| Previous changeset 19:a3d31a68f291 (2022-11-21) Next changeset 21:fa84bba02a62 (2023-10-28) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit e532d288f092df22f32805cea50583fe16a1070f |
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modified:
lotus2.xml test-data/OTU_paired.fna test-data/OTU_paired.txt test-data/mapping_paired.txt |
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| diff -r a3d31a68f291 -r 1d660ee0b1c8 lotus2.xml --- a/lotus2.xml Mon Nov 21 11:49:15 2022 +0000 +++ b/lotus2.xml Sat Dec 03 16:37:26 2022 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.09"> <description>fast OTU processing pipeline</description> <macros> - <token name="@VERSION@">2.21</token> + <token name="@VERSION@">2.23</token> <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz"> <conditional name="refDB_cond"> <param argument="-refDB" type="select" label="Taxonomy reference database"> @@ -264,7 +264,7 @@ </when> --> </conditional> <section name="clu_args" title="Other Clustering Options"> - <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." /> + <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See https://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." /> <param argument="-deactivateChimeraCheck" type="select" label="Chimera check"> <option value="" selected="true">(Default)</option> <option value="0">OTU chimera checks</option> @@ -305,7 +305,7 @@ <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" /> <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB (optional)"/> <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/> - <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" /> + <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use LULU to merge OTUs based on their occurrence" /> <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> <option value="0">Disable</option> <option value="1" selected="true">Use fasttree2</option> @@ -391,25 +391,16 @@ <collection type="list:paired"> <element name="Anh_sample"> <collection type="paired"> - <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" /> - <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" /> + <element name="forward" value="Arabidopsis_R1.fastqsanger.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="Arabidopsis_R2.fastqsanger.gz" ftype="fastqsanger.gz" /> </collection> </element> </collection> </param> </conditional> - <param name="map" value="mapping_paired.txt" /> - <conditional name="clu_cond"> - <param name="clustering" value="3" /> - </conditional> - <section name="clu_args"> - <param name="derepMin" value="1" /> - </section> + <param name="map" value="mapping_paired.txt" ftype="tabular" /> <section name="tax_args"> - <param name="lulu" value="false" /> - </section> - <section name="other_opts"> - <param name="platform" value="454" /> + <param name="lulu" value="true" /> </section> <output name="otu" file="OTU_paired.txt" compare="sim_size" /> <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" /> @@ -421,7 +412,7 @@ .. class:: infomark -The full LotuS2 **documentation** can be found at `<http://lotus2.earlham.ac.uk/>`_. +The full LotuS2 **documentation** can be found at `<https://lotus2.earlham.ac.uk/>`_. ]]></help> <citations> <citation type="doi">10.1186/s40168-022-01365-1</citation> |
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| diff -r a3d31a68f291 -r 1d660ee0b1c8 test-data/OTU_paired.fna --- a/test-data/OTU_paired.fna Mon Nov 21 11:49:15 2022 +0000 +++ b/test-data/OTU_paired.fna Sat Dec 03 16:37:26 2022 +0000 |
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| b'@@ -1,294 +1,464 @@\n->OTU1\n-TACAGATCGTCCGTCAATTCCTTTAAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGATTACTTAATGCGTTTGCGCCGGCACCGAAGGACCTTGGTCCCCCAACACCTAGTAATCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCTTACCTCTCCTGCACTCTAGCTGCACAGTTTCCAAAGCAGTTCCATTGTTAAGCCATGGGATTTCACTCCAGACTTGCGCTGCCGTCTACGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGGGCTTCTTAGTCAGGTACCGTCATTTTCTTCCCTGCTGATAGAGCTTTACGTACCGAAATACTTCTTCACTCACGCGGCGTCGCTGCATCAGGGTTTCCCCCATTGTGCAATAT\n->OTU2\n-ACTACTATGTCCGTCAATTCCTTTAAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTATCGCTTTCGCTTCGCCACCCAGGGGTCAATCCCCCCGGACAGCCAGCATTCATCGTTTACTGCGTGGACTACCAGGGTATCTAATCCTGTTCGATACCCACGCTTTCGTGCCTCAGCGTCAGTGTGGAGCCGGCATGCTGCCTTCGCAATCGGAGTTCTGCGCGATATCTATGCATTTCACCGCTACACCGCGCATTCCGCATACTTCTCTCCAACTCGAGACTGCCAGTTTCAACGGCGGGCTGGGGTTGAGCCCCGGGCTTTGACCGCTGACTTAACAGACCGCCTGCGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGATGCTTTTTCTTCAGGTACACTCATCCGGGGACACGTCCCCGCCTTTGTTCCCTGACAAAAGAGGTTTACGATACTCTGTACCTTCCTCCCTCACGCGGCTTGG\n->OTU3\n-AGACTATACTCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGGATGCTTAACGCTTTCGCTTGGCCGCCGACTGTATATCGCCGACAGCGGGCATCCATCGTTTACCGCGCGGACTACCAGGGTATCTAATCCTGTTCGATACCCGCGCTTTCGAGCTTCAGCGTCAGTAACGCTGCGGCAGGCTGCCTTCGCAATCGGGGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTTCCGCGCACTCAAGGTCTCCAGTTCGCGCCGCACTCTCATGGTTGAGCCACAAAATTTCACGGCACGCTTAAAGACCGGCCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCCCGGACCTTCCGTATTACCGCGGCTGCTGGCACGGAATTAGCCGGTCCTTATTCATGCGGTACCTGCAAACATCCACACGTGGACGCCTTTATCCCCGCATAAAAGAGGTTTACAACCCATAGGGCAGTCTTCCCTCACGCTACTTGGCTGGTTCAGCCT\n->OTU4\n-ACGACTACAGCCGTCAATTCCTTTAAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATACTTAACGCTTTCGCTGTACCACCCAGGCATCATTCTGCCCGGACAGTTAGTATTCATCGTTTACTGCGTGGACTACCAGGGTATCTAATCCTGTTCGATACCCACGCTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAACGCCAGTTTCAACGGCACGACGGGGTTGAGCCCCGAAATTTTACCGCTGACTTGACATTCCGCCTGCGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGATGCTTTTTCTTCAGGTACTCGCAAAGCGCCACACGTGGCGCCCTTTGCTCCCTGACAAAAGAGGTTTACAATCCATAGGACCGTCATCCCTCACGCGA\n->OTU5\n-TACACACACTCCGTCAATTCATTTAAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCAGCACTGAGAGGCGGAAACCTCCCAACACTTAGCACTCATCGTTTACGGCATGGACTACCAGGGTATCTAATCCTGTTCGCTACCCATGCTTTCGAGCCTCAGCGTCAGTTGCAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCTTCCATATATCTACGCATTCCACCGCTACACATGGGAGTTCCACTCTCCTCTTCTGCACTCAAGTTCAACAGTTTCTGATGCAATTCTCCGGTTGAGCCGAAGGCTTTCACATCAGACTTATTGAACCGCCTGCACTCGCTTTACGCCCAATAAATCCGGACAACGCTTGCCACCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGTGACTTTCTAGGTAATTACCGTCAAATAAAGGCCAGTTACTACCTCTATCTTTCTTCACTACCAACAGAGCTTTACGAGCCGAAA\n->OTU6\n-TCTACGTAGCCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGATCACTTAACGCTTTCGCTGTGCCGCTTACTGTGTATCGCAAACAGCTAGTGATCATCGTTTACTGCGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGTGCATCAGCGTCAGTCATGGCTTGGCAGGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTAAGCATTTCACCGCTACACCACGCATTCCGCCTGCCTCAAACATACTCAAGCCTCCCAGTTTCAACGGCAATTCTATGGTTGAGCCACAGACTTTCACCGCTGACTTAAAAGGCCGCCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGGATCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGATCCTTATTCATAAGGTACATACAAAACGGGACACGTCCCGCACTTTATTCCCTTATAAAAGAGGTTTACGATCCATAGAACCTTCATCCCTCACGCGACTGT\n->OTU7\n-ATACGACGTACCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGATTACTTACTGCGTTTGCTGCGGCACCGGAGGGTCCATACCCTCCGACACCTAGTAATCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCTTACCTCTCCTGCACTCCAGCCATACAGTTTCCAGAGCAGTCCGGGGGTTGAGCCCCCGCCTTTCACTCCAGACTTGCACAGCCGTCTACGCTCCCTTTACACCCAGTAATTCCGGATAACGCTTGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGGGCTTCTTGGTCGGGTACCGTCATTGCTTTCTTCCCTGCTGACAGAGCTTTACATACCTAAATACTTCTTCACTCACGCGGCGTCGCTGGATCAGGGTTCCC\n->OTU8\n-TACACGTGATCCGTCAATTCATTTGAGTTTCAACCTTGCGATCGTACTCCCCAGGTGGGATACTTATTGCGTTAGCTGCGGCACGCAGGGGGTCAGTCCCCGCACACCTAGTATCCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTG'..b'ACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTAGACTTGACATCCCCTGCATAACCCAGAGATGGGCGAAGTCCTTCGGGACAGGGTGACAGGTGGG\n+>ASV222\n+TGGTAGTCCACGCCGTAAACGATGAGTGCTAGGTGTGGGGGGTGTCGACTCCCTCCGTGCCGAAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCAGGGCTTGACATGCACTGGAAAGCCGTAGAAATACGGCCTCCCTTCGGGGCCAGTGCACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCCATGTTGCCAGCGCGTAATGGCGGGGACTCATGGGAGACTGCCGGTGACAAATCGGA\n+>ASV223\n+TGGTAGTCCACGCCCTAAACGATGTCGACTAGTTGTCGGAGGGTAACTCCTTCGGTAACGCAGCTAACGCGTGAAGTCGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATG\n+>ASV224\n+TGGTAGTCCTAGCCGTAAACGTTGGGTGCTAGGTGTGGGAGGACATCGACCCCTTCCGTGCCGAAGCTAACGCATTAAGCACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGCGGCTTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCAGGGTGAAACCGTTGAAAGACGGCGCTCTTCGGAGCCTGCACAGGTGGTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGCCTTAAGTGGCGCAACGAGCGCAACCCCTGTCCTTAGTTGCCAGCGGATCATGCCGGGAACTCTAGGGAGACTGCCGGTGCCAAACCGGA\n+>ASV225\n+GGGTAGTCCACGCCGTAAACGGTGGGCACTAGGTGTCGGGGGTATCGACCCCTCCGGTGCCGCAGCTAACGCACTAAGTGCCCTGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTGGTTTAATTCGATGCAACGCGAAGAACCTCACCTAGGCTTGACATGGTCGCAGTAGGAACCCGAAAGGGGGACGACCCGTAAAGTCGGGAACGATCACAGGTGCTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGGCGTTAGTTACCATGTCTAACGCGACTGCCGGTTTCAAACCGGA\n+>ASV226\n+GGGTAGTCCACGCCGTAAACGATGGACACTCGTCCTTTGCGGGGTAACCATTCCTCGTGTGGGGCTCAGCTAACGCGGAAGTGTCCCGCCTGGGAACTACGAGCGCAAGCTTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTGGTTTAATTCGACGCAACGCGCAGAACCTCACCCAGATTTGACATGCAGCTGCAAGCTTCTGAAAGGAAGTCGCCTTCGAGGGTGCTGCACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCCGCGGCTAGTTACTCGTGTCTAGCCGGACTGCCCGATTGGGA\n+>ASV227\n+GGGTAGTCCACGCTGTAAACGATGGGTACTCGGTGTGGGGGGTATCGACCCCCTCCGCGCCCCAGCTAACGCGATAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCTGGGCTTGACA\n+>ASV228\n+GGGTAGTCCACGCCCTAAACGTTGGGTACTAGGTGTGGGGGGTATTGACCCCCTCCGTGCCGAAGCTAACGCGATAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTGGTTCAATTCGATGGTACGCGAAGAACCTTACCAGGGTTTGACATGCTGGTGGTACGGATCCGAAAGGTGAAGGACCCTTCGGGGAGCCAGCACAGGTGTTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCGCTAGTTGGATTTCTCTAGCGAGACTGCCGGGAGCAACCCGGA\n+>ASV229\n+GGGTAGTCCACGCCGTAAACGATGCCGACTCGGTATCCGCTGGGCGAATAGCCCGGGGGGTGCCCCAGCTTACGCGGTAAGTCGGCCGCCTGGGGACTACGAGCGCAAGCTTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTGGTTTAATTCGACGCAACGCGCAGAACCTTACCCAGCCTGGACATGTGCCTGCACACGGGTGAAAGCCCGTCGCCTTCGAGGGTGGCACACAGATGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTACGGTCAGTTACACGTGTCTGACCGGACTGCCCTTTATCGGGA\n+>ASV230\n+GGGTAGTCCACGCAGTAAACGATGCACACCCGGTGTCGGACCGACCGTCATGGTCGGTGCGGTGCCCAAGCTTACGCGATGAGTGTGCCGCCTGGGGACTACGAGCGCAAGCTTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTGGTTTAATTCGACGCAACGCGCAGAACCTTACCTTGCCTTGACATGCTCCTGCAAGCCCGAGAAACCGGGTCGCCTTCGAGGGTGGAGCACCGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTGTGTTATACGTGTCACAGGAGACTGCCCTGGTCAACCAGGGA\n+>ASV231\n+TGGTAGTCCACACTGTAAACGTTGATGACTCGCTGTTGGCGATACACAGCCAGCGGCAGAGAGAAATCGTTAAGTCATCCACCTGGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAATTGACGGGGGTCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTAGAATGCCCTTGATGGGTGCAGAGATGCACTGTTCCGCAAGGACAAGGAGCAAGGTGCTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTCTTAGTTGCCAACATTTAAGGTGGGGACTCTAAGAAGACTGCCTGCGCAAGCAGAGA\n+>ASV232\n+GGGTAGTCCACGCCGTAAACGATGTCGACTCGGTGTGTGGCGCCCGTTTCGGGGGCTGCGTGCCGAAGCTTACGCGGTAAGTCGACCGCCTGGGGACTACGAGCGCAAGCTTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTGGTTTAATTCGACGCAACGCGCAGCACCTCACCCAGACTGGACATGCCCGTGCAAGCTGGTGAAAGCCAGTCGCCTTCGAGGGTCGGGCACAGATGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCGTGTTACCATGTGTCACGGGGGACGGGCGCCTGGATGGGCGCA\n' 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| diff -r a3d31a68f291 -r 1d660ee0b1c8 test-data/OTU_paired.txt --- a/test-data/OTU_paired.txt Mon Nov 21 11:49:15 2022 +0000 +++ b/test-data/OTU_paired.txt Sat Dec 03 16:37:26 2022 +0000 |
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| @@ -1,148 +1,233 @@ OTU SMPL0 -OTU1 39 -OTU2 19 -OTU3 19 -OTU4 18 -OTU5 17 -OTU6 15 -OTU7 10 -OTU8 9 -OTU9 9 -OTU10 9 -OTU11 9 -OTU12 9 -OTU13 8 -OTU14 8 -OTU15 7 -OTU16 7 -OTU17 7 -OTU18 6 -OTU19 6 -OTU20 5 -OTU21 5 -OTU22 5 -OTU23 5 -OTU24 5 -OTU25 4 -OTU26 4 -OTU27 4 -OTU28 4 -OTU29 4 -OTU30 4 -OTU31 4 -OTU32 4 -OTU33 4 -OTU34 4 -OTU35 4 -OTU36 3 -OTU37 3 -OTU38 3 -OTU39 3 -OTU40 3 -OTU41 3 -OTU42 3 -OTU43 3 -OTU44 3 -OTU45 3 -OTU46 3 -OTU47 3 -OTU48 3 -OTU49 3 -OTU50 3 -OTU51 3 -OTU52 2 -OTU53 2 -OTU54 2 -OTU55 2 -OTU56 2 -OTU57 2 -OTU58 2 -OTU59 2 -OTU60 2 -OTU61 2 -OTU62 2 -OTU63 2 -OTU64 2 -OTU65 2 -OTU66 2 -OTU67 2 -OTU68 2 -OTU69 2 -OTU70 2 -OTU71 2 -OTU72 2 -OTU73 2 -OTU74 2 -OTU75 2 -OTU76 2 -OTU77 2 -OTU78 2 -OTU79 2 -OTU80 2 -OTU81 1 -OTU82 1 -OTU83 1 -OTU84 1 -OTU85 1 -OTU86 1 -OTU87 1 -OTU88 1 -OTU89 1 -OTU90 1 -OTU91 1 -OTU92 1 -OTU93 1 -OTU94 1 -OTU95 1 -OTU96 1 -OTU97 1 -OTU98 1 -OTU99 1 -OTU100 1 -OTU101 1 -OTU102 1 -OTU103 1 -OTU104 1 -OTU105 1 -OTU106 1 -OTU107 1 -OTU108 1 -OTU109 1 -OTU110 1 -OTU111 1 -OTU112 1 -OTU113 1 -OTU114 1 -OTU115 1 -OTU116 1 -OTU117 1 -OTU118 1 -OTU119 1 -OTU120 1 -OTU121 1 -OTU122 1 -OTU123 1 -OTU124 1 -OTU125 1 -OTU126 1 -OTU127 1 -OTU128 1 -OTU129 1 -OTU130 1 -OTU131 1 -OTU132 1 -OTU133 1 -OTU134 1 -OTU135 1 -OTU136 1 -OTU137 1 -OTU138 1 -OTU139 1 -OTU140 1 -OTU141 1 -OTU142 1 -OTU143 1 -OTU144 1 -OTU145 1 -OTU146 1 -OTU147 1 +ASV1 608 +ASV2 409 +ASV3 330 +ASV4 292 +ASV5 285 +ASV6 266 +ASV7 245 +ASV8 216 +ASV9 204 +ASV10 200 +ASV11 186 +ASV12 183 +ASV13 155 +ASV14 145 +ASV15 135 +ASV16 126 +ASV17 119 +ASV18 118 +ASV19 114 +ASV20 104 +ASV21 104 +ASV22 103 +ASV23 101 +ASV24 98 +ASV25 97 +ASV26 96 +ASV27 93 +ASV28 93 +ASV29 87 +ASV30 82 +ASV31 81 +ASV32 80 +ASV33 79 +ASV34 79 +ASV35 77 +ASV36 77 +ASV37 76 +ASV38 73 +ASV39 71 +ASV40 69 +ASV41 69 +ASV42 68 +ASV43 67 +ASV44 67 +ASV45 67 +ASV46 66 +ASV47 65 +ASV48 65 +ASV49 64 +ASV50 64 +ASV51 63 +ASV52 62 +ASV53 62 +ASV54 61 +ASV55 61 +ASV56 60 +ASV57 60 +ASV58 59 +ASV59 59 +ASV60 59 +ASV61 59 +ASV62 58 +ASV63 57 +ASV64 57 +ASV65 57 +ASV66 57 +ASV67 57 +ASV68 57 +ASV69 56 +ASV70 55 +ASV71 54 +ASV72 54 +ASV73 54 +ASV74 54 +ASV75 53 +ASV76 53 +ASV77 52 +ASV78 51 +ASV79 51 +ASV80 50 +ASV81 50 +ASV82 50 +ASV83 49 +ASV84 49 +ASV85 49 +ASV86 49 +ASV87 49 +ASV88 48 +ASV89 48 +ASV90 48 +ASV91 47 +ASV92 47 +ASV93 46 +ASV94 45 +ASV95 44 +ASV96 42 +ASV97 42 +ASV98 42 +ASV99 41 +ASV100 41 +ASV101 41 +ASV102 41 +ASV103 41 +ASV104 41 +ASV105 41 +ASV106 40 +ASV107 40 +ASV108 39 +ASV109 39 +ASV110 39 +ASV111 38 +ASV112 38 +ASV113 38 +ASV114 38 +ASV115 38 +ASV116 38 +ASV117 37 +ASV118 37 +ASV119 37 +ASV120 36 +ASV121 36 +ASV122 36 +ASV123 36 +ASV124 35 +ASV125 35 +ASV126 35 +ASV127 34 +ASV128 34 +ASV129 34 +ASV130 34 +ASV131 33 +ASV132 33 +ASV133 33 +ASV134 33 +ASV135 33 +ASV136 32 +ASV137 32 +ASV138 31 +ASV139 31 +ASV140 31 +ASV141 31 +ASV142 31 +ASV143 31 +ASV144 31 +ASV145 30 +ASV146 30 +ASV147 30 +ASV148 30 +ASV149 30 +ASV150 29 +ASV151 29 +ASV152 29 +ASV153 29 +ASV154 29 +ASV155 29 +ASV156 29 +ASV157 29 +ASV158 29 +ASV159 28 +ASV160 28 +ASV161 27 +ASV162 27 +ASV163 27 +ASV164 27 +ASV165 27 +ASV166 26 +ASV167 26 +ASV168 26 +ASV169 26 +ASV170 26 +ASV171 26 +ASV172 25 +ASV173 25 +ASV174 25 +ASV175 24 +ASV176 24 +ASV177 24 +ASV178 24 +ASV179 24 +ASV180 24 +ASV181 23 +ASV182 23 +ASV183 23 +ASV184 23 +ASV185 23 +ASV186 23 +ASV187 23 +ASV188 23 +ASV189 22 +ASV190 22 +ASV191 22 +ASV192 21 +ASV193 20 +ASV194 20 +ASV195 20 +ASV196 20 +ASV197 20 +ASV198 20 +ASV199 20 +ASV200 19 +ASV201 19 +ASV202 19 +ASV203 19 +ASV204 19 +ASV205 18 +ASV206 18 +ASV207 18 +ASV208 17 +ASV209 17 +ASV210 17 +ASV211 17 +ASV212 17 +ASV213 16 +ASV214 16 +ASV215 15 +ASV216 15 +ASV217 15 +ASV218 14 +ASV219 14 +ASV220 14 +ASV221 14 +ASV222 13 +ASV223 13 +ASV224 13 +ASV225 13 +ASV226 13 +ASV227 13 +ASV228 13 +ASV229 13 +ASV230 12 +ASV231 11 +ASV232 10 |
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| diff -r a3d31a68f291 -r 1d660ee0b1c8 test-data/mapping_paired.txt --- a/test-data/mapping_paired.txt Mon Nov 21 11:49:15 2022 +0000 +++ b/test-data/mapping_paired.txt Sat Dec 03 16:37:26 2022 +0000 |
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| @@ -1,2 +1,2 @@ #SampleID fastqFile SequencingRun -SMPL0 Anh_sample1.fastq.gz,Anh_sample2.fastq.gz a +SMPL0 Arabidopsis_R1.fastqsanger.gz,Arabidopsis_R2.fastqsanger.gz a |