| Previous changeset 2:ad1149b4f795 (2022-06-01) Next changeset 4:3fba9c77550a (2022-09-27) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5 |
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modified:
gfastats.xml macros.xml test-data/test_04_stats.tabular test-data/test_07_stats.tabular test-data/test_10.gfa test-data/test_11_stats.tabular |
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added:
test-data/dataset_03.fasta.fai test-data/test_12_stats.tabular |
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| diff -r ad1149b4f795 -r 8ccbf07a5433 gfastats.xml --- a/gfastats.xml Wed Jun 01 15:15:57 2022 +0000 +++ b/gfastats.xml Mon Jul 11 14:13:13 2022 +0000 |
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| @@ -54,12 +54,14 @@ --seq-report $mode_condition.statistics_condition.out_sequence #end if + $mode_condition.discover_paths $mode_condition.tabular > '$stats' #else --agp-to-path $mode_condition.agp_to_path $mode_condition.discover_paths -o dataset.gfa #end if + --threads \${GALAXY_SLOTS:-8} #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding' && mv dataset* output_dataset #end if @@ -155,7 +157,7 @@ </when> <when value="coordinates"> <param argument="--out-coord" type="select" label="BED coordinares feature" - help="Generates bed coordinates of given feature. Default: agp"> + help="Generates bed coordinates of given feature. Default: AGP"> <option value="a">AGP</option> <option value="c">Contigs</option> <option value="g">Gaps</option> @@ -172,10 +174,12 @@ </conditional> <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" label="Tabular-format output" help="Generate output in tabular format"/> + <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly + is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> </when> <when value="scaffolding"> <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" /> - <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="generates the initial set of paths" help="In the graph space an assembly + <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> </when> </conditional> @@ -334,6 +338,19 @@ </conditional> <output name="stats" value="test_11_stats.tabular" ftype="tabular"/> </test> + <!--Test 12 --> + <test expect_num_outputs="1"> + <param name="input_file" value="dataset_04.gfa"/> + <conditional name="mode_condition"> + <param name="selector" value="statistics"/> + <conditional name="statistics_condition"> + <param name="selector" value="assembly"/> + </conditional> + <param name="tabular" value="false"/> + <param name="discover_paths" value="true"/> + </conditional> + <output name="stats" value="test_12_stats.tabular" ftype="tabular"/> + </test> </tests> <help><![CDATA[ |
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| diff -r ad1149b4f795 -r 8ccbf07a5433 macros.xml --- a/macros.xml Wed Jun 01 15:15:57 2022 +0000 +++ b/macros.xml Mon Jul 11 14:13:13 2022 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.2.2</token> + <token name="@TOOL_VERSION@">1.3.0</token> <token name="@SUFFIX_VERSION@">0</token> <xml name="requirements"> <requirements> |
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| diff -r ad1149b4f795 -r 8ccbf07a5433 test-data/dataset_03.fasta.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_03.fasta.fai Mon Jul 11 14:13:13 2022 +0000 |
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| @@ -0,0 +1,3 @@ +contig_1 1680 10 60 61 +contig_2 417540 1728 60 61 +contig_3 356 426237 60 61 |
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| diff -r ad1149b4f795 -r 8ccbf07a5433 test-data/test_04_stats.tabular --- a/test-data/test_04_stats.tabular Wed Jun 01 15:15:57 2022 +0000 +++ b/test-data/test_04_stats.tabular Mon Jul 11 14:13:13 2022 +0000 |
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| @@ -9,6 +9,8 @@ Scaffold auNG 290571.00 Scaffold LG50 1 Largest scaffold 417540 +Smallest scaffold 356 +# contigs 6 Total contig length 419573 Average contig length 69928.83 Contig N50 416949 @@ -18,6 +20,7 @@ Contig auNG 289747.19 Contig LG50 1 Largest contig 416949 +Smallest contig 101 # gaps in scaffolds 3 Total gap length in scaffolds 3 Average gap length in scaffolds 1.00 @@ -25,6 +28,7 @@ Gap auN in scaffolds 1.00 Gap L50 in scaffolds 2 Largest gap in scaffolds 1 +Smallest gap in scaffolds 1 Base composition (A:C:G:T) 102144:112550:104859:100020 GC content % 51.82 # soft-masked bases 0 |
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| diff -r ad1149b4f795 -r 8ccbf07a5433 test-data/test_07_stats.tabular --- a/test-data/test_07_stats.tabular Wed Jun 01 15:15:57 2022 +0000 +++ b/test-data/test_07_stats.tabular Mon Jul 11 14:13:13 2022 +0000 |
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| @@ -6,12 +6,15 @@ Scaffold auN: 415520.91 Scaffold L50: 1 Largest scaffold: 417540 +Smallest scaffold: 356 +# contigs: 6 Total contig length: 419573 Average contig length: 69928.83 Contig N50: 416949 Contig auN: 414345.81 Contig L50: 1 Largest contig: 416949 +Smallest contig: 101 # gaps in scaffolds: 3 Total gap length in scaffolds: 3 Average gap length in scaffolds: 1.00 @@ -19,6 +22,7 @@ Gap auN in scaffolds: 1.00 Gap L50 in scaffolds: 2 Largest gap in scaffolds: 1 +Smallest gap in scaffolds: 1 Base composition (A:C:G:T): 102144:112550:104859:100020 GC content %: 51.82 # soft-masked bases: 0 |
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| diff -r ad1149b4f795 -r 8ccbf07a5433 test-data/test_10.gfa --- a/test-data/test_10.gfa Wed Jun 01 15:15:57 2022 +0000 +++ b/test-data/test_10.gfa Mon Jul 11 14:13:13 2022 +0000 |
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| b'@@ -1,2 +1,2 @@\n-H\tVN:Z:2.0\n-S\tedge_1\t419576\tTTTCCTTTTCCTACTGTACTTCTCAAATATTCCAGGCGACTTTCGTGATGATTCACAGCATGTTTCACGATTCGCTAACCCTAATCCGCTACCGCGGTTAGCCGGGAACCCCGCTTTATCAACGCGATAAAAACGCTTCGGTCAGGCCGCGGAATAATGCTCCGGTGCAATGCCCCGGGTCCGTTATCTTCAACGCTAAATTCGGCACCGTGCGGCACTCGCTGCCAGCGTACGGTGATATGCGTGCCCTTCCGGCGTATGGATTCACGCGTTATTAGACCAGGTTTGAAATCGCACTGCGGTAGCTGATCTTCGTTTGCCAGACACCTTGAGGCCGTTATCTATCTCAAAGGTAAATGTCTGTTTTTCTGACTCAGAGTCTGAGCCTCGCGCTCAACAACGCGCAGCATCATCGGCACAATCAACCTTTTCATTTGAGGAATGCGTCGGTGCGGCTTCTATTTTCGACAGCGTCAGCAAATGCTTCACCAGGTCCTTCCATCCCGCTGGGTCTGCTCGCGCATGGTGTGCAACGCTTTTTCGCGTACCGCGCCTTCCAGCGGCTGCTCAATTCATCATCTCCAGGTAACCCCTGTAACACGGTCCAATGGCGTACGTAACTCATGGCTCACCGTTGGCAAAAAAGTTACGCCGCGCCCCTTCCAGTTGATGCATTTGCGTGACATCACGCGCCACCATCAGCAACTGTTTGTGGGTATAAGGCATGACGCGAATTTCCAGATGCCGCCCGGTGGTTTGAGCACAGATTGAGCGGGCGAGAAAAATCACGCGTTTTCAGATATTGCGTAAACTCCGGGTAAACGCAGTAGTTAAGGATGTTCTGCCCGTTATCTTCCGGCCAGCGCAAACCAAGAAATTTGTTGCGCCAGACCGTTACACCAGAAAATACCGCCCTTTTCCTGGTCAGCACCACCGCGTCGGGCAGCGACTCCGCGCCGCTACGAAAAGCGTTTAATCAGATTGCCCACTGTTCACGGCGGGCGTTTTTTATTTCCGCAGCTGCATCTGGTGTAAGCCGTATAGTAGCGGTTCCCAGCTACCACCGCCCCGGTGGCGGGGTCATACTGCGATCCCACCCAACAGCCACCATGAAAAGGCGCAATAAATTCCAGAAATGCCAGATAAGCAGTCCTGTTACCGATGCCAGCAAAAACCAGGGCAGGTAACCAAAAAATGCACCCAAGGATGAAAGCCGGGAGGCAGCAAAGTAGCAGCTCCAGCACCAGGCCTTTCCACGACAGCCGTTCCAGCACCGTAAGATACTCCAGTTAAGAAAATCATAAGCCCTGCTCTGCGCCGGAGAGCAAGGCGTTAAAAGCGGGGTTGAAAAACGATTATCCTGTACCGCGCACGGTCTGCCACCATGCGGTCATGCCCGCCGGGCTCCAGAGCTTTACGCAGGCGACGAATGTGGACATCGACCGTGCGGTCTTCCACATACACGTTAGTTCCCAGACGTGTTTAACAGCTGCTCGCGCTGTACACGCGCTCAGGATGCGTCATAAAAAAGTGCAGCAGTTTTAAATTCTGTCGGCCCCATCTCCAGCGGCTCTTCGCCCGCCATCACTCGGTGAGATGTCGGGTCGAGACTTAATCCCTGCATCTTAATCACCTCTTCCACCGCCATTGGCGAAATACGGCGCATTACCGCTTTGATTCGCGCCACCAGCTCCTTCGGCGAAAACGGCTTGGTGATATAGTCATCCGCGCCGGTTTCAAGCCGCGCACGCGATCTTCTTCTTTCCCCTCTGGCGGTCAACATCACCACTGGGAATATCCCGGGGTCATCGACTCGCGCTTGAGGTGTTTGATGAACTGGATACCGGAGCCGCCAGGTAACATCCAGTCGAGGAGAATTAAAATCCGGCCAGGGTTCATTCAGTTTGATTCACAGCACTGTCATAATCTTCCGCTTCGACCGGCTGAAAGCCATTTTGTTCGAGCACGAAGAGAGACCAATTTCGGCGAATTGGAGCTTCATCTTCTACGACCAGAATACGTCTCGCCATGATTTGCCCTGTTGTAATAAATAGGTTGCGATCATTAATGCGACGTCATTATGCGTCAGATTTATGACAGATTTATGAAAAGCCTCGTCGCACAATATCTTCAGGTTATTGATTTCCGTGGCGCAGAAAAAAGCAAATGGCACCATCTGTTTGGGTATAATCGCGCCCATGCTTTTTCGCCAGGGAACCGTTATGCGCATCCTTCACACCTCAGACTGGCATCTCTGGCCAGAACTTCTACAGTAAAAGCCGCGAAGCTGAACAATAGGCTTTTCCTTGACTGGCTGCTGGAGACAGCACAAACCCATCAGGTGGATGCGATTATTGTTGCCGGTGATGTTTTCGATACCGGCTCGCCCGCCCAGTTACGCCCGCACGTTATACAACCGTTTTGTTGTCAATTTACAGCAAACTGGCTTTCATCTGGTGGTACTGGCAGGAAACCATGACTCGGTCGCCACGCTGAATGAATCGCGCGATATCATGGCGTCCTCAATACTACCGTGGTCGCCAGCGCCGGACATGCGCCGCAAATCTTGCCTCGTCGCGACGGGACGGCCAGGCGCAGTGCTGTGCCCCATTCCCGTTTTTACGTCCGCGTGACATTATTACCAGCCAGGCGGGGCTTAACGGTATTGAAAAACAGCAGCATTTACTGGCAGCGATTACCGATTATTACCAACAACACTATGCCGATGCCTGCAAACTGCGCGGCGATCAGCCTCTGCCCATCATCGCCACGGGACATTTAACGACCGTGGGGGCCAGTAAAAGTGACGCCGTGCGTGACCATTTATATTGGCACGCTGGACGCGTTTCCGGCACAAAACTTTCCACCAGCCGACTACATCGCGCTCGGGCATATTCACCGCGCACAGATTATTGGCGGCATGGAACATGTTCGCTATTGCGGCTCCCCCATTCCACTGAGTTTTGATGAATGCGGTAAGAGTAAATATGTCCATCTGGTGACATTTTCAAACGGCAAATTAGAGAGCGTGGAAAACCTGAACGTACCGGTAACGCAACCCATGGCAGTGCTGAAAGGCGATCTGGCGTCGATTACCGCACAGCTGGAACAGTGGCGCGATGTATCGCAGGAGCCACCTGTCTGGCTGGATATCGAAATCACTACTGATGAGTATCTGCATGATATTCAGCGCAAAATCCAGGCATTAACCGAATCATTGCCCTGTCGAAGTATTGCTGGTACGTCGGAGTCGTGAACAGCCCGAGCGTGTGTTAGCCAGCCAACAGCGTGAAACCCTCAGCGAACTCAGCGTCGAAGAGGGTGTTCAATCGCCGTCTGGCACTGGAAGAACTGGATGAATCGCAGCAGCAACGTCTGCAGCATCTTTTCACCACGACGTTGCATACCCTCGCCGGGAGAACACGAAGCATGAAAATTCTCAGCCTGCGCCTGAAAAACCTGAACTCATTAAAAGGCGAATGGAAGATTGATTTCACCCGCGAGCCGTTCGCCAGCAACGGCTGTTTGCTATTACCGGCCCAACAGGTGCGGGGAAAACCACCCTGCTGGACGCCATTTGTCTGGCGCTGTATCACGAAACTCCGCGTCTCTCTAACGTTTCACAATCGCAAAATGATCTCATGACCCGCGATACCGCCGAATGTCTGGCGGAGGTGGAGTTTGAAGTGAAAGGTGAAGCGTACCGTGCATTCTGGAGCCAGAATCGGGCGCGTAACCAACCCGACGGTAATTTGCAAGGGCCACGCGTAGAGCTGGCGCGCTGCGCCGACGGCAAAATTCTCGCCGACAAAGTGAAAGATAAGCTGGAACTGACAGCGCGGTTAACCGGGCTGGATTACGGGCGCTTCACCCGTTCGATGCTGCTTTCGCAGGGGCAATTTGCTGCCTTCCTGAATGCCAAACCCAAAGAACGCGCGGGAATTGCTCGAGGAG'..b'ATTTTTCCTGTGGGATTTTCATCACCAATAAACGCCGAGAGGATCTCGCACTTGCGGGTGACAAAATCCAGCTTCAGCATCTCATCAATTTCAGTCAGGCTGAATTCCGGCAGGTCGTGCGGAAAAAACAGCCCCTGATTTTTGCCCAAACCCCTGGGTTACGCTTGCGCAAAGCTGACCTGCCTCGTTGTGATCTTTCAGATTGAGGTTTCATTTAGTTTTCCAGTACTCGTGCGCCCCCCGTATCCAGCCGGCAAATATGACAAAACCTTCCTGATTTTGCAGGTAGTTCTTACCCAACCAGTCGGCAACGCGCGGGGCGGTTTCCGGCTTGTCACACAGAGCGAACAAGGTCCGGGCCGGAGCCGGAGATACCGCTCGCTACCGCGCCATTTCCGCGACCGCCTGCCGCGCCTGCCGGAAGCCTGGCAGTAACCGTTCACGGTAGGTTCACGCGATAACATCTTTTCATACAGCGTTCGCGGCAAGCTCAGGCTGACGGGAATAGCAGGCGTGAATGAAGCCTGCCAGATGTCGCCCGTGCGCAATGCAATCCTGGCGCGATACTGCCCCGGTAAAATAGCCCTGGCTTTTCCGTCGAGACTTTAATCCCCGGATACGCCAGCACCCACAGCCACTCATCCAAACCTGGCACTTGCTGGCTGATGATGTCGTTTTCTTCGATCATCAACTGCATACCACCGAGAAAACACGGTGCCACGTTGTCGTAATGAATGCTGCCGGAGATACGGCCTTCCAGCTCGCCCATCAAAAGCCAGCGAACGAGTGTCATTAAGCGGCTTGCCGCAGTGTTCAATTTCATCCCATCAGCGCCGCGACCACGAAACAGGCACTGGAGCCTAAGCCCGAACCGATCGGCATATTCTTTTCCAGGGTCATCGCCACTGGAATTTGCTTACCCAGTTCCTGGCAAAAACGCCTCCCAGCACTGATAAACGATATTTTCCCGTGGTTTCTGACGGCAGCCTTATCCGGGCAAAGCGTCCGAGGTTGTTGAGACTGAATGTCTCTGCCGCCTCAACCGTGACTACATCTCCGAGCAATGCACCATCAACAGGTGTCACCGCCGCCCCGAGCACATCAAACCCGACGCTCATATTGGCACTGGAAGCCGGGGCATAAACTTTAACCATTTTCAGACTCCTAACTTCCATGAGAGGGTACGTAGCAGATCAGCAAAGACACCGGCAGCTGTAACCGTCAATTTGCCCGCACCATATCCGCGCAGTACCAAACGGCAAGCGGCTGATAATAGTGGCTTAAGAGCCAGGGCGTTTTCGCCATTTTTCACTTTGAACAGCGGATCATTACCATCCACTTCGGCAATCTTCACGCGGCAGACGCCATCTTCATCAATATTGCCAACATAGCGCAAAACCTTTCCCTTCATCACGGGCCTTCGCCACGCGCGCGGCAAAGAGATCGTCGAGTTGTGACAGATTCGCCATAAAAGCGGCAACATCACCCTCGGCGTTAACCTCTGCGGGGCAGCACAGGTTCAATTTCAATATCCGCCAGCTCCAGTTCACTCCCGTTTCACGAGCGAGAATCAATAGTTTACGCGCCACATCCATACCAGAAAGATCATCTCGCCGGGTCCGGTTCGGTATAACCCATTTCCCGACGCAGCGTGGTCGCCTCGGAGAAACTCATGCCTTCGTAAACTTGCCGAAGATATAAGAAAGCCGAACCAGACAAGAATGCCGGAGAACTTCATCAATTCATCACCTGCATTGAGCAGATTTTGCAGGTTCTCAATAACCGGTAATCCAGCCCCAACGTTGGTGTCATAGAGGAATTTACGCCGCGATTTTTCCGCCCGCATAACGCAACTGATGGTAGTAATCCATCGACGAGGTGTTTGCCTTTTTGTTCGGCGTGACAACGTGGAAACCTTCGCGCCAGGAAGTCGGCATATTGATCCGCCACCTGCCTGGCTGGAAGTGCAGTCAACAATGACCGGGTTTCAGCAGATGATATTCTTTTCACAAGGCGAGTTAGCGCCCGGGATAAACGGCTCTTGGCTTGCGCCAGTTCTTCCTGCCAGTTTTCCAGATTAAGGCCCATGTAATTGGTGAGCAGAGCCTTCGAGTTGGCAACACCGCAGACACGTAAGTCGATTATTTTATTCTTCAGCCCAGCTTTGCTGACGCGCTTCAGTTGCTCCAGCAGCGGCACCGCCAACGCCACCGACGCCAATCACAAACACTTCGATAACCTGATCGGTATTGAACAGGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTTACCACGACACGAGATTGAGCGTTCAGAAGATCCCTGAGCAATGGCGACAATGTTGATATTTGGCGCGGCCAGGCGGCAAAGAATTCTCGCCGAGATCCCACGCAAGGTGCGCATACCATCACCTCCCACGAGATAAATGGCCAGCCGTTCCGCACTGCCAGCGGCTCCCAGTAGCCTTCTTTCAGTTCCAGGTAGAACTCTCCTGGCATGCCCGTTCAGCTCGCACACAGTCGCTTTGTGGAACGCAGAAACTAATGCGTATTCGGAAAGATGATTGCGTAATCAGCCACACGGAAATACCGGGCGCGTGACATCGGCTGCAAAGCGCGCCGCCGCCATGCCGACCATCCTATCATCCCCGGACCAGAACGCTGAAACATGCCATGTTAATTCAGATTGGAAATGGTTCCCTTGACCGGTAATTCGTCTTCAACACGGCTGGCACCAATTAGCGTACCTGGTGCTTGAGGATTTCCGGTATTTTTTAATCAGGCAAAGGGATCTGGAACTGGGCGATGGGGGTAATGGTGCGGGTGAAGAACTTTAGCGCCGAAAGTAGGAAACCCATCGCTTCCTGGTAGGAACATCGACTTCAACAACCTCGCATCGGGGCCACCTGACGCGGGTCGCAGGTATAGACCCCCGTCAACGTCCGCCAAATCTCGCAACAATCGGGGCCCGTAAACAGGCAGCCAGCACCGCAGCAGAAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCGGGGGAACCTGCCATCAGCACGCATGTGATCAGCCGGAATGCAGGGCTTGCCGCAATTAGGCGGGTGGACTCAGGAAATCGACGGTAGATTCGAGGTAATGCCCCACCGCCAGCAGTTTTTCGACCGGATCGATAACCTAAGTACTTGTGACGCCGGCGCCGTCTATACGCCGGCATAAATGGCGAGCGACATTTCTCGCCACGGCCAAAATCGAGCGCCAGCGTTTGATGCTAATCCGGCACTGCCCAACAAACTATTGCCATGGGCAGACATGTTTTATTGGGCCAAATTCCTGATCGACGAAAGTTTTCAATGCGCCAGCGGGAACCCCCGGCGGGGCGGCGGCGGTCTACCAGGTCAAAAGGTATCGGCAAAAAATACGTTGGCCATCGCGATTATTGGTAAAGCATCCTGGCCCCTAAATGGTATTTTGTCAATTCATCGACACCAAGGTGTTGGTGATTTTTGCGGGCGGGTCAGAGAGGGACGGTGGGCCTACCTGCCTCCTGCCTTCGGCTCGGCTTTCTAGAATATCGGCAAACACGCGAAAAAACGTTCTGCATTTGCCACTGATGATACCGCCCGAAACTTCAACACTCGCATGGTGTTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCCGCACTGTCTAAAGGTGGCGGGCTTTTATTACATGTGTTTCCGTACGCGTACGGCCCCGCTACCGATACCTGTGGTAATCGGTGAATGTGGGGGTATACGGTGGTGCTATCGTTTTCATGGATGTTGATGAATCTCTGGTATTTTTATCTGTCGGTGCGCTAGGCCTATATTGGTTAAAAATATTTGTGGTTCCGAGTCAATAAAATTTTTAATTTACCACGGGGCCCAAGGAAACCAGTTCAATAAACATGCTATCAGACACCTTTTTTTAGATCCACC\tdp:i:14\n' 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| diff -r ad1149b4f795 -r 8ccbf07a5433 test-data/test_11_stats.tabular --- a/test-data/test_11_stats.tabular Wed Jun 01 15:15:57 2022 +0000 +++ b/test-data/test_11_stats.tabular Mon Jul 11 14:13:13 2022 +0000 |
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| @@ -5,12 +5,15 @@ Scaffold auN 1680.00 Scaffold L50 1 Largest scaffold 1680 +Smallest scaffold 1680 +# contigs 2 Total contig length 1679 Average contig length 839.50 Contig N50 922 Contig auN 847.61 Contig L50 1 Largest contig 922 +Smallest contig 757 # gaps in scaffolds 1 Total gap length in scaffolds 1 Average gap length in scaffolds 1.00 @@ -18,6 +21,7 @@ Gap auN in scaffolds 1.00 Gap L50 in scaffolds 1 Largest gap in scaffolds 1 +Smallest gap in scaffolds 1 Base composition (A:C:G:T) 388:497:402:392 GC content % 53.54 # soft-masked bases 0 |
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| diff -r ad1149b4f795 -r 8ccbf07a5433 test-data/test_12_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_12_stats.tabular Mon Jul 11 14:13:13 2022 +0000 |
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| @@ -0,0 +1,93 @@ ++++Summary+++: +# scaffolds: 2 +Total scaffold length: 839152 +Average scaffold length: 419576.00 +Scaffold N50: 419576 +Scaffold auN: 419576.00 +Scaffold L50: 1 +Largest scaffold: 419576 +Smallest scaffold: 419576 +# contigs: 2 +Total contig length: 839152 +Average contig length: 419576.00 +Contig N50: 419576 +Contig auN: 419576.00 +Contig L50: 1 +Largest contig: 419576 +Smallest contig: 419576 +# gaps in scaffolds: 0 +Total gap length in scaffolds: 0 +Average gap length in scaffolds: 0.00 +Gap N50 in scaffolds: 0 +Gap auN in scaffolds: 0.00 +Gap L50 in scaffolds: 0 +Largest gap in scaffolds: 0 +Smallest gap in scaffolds: 0 +Base composition (A:C:G:T): 204288:225102:209720:200042 +GC content %: 51.82 +# soft-masked bases: 0 +# segments: 1 +Total segment length: 419576 +Average segment length: 419576.00 +# gaps: 0 +# paths: 2 +Scaffold N10: 419576 +Scaffold N20: 419576 +Scaffold N30: 419576 +Scaffold N40: 419576 +Scaffold N50: 419576 +Scaffold N60: 419576 +Scaffold N70: 419576 +Scaffold N80: 419576 +Scaffold N90: 419576 +Scaffold N100: 419576 +Scaffold L10: 1 +Scaffold L20: 1 +Scaffold L30: 1 +Scaffold L40: 1 +Scaffold L50: 1 +Scaffold L60: 2 +Scaffold L70: 2 +Scaffold L80: 2 +Scaffold L90: 2 +Scaffold L100: 2 +Contig N10: 419576 +Contig N20: 419576 +Contig N30: 419576 +Contig N40: 419576 +Contig N50: 419576 +Contig N60: 419576 +Contig N70: 419576 +Contig N80: 419576 +Contig N90: 419576 +Contig N100: 419576 +Contig L10: 1 +Contig L20: 1 +Contig L30: 1 +Contig L40: 1 +Contig L50: 1 +Contig L60: 2 +Contig L70: 2 +Contig L80: 2 +Contig L90: 2 +Contig L100: 2 +Gap N10: 0 +Gap N20: 0 +Gap N30: 0 +Gap N40: 0 +Gap N50: 0 +Gap N60: 0 +Gap N70: 0 +Gap N80: 0 +Gap N90: 0 +Gap N100: 0 +Gap L10: 0 +Gap L20: 0 +Gap L30: 0 +Gap L40: 0 +Gap L50: 0 +Gap L60: 0 +Gap L70: 0 +Gap L80: 0 +Gap L90: 0 +Gap L100: 0 |