCAATA\n+TGAAATATCCTATCGGCATACAGAGTTTCGAACAAATCATAGAAGATGGTTATGTTTATC\n+TCGATAAGACGGCATTGGTCTATGACTTAGTGACTAATGGTAAAATATACTTTCTGAGTC\n+GTCCACGACGATTTGGAAAGTCATTGCTCGTATCTACCTTGAAATGCTATTTCGAGGGTA\n+AGAAGGAACTGTTCAAGGGGCTTGCCATCGACAAGCTGGAGAAGGAGTGGAAGCAATATC\n+CTGTGTTTCATCTCTCTTTTGGTGGTCAAAACTTTGTAGAGCCTTATGCGTTAGACAAAG\n+TGTTGGAGGAGTTTGTTGCCATGGCAGAACGTATCTATGGGCGTGAGGAGTTGGCCGAGA\n+CTTTAGGTAGTCGCTTTAAGGCTGTGTTAGGGAATGCTCATAAAAAAACAGGAATGAGAG\n+CTGTCGTACTCATTGATGAGTATGACAAGCCTTTGCTT'..b'CTTTCTTTCGACCCAGGTCATTACAGTCCT\n+TATCATCCGGCAAATATACCACCTTAACCTTCTTGTATGATACAAGTTTCAAGGCTAAGT\n+TTATTGCCTGTTCCTTAGCATCTGGGTCAAGCAGTATGATGATACGTTCTACTGGAGATT\n+TGATTATCTCGTTTATCTGATAAGCAGATATTGCCTTACCCATAGTAGCAATTCCCCGTT\n+CTCCCATAGTCATGGCATTGATTGCTCCCTCACACAGATAAACGGACCTGTACATATAAA\n+GAGCATCATAATTGTATATGATAAACTCTTTGCCAAGTCCGGTAATATCTTTATTAGGAT\n+TATTGTAACGAGGTCCATTGCCTATAACTAGACGAGCATTATAATACCTTAGCTCTCCGT\n+TATAATAGAACGGGATAATCAGATATCCGAAAAGAGGTCCATCATTACAGTAACCTACTC\n+CCATACGAGATAAAGCCTGTACATCGAAACCTCTTTTCTTAACGTAGCCTCTCATAGTAT\n+TAGCCAGTTGAGAATCCCCATATTTAATGTTCTGAAAACCTTCTGGGAGATATACTGGCT\n+TCTTTTCGGCAAGTTCTACCTTCTCTTCATGAAAGGTGTAAGTGTCAAAGTCTGCAGAGT\n+TTAAGAACCTAAGGAGTTCTGACCATTCGTCAAGGTTCTCTATATCCATTACCATTTGTG\n+CAGGTCTGGGGTGTTCTCCACATCTGAAACAGTTGGACCTATAAGTGGATAAGTTTATAC\n+CCATCTTATTCTCCCTGCCACAGTAAGGACATACGGGAAGTTTCATCCAACCGTTTCTAT\n+ATTCGTATGCTCCTAACCTTTTGATGAAATAGGTCTTAAGCTTACTCTTAAATTCATTAG\n+TGACTTGCATTACTTGGTTCTCCTTAAGATTCTAATACCTCGGTCTATTACCCTACGTAA\n+CCTCAAAAGGTCAGTTAAAGTCATAGGACCTAAGTATTCTGTGTAATTTTCGGAAGTTCT\n+ACACATACCTATCTCAACTCCCCACTCTTGGTTTTCATGATTATGATTACCGTCTGGTGA\n+ATACCTAACAGGTTCAAGTTTCTTCTTTATCTTGAACTTCTTATAATGCCTTATCATGAC\n+GGTGATGATTAGTGATGATTAAACTTCTGTCATATACGAAATACAGTATAGCCTTGATGA\n+TATCACTTGCACTGATACCTAAAGCCATGGACAGTTGTTTTACTGCATTCTTCTGATTTT\n+TATCCAAAGACAGTTCTGCTTTGCTTAAAGCTTCTTTGTATGCCTCAGGAGAATAAACTC\n+CCTTGACAACGAGTGGTTTTACTTCTTCCATTGTGTTTATATTTTTACTTGTTATATGTC\n+TCCAGTTGTATGTGCTCTCTTATCAGCATTGGCATCAGGATTACTTTTCTTGCCGGGAGC\n+CTTTGCAATCATTTCATCCAATTTTCCACCATATACTTCATCGTACTTCTTACGTTGTTC\n+TATGGTGAATTCTTTAGCTTTCTGCTTCTCTATATCTACATGGAACAAAGCTCTTCCCGA\n+CGGTTTACCATCTCTTTGAACTACCAATTCCAATCTCTGGATACCGTCCTTATCTTCTTG\n+TTCAGTAGCATTAAGTCCGTAGATTACATGGACATGACGAACAATATCTACACACTTAGC\n+AATATCGTTCTCATCGTATCTAGTAGCTCTGTGTTTACTACCTTCACGAGTAATATGGTT\n+AGCTGTCCATATCATATCCAGATTCTCAGCTTCTGCCATGTTCTGCATATCTATAAACAC\n+ATTAGAGATTCTCTCGGTATCTTCCTTGTCCCGATTGATAGAGGCAAGCTTTGCTCCGTA\n+GTCAATAATAACTACCTTGATATAAATCCCTTGGTTTGCTAGTTTATGTATAAGTTCAGT\n+AATATAATTGCAGTCAGTTACCATTGCAGGAACTCTTTCAACTACCAATTCTACTCCAAA\n+CCGCATAAGTTTTCTTATATGGCGTGATTCCAAATCATCATATTCTCCTGAGTAAACTTC\n+CTTCTTAGTTTTACTGATGGAAGCCTGGATAACACGGTCCATAATTTGGTCCTTACCGTT\n+CTCAGTATCTATATATAAAACTGACTTCTTCATACGAAGATAACCCAAAGCCAAGTTCAC\n+CAGGAAAAATGTCTTCCTCGCTTTAGGTTTATCAAGAAGTACTCCTATTGAGTGAGCAGG\n+GAATCCTCCAGCATTAGTTAACTTATTTATTTGTCTAAACGGACATGGGATAATTGCAGG\n+GTCTGCTTGACGTTTGAATTGTCTATCTACCAAGTCTCTGGTGAGATATAGTGGTTCGTC\n+TTCCTTTTTAGGTTTGGACTGTTGGAGTATCTTCTCCAGTTTACGAGAGTACTCTTCATA\n+TTGAGTGAAATCATTTAAGTCCAGGGATTCATTCAGATTCTTAACACCTATATAAGTTAC\n+GAACTGATAAACCTTTTCCTGGATATAATCCCGGTCACTCAACGGTAAAGTGTAAAGATT\n+ATCGATTATTTTAAGGATATTCGGTACATCATCCTTAGTTACTAAATCTACATAATCCTT\n+ACTTTCTAGTAAATCTTTTAATACCTCCTTTAATATATTCTTGGAGGGAATTCTACCTTC\n+TTTCTTGAAGAACTTAGTTATGCCCTCGGCAATAATCGAATGCTCAATCAAAGTTAGATA\n+ACTTGGCTTTATCTTTTTCAGGACCAAACCTCCTTCTTTATCTTGGACAATAAACCTAAG\n+AATCTCCAATTGAAAGTCAGTATTGAACTCAAACTTAAATTTGTTCTTTCTGGCCATTTC\n+TACGAGAGTTTAATTATTTATAATATATAGAACTACTTAGTCTCGGTTTACTACCAGAGA\n+GTAGCCACTTCTACTCCAGTATTCAAATCCTCAGCTCTTAGGTGAAATTTTAGGATATTT\n+CTTTGCATATATAAAAATAATGTAGTAATTTTGCAATATCAAAATAAATTTAATTTAGTC\n+AAGGCAATGAACAGAACTAATGGAAACGACGGCTCAGAATTGCATAGACTCAAACCTATG\n+CAAGAGGGCTATGACCAGGACCTATTTAATAGGCTCTACAAGCTTTGCAAACCGGTCATA\n+AAGAACCTGGTTAGGCAAATTGATGCAAGGAGATATAATGTAACTCCAGACATCATCCAA\n+TCTCAGTTTGAAGACAAGATGCTTTTCGTCTTCAACAAGTACTACGGAAAAGTAAGTGAG\n+GAACATCTCAAGGCTAATATCCTCCGTTCCCTATCCACTTATAAAGTCCATCTCCTCAAG\n+TATGCTTATAATGAACGAGCAGAATTCAATCAAAGCTTAGCTTCATTGGATGAGTTATTC\n+GATGATAGCAAAGAATATATAGATGACTCTGAAGAAACTGTATTTAAGGAAGAACTCCTG\n+GATAAAGTTCATCAATATATGAAGGAGCATTTATCTGATGATGCTTATATGGTTTGGCAA\n+GTAGTCACCAATCCTCCCCCTTATGTAGAAGAAAGAATGTTAGGACCAAGAGTTACTAAC\n+ATAGTTATTGCAGAATTCTTCGACCTCCCCAAAACTCGTTCAGCAGTTAAATGGATTGGG\n+GAACTTAGAGAAGATATTAGGTATTGGATGGAAAGAGCTGGAGAAGAAATAAATCTAGAT\n+TAACACACAAAAAGGGAGAACCCATTACTGAGCTCTCCCACATCCAATCAACCTAAAAAC\n+TTATGGCAAGAAAGAACAAGCTTATTCGGAAGTTTGTGTTGTGATTGTTTTGTACGAATT\n+ACTCTTACGGATATAACGGAGGGTAATTGCAGGAACCAGTTTGTCTATCTCCAACTTTTC\n+CTTAGAGGTTTCTGTAATAGAACCACTATCGCTTATAGTACTAAGGTTAAAGCTAGTACG\n' |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/contigs3.fasta.textClipping |
| b |
| Binary file test-data/contigs3.fasta.textClipping has changed |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.tabular Wed Mar 06 14:09:08 2019 -0500 |
| b |
| @@ -0,0 +1,50 @@ +Assembly contig1 contigs2_fna +# contigs (>= 0 bp) 3 1 +# contigs (>= 1000 bp) 3 1 +Total length (>= 0 bp) 6710 6650 +Total length (>= 1000 bp) 6710 6650 +# contigs 3 1 +Largest contig 3980 6650 +Total length 6710 6650 +Reference length 6650 6650 +GC (%) 51.28 52.00 +Reference GC (%) 52.00 52.00 +N50 3980 6650 +NG50 3980 6650 +N75 1610 6650 +NG75 1610 6650 +L50 1 1 +LG50 1 1 +L75 2 1 +LG75 2 1 +# misassemblies 0 0 +# misassembled contigs 0 0 +Misassembled contigs length 0 0 +# local misassemblies 0 0 +# scaffold gap ext. mis. 0 0 +# scaffold gap loc. mis. 0 0 +# possible TEs 0 0 +# unaligned mis. contigs 0 0 +# unaligned contigs 0 + 1 part 0 + 0 part +Unaligned length 1950 0 +Genome fraction (%) 71.579 100.000 +Duplication ratio 1.000 1.000 +# N's per 100 kbp 0.00 0.00 +# mismatches per 100 kbp 0.00 0.00 +# indels per 100 kbp 0.00 0.00 +# genomic features 7 + 7 part 13 + 1 part +# predicted rRNA genes 0 + 0 part 0 + 0 part +Largest alignment 2030 6650 +Total aligned length 4760 6650 +NA50 1610 6650 +NGA50 1610 6650 +NA75 - 6650 +NGA75 - 6650 +LA50 2 1 +LGA50 2 1 +LA75 - 1 +LGA75 - 1 +K-mer-based compl. (%) 68.09 100.00 +K-mer-based cor. length (%) 100.00 100.00 +K-mer-based mis. length (%) 0.00 0.00 +# k-mer-based misjoins 0 0 |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test1_kmers.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_kmers.tabular Wed Mar 06 14:09:08 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). + +Assembly contig1 contigs2_fna +K-mer-based compl. (%) 68.09 100.00 +K-mer-based cor. length (%) 100.00 100.00 +K-mer-based mis. length (%) 0.00 0.00 +K-mer-based undef. length (%) 0.00 0.00 +# k-mer-based misjoins 0 0 + # k-mer-based translocations 0 0 + # k-mer-based 100kbp relocations 0 0 |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test1_mis_ass.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_mis_ass.tabular Wed Mar 06 14:09:08 2019 -0500 |
| b |
| @@ -0,0 +1,25 @@ +All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). + +Assembly contig1 contigs2_fna +# misassemblies 0 0 + # contig misassemblies 0 0 + # c. relocations 0 0 + # c. translocations 0 0 + # c. inversions 0 0 + # scaffold misassemblies 0 0 + # s. relocations 0 0 + # s. translocations 0 0 + # s. inversions 0 0 +# misassembled contigs 0 0 +Misassembled contigs length 0 0 +# local misassemblies 0 0 +# scaffold gap ext. mis. 0 0 +# scaffold gap loc. mis. 0 0 +# misassemblies caused by fragmented reference 0 0 +# possible TEs 0 0 +# unaligned mis. contigs 0 0 +# mismatches 0 0 +# indels 0 0 + # indels (<= 5 bp) 0 0 + # indels (> 5 bp) 0 0 +Indels length 0 0 |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test1_output.tsv --- a/test-data/test1_output.tsv Tue Dec 04 06:49:05 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,45 +0,0 @@ -Assembly contigs2_fna contigs1_fna -# contigs (>= 0 bp) 1 3 -# contigs (>= 1000 bp) 1 3 -Total length (>= 0 bp) 6650 6710 -Total length (>= 1000 bp) 6650 6710 -# contigs 1 3 -Largest contig 6650 3980 -Total length 6650 6710 -Reference length 6650 6650 -GC (%) 52.00 51.28 -Reference GC (%) 52.00 52.00 -N50 6650 3980 -NG50 6650 3980 -N75 6650 1610 -NG75 6650 1610 -L50 1 1 -LG50 1 1 -L75 1 2 -LG75 1 2 -# misassemblies 0 0 -# misassembled contigs 0 0 -Misassembled contigs length 0 0 -# local misassemblies 0 0 -# scaffold gap ext. mis. 0 0 -# scaffold gap loc. mis. 0 0 -# possible TEs 0 0 -# unaligned mis. contigs 0 0 -# unaligned contigs 0 + 0 part 0 + 1 part -Unaligned length 0 1950 -Genome fraction (%) 100.000 71.579 -Duplication ratio 1.000 1.000 -# N's per 100 kbp 0.00 0.00 -# mismatches per 100 kbp 0.00 0.00 -# indels per 100 kbp 0.00 0.00 -# genomic features 13 + 1 part 7 + 7 part -Largest alignment 6650 2030 -Total aligned length 6650 4760 -NA50 6650 1610 -NGA50 6650 1610 -NA75 6650 - -NGA75 6650 - -LA50 1 2 -LGA50 1 2 -LA75 1 - -LGA75 1 - |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test1_unalign.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_unalign.tabular Wed Mar 06 14:09:08 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +Assembly contig1 contigs2_fna +# fully unaligned contigs 0 0 +Fully unaligned length 0 0 +# partially unaligned contigs 1 0 +Partially unaligned length 1950 0 +# N's 0 0 |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.tabular Wed Mar 06 14:09:08 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +Assembly contigs1_fna contigs2_fna +# contigs (>= 0 bp) 3 1 +# contigs (>= 1000 bp) 3 1 +# contigs (>= 500 bp) 3 1 +Total length (>= 0 bp) 6710 6650 +Total length (>= 1000 bp) 6710 6650 +Total length (>= 500 bp) 6710 6650 +# contigs 3 1 +Largest contig 3980 6650 +Total length 6710 6650 +GC (%) 51.28 52.00 +N50 3980 6650 +N75 1610 6650 +L50 1 1 +L75 2 1 +# N's per 100 kbp 0.00 0.00 |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test2_output.tsv --- a/test-data/test2_output.tsv Tue Dec 04 06:49:05 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -Assembly contigs2_fna contigs1_fna -# contigs (>= 0 bp) 1 3 -# contigs (>= 1000 bp) 1 3 -Total length (>= 0 bp) 6650 6710 -Total length (>= 1000 bp) 6650 6710 -# contigs 1 3 -Largest contig 6650 3980 -Total length 6650 6710 -GC (%) 52.00 51.28 -N50 6650 3980 -N75 6650 1610 -L50 1 1 -L75 1 2 -# N's per 100 kbp 0.00 0.00 |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test2_report.pdf |
| b |
| Binary file test-data/test2_report.pdf has changed |
| b |
| diff -r 81df4950d65b -r f30d03867854 test-data/test3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.tabular Wed Mar 06 14:09:08 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +Assembly contigs3_fasta +# contigs (>= 0 bp) 30 +# contigs (>= 1000 bp) 30 +# contigs (>= 500 bp) 30 +Total length (>= 0 bp) 1197377 +Total length (>= 1000 bp) 1197377 +Total length (>= 500 bp) 1197377 +# contigs 30 +Largest contig 78752 +Total length 1197377 +GC (%) 42.28 +N50 38725 +N75 34003 +L50 12 +L75 20 +# N's per 100 kbp 0.00 |