Mercurial > repos > iuc > qiime_make_otu_table
changeset 0:e00b6983b175 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,7 @@ +QIIME 1.9.1 Galaxy Wrapper +-------------------------- + +Note: Many of these tools output html files that will not display properly +unless sanitization is turned off in Galaxy. This can be done globally via the +`santize_all_html` option in `galaxy.ini` or on a per tool basis using the +`santize_whitelist_file` in `galaxy.ini`.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_test_data.sh Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,50 @@ +#!/usr/bin/env bash + +# make_otu_table +make_otu_table.py \ + --otu_map_fp 'test-data/make_otu_table/otu_map.txt' \ + --taxonomy 'test-data/make_otu_table/tax_assignments.txt' \ + --exclude_otus_fp 'test-data/make_otu_table/chimeric_seqs.txt' \ + --mapping_fp 'test-data/make_otu_table/mapping_file.txt' \ + --output_biom_fp 'test-data/make_otu_table/OTU_table_chimeric.biom' +biom convert \ + -i 'test-data/make_otu_table/OTU_table_chimeric.biom' \ + -o 'test-data/make_otu_table/OTU_table_chimeric.biom' \ + --to-json + +make_otu_table.py \ + --otu_map_fp 'test-data/make_otu_table/otu_map.txt' \ + --taxonomy 'test-data/make_otu_table/tax_assignments.txt' \ + --exclude_otus_fp 'test-data/make_otu_table/pynast_failures.fna' \ + --mapping_fp 'test-data/make_otu_table/mapping_file.txt' \ + --output_biom_fp 'test-data/make_otu_table/OTU_table_pynast.biom' +biom convert \ + -i 'test-data/make_otu_table/OTU_table_pynast.biom' \ + -o 'test-data/make_otu_table/OTU_table_pynast.biom' \ + --to-json + +# collapse_samples +collapse_samples.py \ + --input_biom_fp 'test-data/collapse_samples/table.biom' \ + --mapping_fp 'test-data/collapse_samples/map.txt' \ + --collapse_mode 'sum' \ + --collapse_fields 'SampleType' \ + --output_biom_fp 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \ + --output_mapping_fp 'test-data/collapse_samples/collapsed_sum_SampleType_map.txt' +biom convert \ + -i 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \ + -o 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \ + --to-json + +collapse_samples.py \ + --input_biom_fp 'test-data/collapse_samples/table.biom' \ + --mapping_fp 'test-data/collapse_samples/map.txt' \ + --collapse_mode 'first' \ + --collapse_fields 'subject','year' \ + --normalize \ + --output_biom_fp 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \ + --output_mapping_fp 'test-data/collapse_samples/collapsed_first_2fields_map.txt' +biom convert \ + -i 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \ + -o 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \ + --to-json \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,70 @@ +<?xml version="1.0" ?> +<macros> + <token name="@WRAPPER_VERSION@">1.9.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@WRAPPER_VERSION@">qiime</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citation type="doi">10.1038/nmeth.f.303</citation> + </xml> + <xml name="pick_otus_reference_source"> + <conditional name="references"> + <param name="source_selector" type="select" label="Use reference sequences from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param argument="--refseqs_fp" label="Reference sequences" type="select"> + <options from_data_table="qiime_rep_set"/> + </param> + </when> + <when value="history"> + <param argument="--refseqs_fp" type="data" format="fasta" label="Reference sequences to search against"/> + </when> + </conditional> + </xml> + <xml name="assign_taxonomy_reference_source"> + <conditional name="references"> + <param name="source_selector" type="select" label="Select a reference sequence file from"> + <option value="cached">The local cache</option> + <option value="history">The active history</option> + </param> + <when value="cached"> + <param argument="--reference_seqs_fp" label="Reference sequences either used to generate a blast database (Blast) or used as training sequences for the selected classifier (RDP, Mothur)" type="select"> + <options from_data_table="qiime_rep_set"/> + </param> + </when> + <when value="history"> + <param argument="--reference_seqs_fp" type="data" format="fasta" label="Reference sequences to search against"/> + </when> + </conditional> + </xml> + <xml name="pick_otus_similarity"> + <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/> + </xml> + <xml name="pick_otus_denovo_otu_id_prefix"> + <param argument="--denovo_otu_id_prefix" type="text" value="denovo" label="OTU identifier prefix for the de novo OTU pickers"/> + </xml> + <xml name="pick_otus_enable_rev_strand_match"> + <param argument="--enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="Enable reverse strand matching?" help="Will double the amount of memory used"/> + </xml> + <xml name="pick_otus_suppress_presort_by_abundance_uclust"> + <param argument="--suppress_presort_by_abundance_uclust" type="boolean" truevalue="--suppress_presort_by_abundance_uclust" falsevalue="" checked="false" label="Suppress presorting of sequences by abundance?"/> + </xml> + <xml name="pick_otus_max"> + <param argument="--max_accepts" type="integer" value="1" label="Max_accepts value"/> + <param argument="--max_rejects" type="integer" value="8" label="Max_rejects value"/> + </xml> + <xml name="pick_otus_stepwords"> + <param argument="--stepwords" type="integer" value="8" label="Stepwords value"/> + </xml> + <xml name="pick_otus_word_length"> + <param argument="--word_length" type="integer" value="8" label="Word length value"/> + </xml> + <xml name="pick_otus_suppress_prefilter_exact_match"> + <param argument="--suppress_prefilter_exact_match" type="boolean" truevalue="--suppress_prefilter_exact_match" falsevalue="" checked="false" label="Don't collapse exact matches before calling?"/> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_otu_table.xml Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,66 @@ +<tool id="qiime_make_otu_table" name="Make OTU table" version="@WRAPPER_VERSION@.0"> + <description>Make an OTU table from an OTU map and a taxonomy assignment file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>make_otu_table.py --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + make_otu_table.py + --otu_map_fp '$otu_map_fp' + --output_biom_fp '$output_biom_fp' + #if $taxonomy + --taxonomy '$taxonomy' + #end if + #if $exclude_otus_fp + --exclude_otus_fp '$exclude_otus_fp' + #end if + #if $mapping_fp + --mapping_fp '$mapping_fp' + #end if + ]]></command> + <inputs> + <param argument="--otu_map_fp" type="data" format="tabular,txt,biom" label="OTU map" help="An OTU map file generated by the pick_otus.py script" /> + <param argument="--taxonomy" type="data" format="txt" optional="True" label="Taxonomy assignment" help="Text file generated by the assign_taxonomy.py script and contains the assignments of taxons to sequences" /> + <param argument="--exclude_otus_fp" type="data" format="tabular,fasta,txt" optional="True" label="List of OTU identifiers to reject" help="A text file listing OTU identifiers that should not be included in the OTU table (generated by the identify_chimeric_seqs.py script) or a failure file in fasta format (generated by the align_seqs.py script)" /> + <param argument="--mapping_fp" type="data" format="tabular,txt" optional="True" label="Validated mapping file" help="A mapping file in tabular format verified by the validate_mapping_file.py script" /> + </inputs> + <outputs> + <data name="output_biom_fp" format="biom1" label="${tool.name} on ${on_string}: OTU table (biom format)"/> + </outputs> + <tests> + <!-- Qiime make_otu_table.py generates a binary file that can't be compared directly with diff --> + <!-- In addition, the files generated by 2 different executions of make_otu_table with the same input data are different --> + <!-- As a consequence, standard comparisons based on "diff" or md5 checksums/SHA hash are impossible --> + <!-- The following tests are then based on a comparison of file sizes with a maximum delta of 0 bytes --> + <test> + <param name="otu_map_fp" value="make_otu_table/otu_map.txt" /> + <param name="taxonomy" value="make_otu_table/tax_assignments.txt" /> + <param name="exclude_otus_fp" value="make_otu_table/chimeric_seqs.txt" /> + <param name="mapping_fp" value="make_otu_table/mapping_file.txt" /> + <output name="output_biom_fp" file="make_otu_table/OTU_table_chimeric.biom" compare="sim_size" /> + </test> + <test> + <param name="otu_map_fp" value="make_otu_table/otu_map.txt" /> + <param name="taxonomy" value="make_otu_table/tax_assignments.txt" /> + <param name="exclude_otus_fp" value="make_otu_table/pynast_failures.fna" /> + <param name="mapping_fp" value="make_otu_table/mapping_file.txt" /> + <output name="output_biom_fp" file="make_otu_table/OTU_table_pynast.biom" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +The script `make_otu_table.py <http://qiime.org/scripts/make_otu_table.html>`_ tabulates the number of times an OTU is found in each +sample, and adds the taxonomic predictions for each OTU in the last column if a taxonomy file is supplied. + +The output of `make_otu_table.py <http://qiime.org/scripts/make_otu_table.html>`_ is a `biom file <http://biom-format.org/>`_, where the columns correspond to +Samples and rows correspond to OTUs and the number of times a sample appears in a particular OTU. + +More information about this tool is available on +`QIIME documentation <http://qiime.org/scripts/make_otu_table.html>`_. + ]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/collapse_samples/collapsed_first_2fields_map.txt Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,3 @@ +#SampleID original-sample-ids BarcodeSequence LinkerPrimerSequence SampleType month day replicate-group days_since_epoch Description +1.2008 (f1, f2, f5, f6, p1, not16S.1) (ACACTGTTCATG, ACCAGACGATGC, ACCAGACGATGC, ACCAGACGATGC, AACGCACGCTAG, ATACTATTGCGC) GTGCCAGCMGCCGCGGTAA (feces, feces, feces, feces, L_palm, Other) 10 (22, 23, 23, 23, 21, 22) (1, 1, 2, 2, 2, 3) (14174, 14175, 14175, 14175, 14173, 14174) (fecal1, fecal2, derived from f3 with some changes to sequences to add one new otu, derived from f4 with some changes to sequences to add one new otu, palm1, contains one randomly generated sequence, randomly generated sequence plus some variants, these should not map to 16S) +2.2008 (f3, f4, p2, t1, t2) (ACCAGACGATGC, ACCAGACGATGC, ACACTGTTCATG, AGTGAGAGAAGC, ATACTATTGCGC) GTGCCAGCMGCCGCGGTAA (feces, feces, L_palm, Tongue, Tongue) 10 (23, 23, 22, 21, 22) (1, 1, 2, 2, 2) (14175, 14175, 14174, 14173, 14174) (identical sequences to fecal2, all sequences identical, map to GG 295053 at 97 percent id, palm2, tongue1, contains one randomly generated sequence, tongue2) \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/collapse_samples/collapsed_first_2fields_table.biom Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,1 @@ +{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-05-19T14:27:09.894251","type": "OTU table","matrix_element_type": "float","shape": [14, 2],"data": [[0,0,0.81818181818181823],[0,1,0.90909090909090906],[2,1,0.045454545454545456],[13,0,0.18181818181818182],[13,1,0.045454545454545456]],"rows": [{"id": "295053", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "42684", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria"]}},{"id": "None11", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None10", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None7", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None6", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None5", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None4", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None3", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None2", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None1", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "879972", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None9", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None8", "metadata": {"taxonomy": ["k__Bacteria"]}}],"columns": [{"id": "2.2008", "metadata": {"collapsed_ids": ["f3", "f4", "p2", "t1", "t2"]}},{"id": "1.2008", "metadata": {"collapsed_ids": ["f2", "f1", "p1", "not16S.1"]}}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/collapse_samples/collapsed_sum_SampleType_map.txt Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,5 @@ +#SampleID original-sample-ids BarcodeSequence LinkerPrimerSequence year month day subject replicate-group days_since_epoch Description +L_palm (p1, p2) (AACGCACGCTAG, ACACTGTTCATG) GTGCCAGCMGCCGCGGTAA 2008 10 (21, 22) (1, 2) 2 (14173, 14174) (palm1, contains one randomly generated sequence, palm2) +Other not16S.1 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA 2008 10 22 1 3 14174 randomly generated sequence plus some variants, these should not map to 16S +Tongue (t1, t2) (AGTGAGAGAAGC, ATACTATTGCGC) GTGCCAGCMGCCGCGGTAA 2008 10 (21, 22) 2 2 (14173, 14174) (tongue1, contains one randomly generated sequence, tongue2) +feces (f1, f2, f3, f4, f5, f6) (ACACTGTTCATG, ACCAGACGATGC, ACCAGACGATGC, ACCAGACGATGC, ACCAGACGATGC, ACCAGACGATGC) GTGCCAGCMGCCGCGGTAA 2008 10 (22, 23, 23, 23, 23, 23) (1, 1, 2, 2, 1, 1) (1, 1, 1, 1, 2, 2) (14174, 14175, 14175, 14175, 14175, 14175) (fecal1, fecal2, identical sequences to fecal2, all sequences identical, map to GG 295053 at 97 percent id, derived from f3 with some changes to sequences to add one new otu, derived from f4 with some changes to sequences to add one new otu) \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/collapse_samples/collapsed_sum_SampleType_table.biom Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,1 @@ +{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-05-19T14:27:05.204426","type": "OTU table","matrix_element_type": "float","shape": [14, 4],"data": [[0,1,78.0],[0,3,4.0],[1,3,1.0],[2,1,1.0],[2,3,2.0],[3,0,1.0],[4,3,1.0],[5,2,20.0],[6,3,1.0],[7,3,2.0],[8,0,5.0],[8,3,1.0],[9,2,2.0],[10,3,1.0],[11,0,5.0],[11,3,29.0],[12,0,34.0],[12,3,3.0],[13,1,9.0]],"rows": [{"id": "295053", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "42684", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria"]}},{"id": "None11", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None10", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None7", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None6", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None5", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None4", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None3", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None2", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None1", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "879972", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None9", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None8", "metadata": {"taxonomy": ["k__Bacteria"]}}],"columns": [{"id": "Tongue", "metadata": {"collapsed_ids": ["t1", "t2"]}},{"id": "feces", "metadata": {"collapsed_ids": ["f2", "f1", "f3", "f4"]}},{"id": "Other", "metadata": {"collapsed_ids": ["not16S.1"]}},{"id": "L_palm", "metadata": {"collapsed_ids": ["p2", "p1"]}}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/collapse_samples/map.txt Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,12 @@ +#SampleID BarcodeSequence LinkerPrimerSequence SampleType year month day subject replicate-group days_since_epoch Description +f1 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA feces 2008 10 22 1 1 14174 fecal1 +f2 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 1 14175 fecal2 +f3 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 2 1 14175 identical sequences to fecal2 +f4 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 2 1 14175 all sequences identical, map to GG 295053 at 97 percent id +f5 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 2 14175 derived from f3 with some changes to sequences to add one new otu +f6 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 2 14175 derived from f4 with some changes to sequences to add one new otu +p1 AACGCACGCTAG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 21 1 2 14173 palm1, contains one randomly generated sequence +p2 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 22 2 2 14174 palm2 +t1 AGTGAGAGAAGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 21 2 2 14173 tongue1, contains one randomly generated sequence +t2 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 22 2 2 14174 tongue2 +not16S.1 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Other 2008 10 22 1 3 14174 randomly generated sequence plus some variants, these should not map to 16S \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/collapse_samples/table.biom Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "QIIME 1.6.0-dev","date": "2013-02-09T09:30:11.550590","matrix_type": "sparse","matrix_element_type": "int","shape": [14, 9],"data": [[0,0,20],[0,1,18],[0,2,18],[0,3,22],[0,4,4],[1,4,1],[2,0,1],[2,4,1],[2,5,1],[3,6,1],[4,4,1],[5,7,20],[6,4,1],[7,4,1],[7,5,1],[8,4,1],[8,6,2],[8,8,3],[9,7,2],[10,5,1],[11,4,9],[11,5,20],[11,6,1],[11,8,4],[12,4,3],[12,6,19],[12,8,15],[13,0,1],[13,1,4],[13,2,4]],"rows": [{"id": "295053", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "42684", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria"]}},{"id": "None11", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None10", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None7", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None6", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None5", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None4", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None3", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None2", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None1", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "879972", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None9", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None8", "metadata": {"taxonomy": ["k__Bacteria"]}}],"columns": [{"id": "f2", "metadata": null},{"id": "f1", "metadata": null},{"id": "f3", "metadata": null},{"id": "f4", "metadata": null},{"id": "p2", "metadata": null},{"id": "p1", "metadata": null},{"id": "t1", "metadata": null},{"id": "not16S.1", "metadata": null},{"id": "t2", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/make_otu_table/OTU_table_chimeric.biom Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,1 @@ +{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-05-19T14:25:37.660678","type": "OTU table","matrix_element_type": "float","shape": [2, 2],"data": [[0,0,1.0],[1,1,3.0]],"rows": [{"id": "1", "metadata": {"taxonomy": ["A", "B", "C", "D"]}},{"id": "x", "metadata": {"taxonomy": ["A", "B", "C"]}}],"columns": [{"id": "ABC", "metadata": {"LinkerPrimerSequence": "AAAAAA", "BarcodeSequence": "ATGC", "Description": "First Sample"}},{"id": "GHI", "metadata": {"LinkerPrimerSequence": "AAAAAA", "BarcodeSequence": "CATG", "Description": "Third Sample"}}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/make_otu_table/OTU_table_pynast.biom Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,1 @@ +{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-05-19T14:26:19.586158","type": "OTU table","matrix_element_type": "float","shape": [2, 2],"data": [[0,0,1.0],[1,1,3.0]],"rows": [{"id": "1", "metadata": {"taxonomy": ["A", "B", "C", "D"]}},{"id": "x", "metadata": {"taxonomy": ["A", "B", "C"]}}],"columns": [{"id": "ABC", "metadata": {"LinkerPrimerSequence": "AAAAAA", "BarcodeSequence": "ATGC", "Description": "First Sample"}},{"id": "GHI", "metadata": {"LinkerPrimerSequence": "AAAAAA", "BarcodeSequence": "CATG", "Description": "Third Sample"}}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/make_otu_table/chimeric_seqs.txt Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,3 @@ +0 some comment +42 not a real otu id +z \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/make_otu_table/mapping_file.txt Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,5 @@ +#SampleID BarcodeSequence LinkerPrimerSequence Description +ABC ATGC AAAAAA First Sample +XYZ TGCA AAAAAA Fourth Sample +GHI CATG AAAAAA Third Sample +DEF GCAT AAAAAA Second Sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/make_otu_table/otu_map.txt Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,4 @@ +0 ABC_0 DEF_1 +1 ABC_1 +x GHI_2 GHI_3 GHI_77 +z DEF_3 XYZ_1 \ No newline at end of file