| Next changeset 1:85da3173a488 (2021-05-19) |
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Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit d05728af3d4d2ffd49548a320e8e8b4c6cc2f5e7" |
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added:
lotus2.xml test-data/Anh_sample1.fastq.gz test-data/Anh_sample2.fastq.gz test-data/OTU.fna test-data/OTU.txt test-data/hiera_RDP.txt |
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| diff -r 000000000000 -r 478e767a0e7a lotus2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lotus2.xml Thu May 13 17:38:45 2021 +0000 |
| [ |
| b'@@ -0,0 +1,202 @@\n+<tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01">\n+ <description>fast OTU processing pipeline</description>\n+ <macros>\n+ <token name="@VERSION@">2.04</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">lotus2</requirement>\n+ </requirements>\n+ <version_command>lotus2 --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+mkdir input\n+&&\n+#if $inputs.paired_or_single == \'single\':\n+ #for i, f in enumerate($inputs.input):\n+ #set ext = $f.ext.replace(\'sanger\', \'\')\n+ ln -s \'$f\' \'input/input${i}.${ext}\' &&\n+ #end for\n+#elif $inputs.paired_or_single == \'paired\':\n+ #for i, f in enumerate($inputs.left_input):\n+ #set ext = $f.ext.replace(\'sanger\', \'\')\n+ ln -s \'$f\' \'input/input${i}.1.${ext}\' &&\n+ #end for\n+ #for i, f in enumerate($inputs.right_input):\n+ #set ext = $f.ext.replace(\'sanger\', \'\')\n+ ln -s \'$f\' \'input/input${i}.2.${ext}\' &&\n+ #end for\n+#else:\n+ #for i, f in enumerate($inputs.pair_input):\n+ #set ext = $f.forward.ext.replace(\'sanger\', \'\')\n+ ln -s \'$f.forward\' \'input/input${i}.1.${ext}\' &&\n+ #set ext = $f.reverse.ext.replace(\'sanger\', \'\')\n+ ln -s \'$f.reverse\' \'input/input${i}.2.${ext}\' &&\n+ #end for\n+#end if\n+\n+lotus2 -create_map mapping.txt -i input/ &&\n+cat mapping.txt &&\n+\n+lotus2\n+-i input/\n+-o output\n+-tmpDir tmp_folder\n+-threads "\\${GALAXY_SLOTS:-1}"\n+-map mapping.txt\n+-platform $platform\n+#if $barcode:\n+ -barcode \'$barcode\'\n+#end if\n+#if $forwardPrimer:\n+ -forwardPrimer \'$forwardPrimer\'\n+#end if\n+#if $reversePrimer:\n+ -reversePrimer \'$reversePrimer\'\n+#end if\n+\n+-clustering $clu_args.clustering\n+-id $clu_args.id\n+-derepMin $clu_args.derepMin\n+-chim_skew $clu_args.chim_skew\n+-deactivateChimeraCheck $clu_args.deactivateChimeraCheck\n+-readOverlap $clu_args.readOverlap\n+\n+-refDB $tax_args.refDB\n+-amplicon_type $tax_args.amplicon_type\n+-tax_group $tax_args.tax_group\n+-rdp_thr $tax_args.rdp_thr\n+-utax_thr $tax_args.utax_thr\n+-keepUnclassified $tax_args.keepUnclassified\n+-taxAligner $tax_args.taxAligner\n+-useBestBlastHitOnly $tax_args.useBestBlastHitOnly\n+-LCA_cover $tax_args.LCA_cover\n+-LCA_frac $tax_args.LCA_frac\n+-greengenesSpecies $tax_args.greengenesSpecies\n+-pseudoRefOTUcalling $tax_args.pseudoRefOTUcalling\n+\n+&&\n+\n+cd output/ &&\n+tar -cvzf higherLvl.tar.gz higherLvl/ &&\n+tar -cvzf ExtraFiles.tar.gz ExtraFiles/ &&\n+tar -cvzf LotuSLogS.tar.gz LotuSLogS/ &&\n+tar -cvzf primary.tar.gz primary/\n+ ]]></command>\n+\n+ <inputs>\n+ <conditional name="inputs">\n+ <param name="paired_or_single" type="select" label="Paired or Single-end data?">\n+ <option value="single" selected="true">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ <option value="paired_collection">Paired-end collection</option>\n+ </param>\n+ <when value="single">\n+ <param name="input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" />\n+ </when>\n+ <when value="paired">\n+ <param name="left_input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />\n+ <param name="right_input" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" />\n+ </when>\n+ <when value="paired_collection">\n+ <param name="pair_input" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="List of paired reads" />\n+ </when>\n+ </conditional>\n+ <param argument="-platform" type="select" label="Sequencing platform">\n+ <option value="miSeq" selected="true">miSeq</option>\n+ <option value="hiSeq">hiSeq</option>\n+ <option value="454">454</option>\n+ '..b' <param argument="-taxAligner" type="select" label="Taxonomy aligner">\n+ <option value="0" selected="true">Deactivated (just use RDP)</option>\n+ <option value="1">Blast</option>\n+ <option value="2">Use LAMBDA to search against a 16S reference database for taxonomic profiling of OTUs</option>\n+ <option value="3">Use UTAX with custom databases</option>\n+ <option value="4">Use VSEARCH to align OTUs to custom databases</option>\n+ <option value="5">Use USEARCH to align OTUs to custom databases</option>\n+ </param>\n+ <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use best blast hit only" help="If selected, do not use LCA (lowest common ancestor) to determine most likely taxonomic level (not recommended)" />\n+ <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>\n+ <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/>\n+ <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />\n+ <param argument="-pseudoRefOTUcalling" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create Reference based (open) OTUs" />\n+ </section>\n+ </inputs>\n+\n+ <outputs>\n+ <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />\n+ <data name="otu_biom" format="biom" label="${tool.name} on ${on_string}: biom-formatted OTU abundance matrix" from_work_dir="output/OTU.biom" />\n+ <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />\n+ <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />\n+ <data name="hiera_blast" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on Blastn" from_work_dir="output/hiera_BLAST.txt" />\n+ <data name="hiera_rdp" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on RDP classifier" from_work_dir="output/hiera_RDP.txt" />\n+ <data name="primary" format="tar" label="${tool.name} on ${on_string}: Copies of sdm options and mapping file" from_work_dir="output/primary.tar.gz" />\n+ <data name="higherlvl" format="tar" label="${tool.name} on ${on_string}: Abundance matrices" from_work_dir="output/higherLvl.tar.gz" />\n+ <data name="lotuslogs" format="tar" label="${tool.name} on ${on_string}: Log files" from_work_dir="output/LotuSLogS.tar.gz" />\n+ <data name="extrafiles" format="tar" label="${tool.name} on ${on_string}: Extra files" from_work_dir="output/ExtraFiles.tar.gz" />\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="paired_or_single" value="single"/>\n+ <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="platform" value="454" />\n+ <output name="otu" file="OTU.txt" compare="sim_size" />\n+ <output name="otu_fna" file="OTU.fna" compare="sim_size" />\n+ <output name="hiera_rdp" file="hiera_RDP.txt" compare="sim_size" />\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool.\n+\n+Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1186/2049-2618-2-30</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 478e767a0e7a test-data/Anh_sample1.fastq.gz |
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| Binary file test-data/Anh_sample1.fastq.gz has changed |
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| diff -r 000000000000 -r 478e767a0e7a test-data/Anh_sample2.fastq.gz |
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| Binary file test-data/Anh_sample2.fastq.gz has changed |
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| diff -r 000000000000 -r 478e767a0e7a test-data/OTU.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OTU.fna Thu May 13 17:38:45 2021 +0000 |
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| b'@@ -0,0 +1,374 @@\n+>OTU1\n+TACAGATCGTCCGTCAATTCCTTTAAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGATTACTTAATGCGTTTGCGCCGGCACCGAAGGACCTTGGTCCCCCAACACCTAGTAATCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCTTACCTCTCCTGCACTCTAGCTGCACAGTTTCCAAAGCAGTTCCATTGTTAAGCCATGGGATTTCACTCCAGACTTGCGCTGCCGTCTACGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGGGCTTCTTAGTCAGGTACCGTCATTTTCTTCCCTGCTGATAGAGCTTTACGTACCGAAATACTTCTTCACTCACGCGGCGTCGCTGCATCAGGGTTTCCCCCATTGTGCAATAT\n+>OTU2\n+TCTACGTAGCCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGATCACTTAACGCTTTCGCTGTGCCGCTTACTGTGTATCGCAAACAGCTAGTGATCATCGTTTACTGCGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGTGCATCAGCGTCAGTCATGGCTTGGCAGGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTAAGCATTTCACCGCTACACCACGCATTCCGCCTGCCTCAAACATACTCAAGCCTCCCAGTTTCAACGGCAATTCTATGGTTGAGCCACAGACTTTCACCGCTGACTTAAAAGGCCGCCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGGATCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGATCCTTATTCATAAGGTACATACAAAACGGGACACGTCCCGCACTTTATTCCCTTATAAAAGAGGTTTACGATCCATAGAACCTTCATCCCTCACGCGACTGT\n+>OTU3\n+AGTACGCTATCCGTCAATTCATTTAAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATACTTAACGCTTTCGCTGTACCACCCAGACCTCAATCGGCCCGGACAGTTAGTATTCATCGTTTACTGCGTGGACTACCAGGGTATCTAATCCTGTTCGATACCCACGCTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAACGCCAGTTTCAACGGCACGACGGGGTTGAGCCCCGAAATTTTACCGCTGACTTGACATTCCGCCTGCGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGATGCTTTTTCTTCAGGTACTCGCAAAACGCCACACGTGGCGCCCTTTGCTCCCTGACAAAAGAGGTTTACAATCCATAGGACCGTCATCCCTCACGCGACTTGGC\n+>OTU4\n+TACACACACTCCGTCAATTCATTTAAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCAGCACTGAGAGGCGGAAACCTCCCAACACTTAGCACTCATCGTTTACGGCATGGACTACCAGGGTATCTAATCCTGTTCGCTACCCATGCTTTCGAGCCTCAGCGTCAGTTGCAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCTTCCATATATCTACGCATTCCACCGCTACACATGGGAGTTCCACTCTCCTCTTCTGCACTCAAGTTCAACAGTTTCTGATGCAATTCTCCGGTTGAGCCGAAGGCTTTCACATCAGACTTATTGAACCGCCTGCACTCGCTTTACGCCCAATAAATCCGGACAACGCTTGCCACCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGTGACTTTCTAGGTAATTACCGTCAAATAAAGGCCAGTTACTACCTCTATCTTTCTTCACTACCAACAGAGCTTTACGAGCCGAAA\n+>OTU5\n+CGAGAGATACCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATACTTAACGCTTTCGCTTGGCCGCTTGCTGTATATCGCAAACAGCGAGTATTCATCGTTTACCGTGTGGACTACCAGGGTATCTAATCCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTCAACTGCACTCAAGATATCCAGTATCAACTGCAATTTTACGGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCCATCTACGCTCCCTTTAAACCCGATAAATCCGGATAACGCTCGGATCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATGCATACCCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTA\n+>OTU6\n+TCTCTATGCGCCGTCAATTCCTTTGAGTTTCACCGTTACCGGCGTACTCCCCAGGTGGGATGCTTAACGCTTTCGCTTGGCCGCCGACTGTATATCGCCGACAGCGGGCATCCATCGTTTACCGCGCGGACTACCAGGGTATCTAATCCTGTTCGATACCCGCGCTTTCGAGCTTCAGCGTCAGTAACGCTGCGGCAGGCTGCCTTCGCAATCGGGGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTTCCGCGCACTCAAGGTCTCCAGTTCGCGCCGCACTCTCATGGTTGAGCCACAAAATTTCACGGCACGCTTAAAGACCGGCCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCCCGGACCTTCCGTATTACCGCGGCTGCTGGCACGGAATTAGCCGGTCCTTATTCATGCGGTACCTGCAAACATCCACACGTGGACGCCTTTATCCCCGCATAAAAGAGGTTTACAACCCATAGGGCAGTCTTCCCTCACGCTACTTGGCTGGTTCAGCCT\n+>OTU7\n+TACAGATCGTCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGATTACTTAATGCGTTTGCGCCGGCACCGAAGGACCTTGGTCCCCCAACACCTAGTAATCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCTTACCTCTCCTGCACTCTAGCTGCACAGTTTCCAAAGCAGTTCCATGGTTAAGCCATGGGATTTCACTCCAGACTTGCGCTGCCGTCTACGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGGGCTTCTTAGTCAGGTACCGTCCAAAGTCCAAAGGACTTTATTTCTTCCCTGCTGATAGAGCTTTACATACCGAAATACTTCTTCACTCACGCGGCGTCGCTGCATCAGGGTTCC\n+>OTU8\n+ACTACTATGTCCGTCAATTCCTTTAAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTATCGCTTTCGCTTCGCCACCCAGGGGTCAATCCCCCCGGACAGCCAGCATTCATCGTTTACTGCGTGGACTACCAGGGTA'..b'TCTTCTTCCCTGCTGACAGAGCTTTACGTGCCGAAACACTTCTTCACTCACGCGGCGTCGCTGCATCAGGGTTTCCCCCATTGTGCAATATCT\n+>OTU181\n+ACGCGAGTATCCGTCAATTCCTTTAAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGATCACTTACTGCGTTTGCTGCGGCACCGATGGGTCCATACCCACCGACACCTAGTGATCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCACTTACCTCTCCTGCACTCCAGCCATACAGTTTCCAAAGCAATTCCCAGGTTGAGCCCGGGGCTTTCACTTCAGACTTGCCATACCGTCTACGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGGGCTTCTTACTCAGGTACCGTCTTTCTTCTTCCCTGCTGATAGAGCTTTACATACCGAAATACTTCTTCACTCACGCGGCGTCGCTGCATCAGGGTTCCCCCCATTGTGCAATA\n+>OTU182\n+CGTCTAGTACCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGGATACTTACTGCGTTTGCGGCGGCACCGATGGGCTTTGCCCACCGACACCTAGTATCCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTCACTGTCCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCACTTACCTCTCCAGCACTCTAGCCCACCAGTTTCCAGAGCAGTCCCGGGGTTGGGCCCCGGGCTTTCACTCCAGACTTGATCGGCCGTCTACGCTCCCTTTACACCCAGTGAATCCGGATAACGCTCGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGGGCTTCTTGGTCAGGTACCGTCTTTGTTCTTCCCTGCTGATAGAGCTTTACATACCGGAGTACTCCTTCACTCACGCGGCGTCGCTGCATCACGGGTTCCCCCCATTGTGCAATACTCCCCCA\n+>OTU183\n+CGTCTAGTATCCGTCATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGAATACTTATTGCGTTTGCTGCGGCACCAAAGAGCTTTGCTCCCTGACACCTAGTATTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCTTACCTCTCCTGCACTCTAGTCATACAGTTTCAAAAGCAGTCCCGCAGTTGAGCCGCGGGCTTTCACTTCTGACTTGCATCACCGTCTACGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGGGCTTCTTAGTCAGGTACCGTCATTTTCTTCCCTGCTGATAGAGCTTACGACGACCGAAATACTTCTTCACTCACGCGGCGTCGCTGCATCAGGGTTTCCCCCATT\n+>OTU184\n+AGCGTCGTCTCCGTCAATTCCTTTAAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGAATACTTACTGCGTTTGCTGCGGCACCGGGGAGCTTTGCTCCCCGACACCTAGTATTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGTGTCAGTTACAGTCCAGCAGGCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTACGCATTTCACCGCTACACCAGGAATTCCGCCTGCCCCTCCTGCACTCCAGCCAGACAGTTCCAAAAGCAATCCGCGGGGTTAAGCCCCGGGTTTTCACTTCTGGCTTGCCTTGCCACCTGCGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGGGCTTCTTAGTCAGGTACTGTCATCTTCTTCCCTGCTGATAGGGCTTTACATACCGAAATACTTCCTCACCCACGCGGCGTCGCTGCATCAGGGTTTCCCCCATTGTGCAATATCCCCCA\n+>OTU185\n+AGACTATACTCCGTCAATTCCTTTAAGTTTCAACCTTGCGGTCGTACTCCCCAGGTGGATAACTTATCGCTTTCGCTGGGTTACCGACTGTCTATCGCCGACAACTAGTTATCATCGTTTACTGCGTGGACTACCAGGGTATCTAATCCTGTTCGATACCCACGCTTTCGTGCATCAGTGTCAGAACAGGCCTAGCAAGCTGCCTTCGCAATCGGTGTTCTGTGTAATATCTATGCATTTCACCGCTACACTACACATTCCGCCTGCTGCTACCTGTCTCAAGTCATACAGTATTAGCGGCAGCCCCGATGTTGAGCATCGGTATTTCACCGCTAACTTATACCACAACCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGGATCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGATCCTTATTCGTACCGTACTTTCAAAATCCTATCTCGTAGAACCCTTTACCCGGTACAAAAGCAGTTTACAACTCGTAGAGCCGTCTTCCTGCACGCGGCATGG\n+>OTU186\n+ATATCGCGAGCCGTCAATTCCTTTAAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGATCACTTAATGCGTTTGCTGCGGCACCGGTGGGCCCATACCCACCGACACCTAGTGATCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCACTTACCTCTCCTGCACTCTAGCACCACAGTTCCAAAAGCATGTACAGGGTTGAGCCCTGCCCTTTCACTTCTGGCTTGCCTTGCCGTCTACGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGGGCTTCTTAGTCAGGTACCGTTCTTTTTTCGTCCCTGCTGATAGAGCTTTACATACCGAAATACTTCCTCGCTCACGCGGCGTCGCTGCATCACGGGTTTCCCCCATTGTG\n+>OTU187\n+AGCACTGTAGCCGTCAATTCATTTAAGTTTCAGCCTTGCGACCGTACTCCCCAGGCGGGATGCTTAACGCGTTAACTACGGCGCCGAGGAATACTCCCCAACACCTAGCATCCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAATACCGGTCCAGGTGGCCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGGATTTCACTCCTACACCTGGAATTCCGCCACCCTCTCCCGGATTCTAGTCAAGCAGTATCAAAGGCAGTTCCACGGTTAAGCCGTGGGCTTTCACCTCTGACTTACAAAACAGCCTACGTGCGCTTTACGCCCAGTGATTCCGATTAACGCTCGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTCCTTTGGAGGTACCGTCAATATACGGCTGATTAGCACCGTATAACTTCTTCCCTCCTGACAGAGGTTTACGATCCGAAGACCTTCATCCCTCACGCGGCGTCGCTGACGTCA\n' |
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| diff -r 000000000000 -r 478e767a0e7a test-data/OTU.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OTU.txt Thu May 13 17:38:45 2021 +0000 |
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| @@ -0,0 +1,188 @@ +OTU SMPL1 SMPL0 +OTU1 24 39 +OTU2 26 15 +OTU3 12 18 +OTU4 12 17 +OTU5 15 12 +OTU6 6 19 +OTU7 14 9 +OTU8 4 19 +OTU9 11 8 +OTU10 8 9 +OTU11 7 9 +OTU12 15 1 +OTU13 7 8 +OTU14 10 5 +OTU15 5 10 +OTU16 10 4 +OTU17 8 6 +OTU18 10 4 +OTU19 6 7 +OTU20 5 7 +OTU21 3 9 +OTU22 6 5 +OTU23 9 1 +OTU24 7 3 +OTU25 2 8 +OTU26 7 2 +OTU27 3 5 +OTU28 4 4 +OTU29 3 5 +OTU30 4 4 +OTU31 3 4 +OTU32 4 3 +OTU33 0 7 +OTU34 7 0 +OTU35 3 4 +OTU36 5 1 +OTU37 5 1 +OTU38 2 4 +OTU39 4 2 +OTU40 2 4 +OTU41 3 3 +OTU42 3 3 +OTU43 5 1 +OTU44 2 4 +OTU45 2 4 +OTU46 2 4 +OTU47 5 1 +OTU48 2 4 +OTU49 2 3 +OTU50 3 2 +OTU51 3 2 +OTU52 5 0 +OTU53 3 2 +OTU54 3 2 +OTU55 5 0 +OTU56 4 1 +OTU57 3 2 +OTU58 3 2 +OTU59 1 3 +OTU60 2 2 +OTU61 3 1 +OTU62 3 1 +OTU63 2 2 +OTU64 1 3 +OTU65 2 2 +OTU66 1 3 +OTU67 2 2 +OTU68 2 2 +OTU69 2 2 +OTU70 4 0 +OTU71 4 0 +OTU72 1 3 +OTU73 2 2 +OTU74 1 3 +OTU75 0 4 +OTU76 2 1 +OTU77 1 2 +OTU78 0 3 +OTU79 3 0 +OTU80 1 2 +OTU81 0 3 +OTU82 0 3 +OTU83 2 1 +OTU84 1 2 +OTU85 3 0 +OTU86 3 0 +OTU87 0 3 +OTU88 1 2 +OTU89 1 2 +OTU90 2 1 +OTU91 1 1 +OTU92 0 2 +OTU93 1 1 +OTU94 1 1 +OTU95 1 1 +OTU96 0 2 +OTU97 2 0 +OTU98 2 0 +OTU99 0 2 +OTU100 1 1 +OTU101 1 1 +OTU102 1 1 +OTU103 1 1 +OTU104 1 1 +OTU105 2 0 +OTU106 0 2 +OTU107 1 1 +OTU108 1 1 +OTU109 1 1 +OTU110 1 1 +OTU111 0 2 +OTU112 2 0 +OTU113 2 0 +OTU114 0 2 +OTU115 1 1 +OTU116 2 0 +OTU117 0 2 +OTU118 2 0 +OTU119 0 2 +OTU120 2 0 +OTU121 2 0 +OTU122 1 1 +OTU123 1 1 +OTU124 1 0 +OTU125 0 1 +OTU126 1 0 +OTU127 1 0 +OTU128 1 0 +OTU129 0 1 +OTU130 0 1 +OTU131 1 0 +OTU132 1 0 +OTU133 1 0 +OTU134 0 1 +OTU135 0 1 +OTU136 1 0 +OTU137 0 1 +OTU138 0 1 +OTU139 0 1 +OTU140 0 1 +OTU141 1 0 +OTU142 0 1 +OTU143 0 1 +OTU144 0 1 +OTU145 0 1 +OTU146 0 1 +OTU147 0 1 +OTU148 1 0 +OTU149 1 0 +OTU150 0 1 +OTU151 0 1 +OTU152 1 0 +OTU153 0 1 +OTU154 0 1 +OTU155 1 0 +OTU156 1 0 +OTU157 0 1 +OTU158 1 0 +OTU159 0 1 +OTU160 1 0 +OTU161 1 0 +OTU162 1 0 +OTU163 0 1 +OTU164 1 0 +OTU165 0 1 +OTU166 0 1 +OTU167 1 0 +OTU168 1 0 +OTU169 1 0 +OTU170 0 1 +OTU171 1 0 +OTU172 0 1 +OTU173 1 0 +OTU174 1 0 +OTU175 1 0 +OTU176 1 0 +OTU177 1 0 +OTU178 1 0 +OTU179 0 1 +OTU180 1 0 +OTU181 0 1 +OTU182 0 1 +OTU183 1 0 +OTU184 0 1 +OTU185 0 1 +OTU186 0 1 +OTU187 0 1 |
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| diff -r 000000000000 -r 478e767a0e7a test-data/hiera_RDP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hiera_RDP.txt Thu May 13 17:38:45 2021 +0000 |
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| b'@@ -0,0 +1,188 @@\n+domain\tphylum\tclass\torder\tfamily\tgenus\tspecies\tOTU\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU1\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tPorphyromonadaceae\tParabacteroides\t?\tOTU2\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\tDuncaniella\t?\tOTU3\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLactobacillus\t?\tOTU4\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tBacteroidaceae\tPhocaeicola\t?\tOTU5\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tPrevotellaceae\t?\t?\tOTU6\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU7\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU8\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU9\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU10\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\tParamuribaculum\t?\tOTU11\n+Bacteria\tCampilobacterota\tCampylobacteria\tCampylobacterales\tHelicobacteraceae\tHelicobacter\t?\tOTU12\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU13\n+Bacteria\t?\t?\t?\t?\t?\t?\tOTU14\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU15\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\t?\tOTU16\n+Bacteria\tVerrucomicrobia\tVerrucomicrobiae\tVerrucomicrobiales\tAkkermansiaceae\tAkkermansia\t?\tOTU17\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tAcetatifactor\t?\tOTU18\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\t?\t?\tOTU19\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU20\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\t?\t?\tOTU21\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tLachnospira\t?\tOTU22\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU23\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tRikenellaceae\tAlistipes\t?\tOTU24\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\t?\t?\tOTU25\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU26\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU27\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\tMuribaculum\t?\tOTU28\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU29\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\tDuncaniella\t?\tOTU30\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU31\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tOscillibacter\t?\tOTU32\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU33\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU34\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tEnterocloster\t?\tOTU35\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU36\n+Bacteria\tProteobacteria\tDeltaproteobacteria\tDesulfovibrionales\tDesulfovibrionaceae\tMailhella\t?\tOTU37\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU38\n+Bacteria\tProteobacteria\tAlphaproteobacteria\t?\t?\t?\t?\tOTU39\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU40\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU41\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLimosilactobacillus\t?\tOTU42\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\t?\tOTU43\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU44\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU45\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tRikenellaceae\tAlistipes\t?\tOTU46\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU47\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tDysosmobacter\t?\tOTU48\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU49\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\tDuncaniella\t?\tOTU50\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospirace'..b'icutes\tClostridia\tClostridiales\tLachnospiraceae\tAcetatifactor\t?\tOTU134\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU135\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\t?\t?\tOTU136\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tAnaerotruncus\t?\tOTU137\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU138\n+Bacteria\tProteobacteria\tGammaproteobacteria\tXanthomonadales\tXanthomonadaceae\tStenotrophomonas\t?\tOTU139\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\t?\t?\tOTU140\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU141\n+Bacteria\tProteobacteria\tGammaproteobacteria\tEnterobacterales\tMorganellaceae\tProteus\t?\tOTU142\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\t?\t?\t?\tOTU143\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU144\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU145\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU146\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU147\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU148\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\t?\t?\tOTU149\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tAcutalibacter\t?\tOTU150\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU151\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU152\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\t?\t?\tOTU153\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\t?\t?\t?\tOTU154\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\t?\t?\t?\tOTU155\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU156\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU157\n+Bacteria\tProteobacteria\tDeltaproteobacteria\tDesulfovibrionales\t?\t?\t?\tOTU158\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU159\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU160\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU161\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\t?\t?\t?\tOTU162\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU163\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU164\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\t?\t?\t?\tOTU165\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU166\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tOdoribacteraceae\tOdoribacter\t?\tOTU167\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU168\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU169\n+Bacteria\tProteobacteria\tBetaproteobacteria\tBurkholderiales\tComamonadaceae\tOttowia\t?\tOTU170\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU171\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\tParamuribaculum\t?\tOTU172\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\tDuncaniella\t?\tOTU173\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tPorphyromonadaceae\tParabacteroides\t?\tOTU174\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\t?\t?\t?\tOTU175\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tMuribaculaceae\t?\t?\tOTU176\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU177\n+Bacteria\tBacteroidetes\t?\t?\t?\t?\t?\tOTU178\n+?\t?\t?\t?\t?\t?\t?\tOTU179\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU180\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU181\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU182\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU183\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU184\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tRikenellaceae\t?\t?\tOTU185\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\t?\t?\tOTU186\n+Bacteria\tProteobacteria\tDeltaproteobacteria\tDesulfovibrionales\tDesulfovibrionaceae\t?\t?\tOTU187\n' 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