| Previous changeset 12:875d0f36d66f (2022-02-06) Next changeset 14:3061c8b029e5 (2022-08-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" |
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modified:
macros.xml quast.xml |
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added:
test-data/test8.fasta test-data/test8_result.tab |
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| diff -r 875d0f36d66f -r 675488238c96 macros.xml --- a/macros.xml Sun Feb 06 21:02:38 2022 +0000 +++ b/macros.xml Fri Mar 25 17:36:59 2022 +0000 |
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| @@ -11,7 +11,7 @@ </xrefs> </xml> <token name="@TOOL_VERSION@">5.0.2</token> - <token name="@VERSION_SUFFIX@">4</token> + <token name="@VERSION_SUFFIX@">5</token> <xml name="gene_thresholds"> <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"/> </xml> |
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| diff -r 875d0f36d66f -r 675488238c96 quast.xml --- a/quast.xml Sun Feb 06 21:02:38 2022 +0000 +++ b/quast.xml Fri Mar 25 17:36:59 2022 +0000 |
| [ |
| b'@@ -8,6 +8,7 @@\n <command detect_errors="exit_code">\n <![CDATA[\n #import re\n+#import os\n \n #if str($in.custom) == \'false\'\n #set $labels = \',\'.join( [re.sub(\'[^\\w\\-_]\', \'_\', str($x.element_identifier)) for $x in $in.inputs])\n@@ -47,7 +48,7 @@\n #end for\n #for $read in $reads.input_2\n --pe2 \'$read\'\n- #end for \n+ #end for\n #else if $reads.reads_option == \'paired_interlaced\'\n #for $read in $reads.input_1\n --pe12 \'$read\'\n@@ -69,8 +70,8 @@\n #end for\n #end if\n \n---labels $labels\n--o outputdir\n+--labels \'$labels\'\n+-o \'outputdir\'\n \n #if $assembly.type == \'genome\'\n #if $assembly.ref.use_ref == \'true\'\n@@ -97,7 +98,7 @@\n --references-list \'$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+ --max-ref-num $assembly.ref.max_ref_num\n #end if\n #end if\n \n@@ -119,7 +120,7 @@\n --min-alignment $alignments.min_alignment\n --min-identity $alignments.min_identity\n --ambiguity-usage \'$alignments.ambiguity_usage\'\n---ambiguity-score \'$alignments.ambiguity_score\'\n+--ambiguity-score $alignments.ambiguity_score\n $alignments.fragmented\n $alignments.upper_bound_assembly\n #if $alignments.upper_bound_min_con\n@@ -159,6 +160,14 @@\n && cp -R outputdir/icarus_viewers \'$report_html.files_path\'\n #end if\n \n+#if $assembly.type == \'metagenome\'\n+ && if [[ -d "outputdir/combined_reference/" ]]; then mkdir -p \'$report_html_meta.files_path\' && cp outputdir/combined_reference/*.html \'$report_html_meta.files_path\'; fi\n+ #if $assembly.ref.origin != \'none\'\n+ && if [[ -d "outputdir/combined_reference/" ]]; then cp -R outputdir/combined_reference/icarus_viewers \'$report_html_meta.files_path\'; fi\n+ && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p \'$krona.files_path\' && cp outputdir/krona_charts/*.html \'$krona.files_path\'; fi\n+ #end if\n+#end if\n+\n ]]>\n </command>\n <inputs>\n@@ -188,11 +197,9 @@\n <option value="nanopore">Nanopore reads</option>\n </param>\n <when value="disabled"/>\n-\n <when value="single">\n <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />\n </when>\n-\n <when value="paired">\n <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />\n <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />\n@@ -201,21 +208,17 @@\n <when value="paired_interlaced">\n <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />\n </when>\n-\n <when value="mate_paired">\n <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />\n <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />\n </when>\n-\n <when value="pacbio">\n <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />\n </when>\n-\n <when value="nanopore">\n <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />\n </when>\n </conditional>\n-\n <conditional name="assembly">\n <param name="type" type="select" label="Type of assembly">\n <option value="genome">Genome</option>\n@@ -321,24 +324,35 @@\n <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the end'..b'ame="report_tabular_meta" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="contigs (>= 0 bp)" />\n+ </assert_contents>\n+ </output>\n+ <output_collection name="metrics_tabular" type="list" count="14"/>\n+ <output_collection name="metrics_pdf" type="list" count="15"/>\n+ </test>\n+ <!-- Test 09: metagenomics log, html and krona outputs-->\n+ <test expect_num_outputs="4">\n+ <conditional name="in">\n+ <param name="custom" value="false"/>\n+ <param name="inputs" value="test8.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+ <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="alignments">\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="all"/>\n+ <param name="ambiguity_score" value="0.99"/>\n+ <param name="fragmented" value="false"/>\n+ </section>\n+ <section name="advanced">\n+ <param name="contig_thresholds" value="0,1000"/>\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+ </section>\n+ <param name="output_files" value="html,log,krona"/>\n+ <output name="report_html" ftype="html">\n+ <assert_contents>\n+ <has_text text="Vibrio_parahaemolyticus" />\n+ </assert_contents>\n+ </output>\n+\t\t\t<output name="report_html_meta" ftype="html">\n+ <assert_contents>\n+ <has_text text="Total length (>= 1000 bp)" />\n+ </assert_contents>\n+ </output>\n+\t\t\t<output name="log_meta" ftype="txt">\n+ <assert_contents>\n+ <has_text text="Vibrio_parahaemolyticus | successfully downloaded" />\n+ </assert_contents>\n+ </output>\n+ <output name="krona" ftype="html">\n+ <assert_contents>\n+ <has_text text="Vibrio_parahaemolyticus" />\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help>\n@@ -622,7 +758,7 @@\n **Using Quast without reference**\n \n Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:\n- \n+\n * Quast report in HTML format\n * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)\n * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format\n' |
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| diff -r 875d0f36d66f -r 675488238c96 test-data/test8.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test8.fasta Fri Mar 25 17:36:59 2022 +0000 |
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| b'@@ -0,0 +1,100 @@\n+>contig_1\n+TCATTATTGCCGCTTTCTCCTGCCTAATTGCGGAAACTACTAAATTCCCCGCTCCTATTCAGCCAGTGCCTAAAGTTTACTCCTGCTTTGGACCGCTTATAGCGCGAAATGCAACCCCATAAAGGAGAAAAAAAGTTAGGCATGGAAAATCCGCGCTGCTTATTACTATAAAGCTAGCTTGTAGCATGGTTTAAGTGCTTTCCGGATGTGTGCAAGCAAGGCTGGCCCATTTGTCACCAATGTAAGCAGTGGATGGTTGATGGCGGGCTGCTAATAGAAAAGTGCCATGGTCCGGCTAGACCGCATGATCAATACTGTTGAAAACGCAGACTGCACTACCAGTCCGATTAAAGCTAAAACGGGCAAGCGCTGGTATTCCGTTAAATTCTCAGAAGATTACTTAACGGGTCCAAACTTGGGTCGCGTAGTAAAGGTGGGAAACATTCTGGAAACTAGCCCCCTTAGAAACCCTCACAAGGCCCCATGTCGCATGGCCTTTGGGCCAAGTTTTCCAGGTTTCCCCCTTATAGAGAGTAAAGAAACCGGAAACTAAGCAAGAATCCTGTAACGGGCTCGAAAGTCGAGCCGGACGACTTCTCTGTAAGCGCAATCCTTAGAAAGTTAGACACATCGAGATACTGCGTGCTCCTCCTCTTCGCGCTACCTGCCTGGGCCTCCTTTAAGCACTCCTCCCAAGCTTTGCTACTTACTAGATCCATATCTATAGCCCTGCGCTTCCATTTGGAAAATAGTGCCCTTAGTAACACCGAATCTCTCGGCCAATTCATTCTTGGGAAGCACAACGCCCAGTTCCTTTCACTGCTCGCACCATTTCCACTATCTTGGCATCTGATCGCGGCTCGACAACCCACTGGGGGGCGCTCTCCAGGGTCATTCTGAAGGCTGACTCTAACGGGTGCTACCCGATCATCTCTAAGACCCCGGTATTTTTCAAAGTCAATGTCAAATGTGGGCTCCTCCTTGTGCGGGGTATCCTGGTCGGGATGATTTTAGACTAATAATCGAATTGAAAATCACCGCTTGCTTAGAGGTTCCCCGGTAGCTTCCATTGCCCGCTTGGGTGTTTCTTCCTGGCATGGTGAACTTAAACATGGCCGCAATACGCCCTTGCTTTAGCTGACGCAGAGAACCGGCATGATCGGGTTTAAAGCTAGAGGCGGCGTTTTCGTCTTCCACTTCACAAAGCGTGCTGAAGTTGTCGAGTATCACAAACTCTGCCCGATTGGTTCTTTTATGTGCTTTCATCACAATGGCTTGCCCCTCATCGGTAGGCCAGGTCAGGAAACTCGACATCCAGGCTTTGATCCTGCTGAGCAAGAAACAATAGGTTATTTCTGGGCTGTTTTAATATTGACATCCAGGGGCTCTATTAGCTTTCTCGCATCGCCTCTTGCAGATTCCTCTATATCCCATTTTCAACCGTCGACGAAGACCACACGCCTAGCTATGGGGGCATCCCAGTGATACAACTTCCCGCCCGCCTGCAACGGCAAGCGCCGCTGATAGCGCCGAACCAAGACTTACCCACGCCCAGCAGGTGCATAGACCCATGCTCAAGTGGCGCTGGGTGAGCCAAGGGAGCTAATAGCTCCCTCTCTTGGTTTAAACTTTTCATCAAGCAAATCCACCTAGGGCTGCGAGATTTTAAATTCCGTGGTTTAGATTTACTACTCACGTTATTCATGACCTGGCCTGGATAAGCAAAAAAGTGAATAACTTTGGGGTCCTTTCTCAGGGATTCCTTGCTGCGGGTAGCGTGCGCGCGCGAGATTTCGGCTAGGCTACAGGTCTTTTCTTAGCATCCTTCCTGAACGCTCCTGGCCGGGCCGATAGGAAACTATCAATCATAAAGGAGTCACCCCAAGGCAAAGGAAGTATCTAGGGCTTCTGTACCGTTCATAGAGAGCATCCCCTGCTTATTCCATTTACGGGGTGGAAAGAAGAAAAACTTTTAAAAGTCTCACATGAGGGTGTTAGACGCCCGCTAATCAGATACTAGGTCTATTGCATAATTTTATAAAGGCTGTACACAACTAACAAGCATAAATCGCGCATTCACTTTTTTGTGATTGAATTTCTGTTCCCATTAAATGCATGCCCTGATACCATCAGCATCTGAAAGTGTATCCCATACATATGATGAAAATGATGACTTTAATGCCGGGATGAAAGTCCTTTTTTCTTTTTCGAATTCGATTTTAGAGCTTTACCGAGGGTCGCCTTTTCATCACCTATTAATATGTTTGGCATAATGATTCAATTGCCGATATTGATTCTTTTATTGAATTACCGATAATCAGGATTTTCTCGATCACTCATCATGCTTAAAGCGGGTTTCTAAATGCTCCCTTACCCCTGCAAATGGGGAAGATCTAGCAATAGCCTTCTTCCAATAGACTGGAATTTCTTCTTCTGCAGTAATTTTCTGTTAACTGACCATTTACAAACCTTATAAGCAGAGGTTTTCACGATTCAAACATGAGTTACAGGCTCTTTATAAAAATCTTTCCTTTGTTCGTAGTGGCCCCTTTAGTGGCCACAAACTCAACAAAATCATAAATCTCAATACCATTGAGCAGAAAAAAAATATCCTCCTTAAATCACCAACGCAATCCCAAAAAGTAAGGAGGTATTGTATCTATAGGCTTCTTGTAATAATATAACCAAAGATTTTGTAATTAAAAGGTTGCATGTTGCTACCTTCTATATAATCAATACGGCCAGCCATACGTGTCATATTTGCGTTTATTGAACTTCTCCCAGTAGAAAAATCCGTAACAAACTCCAGAGACTATTCTTCAGTTTCATCGTCGATAGATTCTCGTTGAATAGCTTTTTCAGCTGCTGATATTTCCTTGTCTTTGAGAAAACTGCATAAAGATTTATCCCCCTTTGGCCGCCATTAAGTTACTGCCCATTATTAGTACGCTAGATCGGCGGCTCCGATGAATATGCTCTAGCTAGATGGCATTTTGCCAAACCGTAGTCAGCAAATTATCCCGGGAAATTAAAGCTAGTAAGAAATTGATCCCGCCCTAATCCGGTGCCTCTCTTTCACAAACCCTCAGCACACAGCCCGATCCACCTCCAGCTCCATAGCTTACCATCGCTACAGCCTCAGCCCATCTTCTCTAGATCCACACCGGGGCTATACAGGCCATAGGTGAGGCCTCTGTTTCTTATGCCCCCAACAATCTGCTGGGCAAGCGTTTCCCGACAACCCCCCGCTTGCTCTAGTGCCCCCGCCAAAAATTCTTGCGAAAACTATGGAAGACGAATCCGGGCTATCTGTAAGGCCCGCCTTCTCGGCGCTTTAAATCTTTCGAAACGCTTCGCAAAGTAATGATGGGCGCTTATTATCTTTCGCCACCTCGGATAAGCCCGCGTGATCAAGTAGCCCCTCTGTGCTGCTCGCTTTCCAGTTGTTCAAATGAACGGTTTCAGAAGGGGGATGAATAGGGGGTATCCCGAAATGCTGCTTTCAGTCTTCCCTTCCGGTATGATGAATGTGAATCGGAATTGAACACTTCAAGGCGGGGTCCTCGCGATCTCGTTCTCGGCGCATGCCAGTTATAAGAGGGCGATCACGGTCATGGGCCCAGAGGGGATCATCCCTCGCCCAAGCCGGGGCCTTAATCTCTAGCTAGTAAAGTGTTTAGAGTTTCTTTCTTGTGCCAGACGCGGCGCCTTGCCCGTTTTTCTTTCCCCTGGAGCCCTCGGGTGGTATCGCGGTACAGAATTTGCTTCATCCCTCTAAAAGGCGATTTGGAGACTGTTTGCCCCCGCTCCATGGCCCAGTTAAAGAAGGCGGACAAAGTCGCTACAATCCGTATCTTTAACCGTCTTCTGGGAGTTACCTCGCTTTAGCACACACCTCGAGCTCACGTAGGCGTCCGGCATCTTTCCCGCGCGAGTTATCCTTTGAGGCTTCCTATCCGCCCCTCCCAA'..b'AGCCACCAGCGTGCATGTATATCCTTGAAACGGTGGTAGGGTGCCTCATTCGGAACAGCGCGCCAGCCGGTAATTCCATGCTTGTTCGATCTAGCAGCGTCGAATAGGCTCGGCTATCGCGTCGTGGTAAAACAGCCGTTTTAACACGTATTCTAACGAGAATACGGTACTGATAATATGGTGGTTTCAATAGAATTGCATCAGTGTTTAGCTGTGAGGCTAGGAGCCAGGCTTGTTTTAATCCCAGTCTTCATGAGGGGATTCTAGCCCGCGTCGTATGTAGGGCAACATCTATAACGGGTTAGACGTGTCTTGCTAGTCTTAGTGGGTGTTTTCTATGTCGAAAATTATTGTCTGTCAGTAGGGAGGCCGGGTTTCGAGGAGCGTGTGGCGTAGATTCTTGGAGCTGGCTATAAAGGCGGTATAACAGGTACCGTGGCGTTGAGTCTACTTGCTAAGCTGCTAGAGGTTAAAGGGGTGATGTAGCCTACGTCGTGTTTGAGGGTAGCTTCTGCGAGACCTGCGGTATCAACGACTGGGTAGATGATCTCAAGTACGTGATCGAGGATCCTTGGTGGAGAGGCTGAGCCTCATAGCCAGTTGGTTGAGCCTCCGTCGAGGGATGAGTTCTTCGACTACCGTATATAGGCGTGTTTAAGATTAGGAAGGTTCCTGAGAACCTGGATGAGCTTGAGAGGTGAGGGAGGAAGAGGCTCGAGAAGTACTTCTTCCCATCAGAACGAGGAGGCGGCACAGAGGGGTCTAGAACCTTCCCTCTGGATAGCATTCCTTCGCGGCTATTGCTGAACGCTAAAGGCTTGCAGGGGCTTGGTTCGCTTATAGCGAAGAGAGCGTCGGTGACATACCCTGAGGCTGTGTTTTTTATTCCAGGCTCCGAGTATGTAGGCTGGCGAGACCCTTTACACCCCCTGGCGGCCAGTTTTACTGTACACCCGCCTACAGTACATTGGTTTCTTCTTATCAACCCCCCCAATATGCTATTGCTGAAGTTCATGAACGCAGCCCGGGGTAGCACAGTGCTCCCAGGCCAAGGGCGTGGCCAAGCTCGTGTAGCGCTTCCTTCAGAAGCCTCCTACGATAGAGAGCTTCGTTTGGCGGCTCACCGTAGAACTCTGGGTGCAGCCTCGCAGTGTAGACCACGGCGACACCCCCGGCCCCAGGAGTTGCCTGGCCAAATACAAAGTTGAGGGCCTGGCGTATAGGCGTCAAAGCCTGCCACAAACCAGTAGGGGCATCGCCCCCTAAGCTTTCTCGTGGAGAATAGCTGCAAGCTCCAGTATAGCGTCGGCTGAGGTACTGGCGGCGCACCGGGTCATAGGCTGACGGAGGCGGCTCCAGCTCCTGCTCCCACGATGTTTTACGTGTGCGTTACTGTAGGCCTCCCTGAGCCCTAGCAGAGAGGAAACACCAGATCATCCCCGCTCAACGTGGTGTACCCGCAATGTGTATGACTACCATGATGTTGTGCCTCCCATACTATGCTAGAGCTAGAGCGGCAGGCTAGTAGTAGTGTGAAGAGAGTCAAGCGTATGAGTTCTACCATGCCTAGAAGCCTTATCCTAGACATTTGTATCTTCCTGGCCCGCAGGGGCGTTCCACACCAGCTTTATGGGTGGGCTCCACGCCATGTCAGCAGTGCAGTGCAGGCTTGACAGCTGCAGCAAGGGGTAGCGCAGGGAGCCATAGCGCTAATGGTAAAGAGAGGACTCGTACTGCGCATGGGAAGCCTCGACTCTACATACGCTGCTGTGCTAGCAGTGTACAGCGCCATGAGGCCTGGCAGCTGTGATGGTTAGAGTTGTTGGGCTCGCCAGCGAGGAACAGAGGCTAGTACAGCGGTATAGGGAAGAGAAGGGGCAGCGTCAGCTATGTAGCCCATAGCGGGTGCCTAGGAAGACCCCCTCACAGCCGCAGCGGTGTAGCCAGGCGAAGAGAGAGGCGAGTAGGCTAGGAGGCGCGGCAGCAACAGCACTACGCCCAAAGAATGAATGCAGCTGCGTACGGCAAAACAATTGACACTGGCAACGGCTGCTACAAGACGTGCACAGCGCCTCTTCGCAGCATCCAAAGGCGGCGTCGAAGGTCAACACGTGCAAGAGATACGGCTGCCGCAGCGAACAACCAAGCCCCACAAGGTGACAGACTCCATCGACACGACACCGACAGCGGGCGCTAAACACTATGATGGCCAGCAGCACTAGGCTCCCGGGGCAGCCTAAACAAGGCCCGCGGAGCCCCTACGCTGCAGCCTCGCCCCCATTAAAGGGACTCCCATCGAGCGGCAAAACAGTAAAACCATGATATGGCTTGGCGTGGGAGCCTCCACCAGCCAGTATGGCAGCCCCTCGCGGCTCAGTGCTAGAGGGAGGAATCCAGCTTGAAGGAACGTCCTGGAGAACGACTTTGCAGCCCTTAAGAAGGGGGGTAGGGTGTTATAGCTCCTTGGGCGGTGAGGATCGCCTGCGACGAAAGAAGGCCGCCACAGTGTTGGCGGCGGATGCTGATGGAAAGAGCCGTGCCGAGCCCTCTCCTCCCCTTCTAGAGTACATCCTTTATGAAGCGGCCCGTTCTCATATATCAGGTCGCCGTCCAGCGTAGACCTTTGTGGCTCCCAGAGGCTCCCTTATCATGTCCCCAGTGGATGCTCGACTGGTTCCCTCCCGCCAGTCCTCGGGGTAGGAATGCTCCTAGTGCTATTGTGCATTGGTGCCCGCCTATCTTCTCGTCGAATAGTATCTCCTTGGTGAACCTGTCAATGTTTGTAGTTTAGCCCGAAGGCTAGCTCTCCCCAGCCTCCTGGCTCCCTCGTCTGTCTGGAGCATCTTACGGAGAAAGTCCTCGCCCTCTCCTCGCAGTGGCCTCTACGACTTCGCCGCCGGCGGAAGACGAGCCGTACACCCCTCCACCCTCGACGCCCCGCCATATGGCGGGGGTAGTCGAAACTCTATGTAGCCCTCAGCTGTGTCCTCCACCGGGGCCGGTAAAGACTTCGCCGCCTGGCATGTTGTAGCGGCCGTCATCGTTTATCCAACTTCCTCCCCGCGACGCTCACCCTTGAAGTCTATACCGGGCCCCTTGATGTGTTAGCTCTGACACCCTGGTTCAACATGTCCACTATCTTCTGCTGCTCCCTAGCCTTCTTCTCTCCACGCAGCTATGGGGTCGGTCGCGGTCAACCATGGTTGCACGATATACGAACTCTTCAAACTCGAGAATAGACATGCCAGCCTCCTGGGCCATAGCCCGTGTTGGGTAGGGCGCCAGGGTCCAGCGCAGCTCGCCTCTCGCGCGCTCCTCTCCATGTATATCCTTGTCAGCTCGAACCGGGCCCGGCTACGCGCCTAGCCATCCTCTCCGGATCAACGCCATTCAAGTGCTTTGGTATGGCCTCGGCGCCAGTTATGGATATGGGAGACGTCAATCTTTTCGGCTAGGAGCTTCTCCACGGGGCTAATATGGTCTAGGACAATTGTCCTTGGCGTACCGGTAGGAATATTTCATCGAGAACCTCGTCTCGGAGGCTTACGAGGAGCGGGTACCCGCCCCGGCTAACGACCTCCCGGTTAAAGCTCCCGCACTAGAGGCAACGCCTCAAGTCCAGCAGAATATAACGACTTCGTCGCCTGGGCGCGATGAGGAGACACAAGTAATTCTGCAATCAGTCCTTGGCAAAGCTTTGAGGATAGAAGGGTCGGGGCAATAGCCTAGCCGCCTATATGACACGCGGGAGTCCCGGCCGTAAAAGAGGCCAAGCGGCCCACGCTTCCCTTAACACCAGCCTCACGGGAAGCTTGGGCAGCAGGGGAGGGGGCGGGCAGTATTGATATATTCGTGATATACCGTGTGTCATAAAGGAGGTTTGGTGTAAGAGAAGCTTTGCCAGCGCGGATAACAATTATCCTTTGTCGCGTTTGCGGGGCTCCAAACCTCGAAGTGCAAGGTGCCATTTTTCAGCGCTATGTCGAATATTGAGTGGT\n' 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| diff -r 875d0f36d66f -r 675488238c96 test-data/test8_result.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test8_result.tab Fri Mar 25 17:36:59 2022 +0000 |
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| @@ -0,0 +1,29 @@ +Assembly test8_fasta +# contigs (>= 0 bp) 50 +# contigs (>= 1000 bp) 50 +Total length (>= 0 bp) 255882 +Total length (>= 1000 bp) 255882 +# contigs 50 +Largest contig 14050 +Total length 255882 +Reference length 4995681 +N50 5163 +N75 4420 +L50 18 +L75 31 +# misassemblies 0 +# misassembled contigs 0 +Misassembled contigs length 0 +# local misassemblies 0 +# scaffold gap ext. mis. 0 +# scaffold gap loc. mis. 0 +# unaligned mis. contigs 1 +# unaligned contigs 49 + 1 part +Unaligned length 254490 +Genome fraction (%) 0.027 +Duplication ratio 1.031 +# N's per 100 kbp 0.00 +# mismatches per 100 kbp 444.44 +# indels per 100 kbp 2888.89 +Largest alignment 657 +Total aligned length 1392 |