Mercurial > repos > iuc > qiime_collapse_samples
changeset 0:242462fc608b 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 16:38:55 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/collapse_samples.xml Mon Jul 10 16:38:55 2017 -0400 @@ -0,0 +1,90 @@ +<tool id="qiime_collapse_samples" name="Collapse samples" version="@WRAPPER_VERSION@.0"> + <description>Collapse samples in a BIOM table and mapping file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>collapse_samples.py --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + collapse_samples.py + --input_biom_fp '$input_biom_fp' + --mapping_fp '$mapping_fp' + --collapse_mode '$collapse_mode' + $normalize + #set allCollapseFields = '' + #for $repeat in ( $collapse_fields_repeat ) + #if $allCollapseFields == '' + #set allCollapseFields += str($repeat.collapse_fields) + #else: + #set allCollapseFields += ',' + str($repeat.collapse_fields) + #end if + #end for + --collapse_fields $allCollapseFields + --output_biom_fp '$output_biom_fp' + --output_mapping_fp '$output_mapping_fp' + ]]></command> + <inputs> + <param argument="--input_biom_fp" type="data" format="biom1" label="Input biom table" help="The biom table containing the samples to be collapsed" /> + <param argument="--mapping_fp" type="data" format="tabular" label="Input mapping file" help="The sample metadata mapping file" /> + <param argument="--collapse_mode" type="select" label="Collapse mode to use" help="The mechanism for collapsing counts within groups"> + <option value="sum" selected="true">sum</option> + <option value="mean">mean</option> + <option value="random">random</option> + <option value="median">median</option> + <option value="first">first</option> + </param> + <param argument="--normalize" type="boolean" label="Do you want to normalize observation counts to relative abundances ?" truevalue="--normalize" falsevalue="" checked="False" help="When this option is used the counts within each sample sum to 1.0" /> + <repeat name="collapse_fields_repeat" title="New field to collapse data on" help="You must specify at least one field to collapse data on" min="1" > + <param argument="--collapse_fields" type="text" label="Name of the field" value="" help="Enter the name of one of the column of your mapping file" /> + </repeat> + </inputs> + <outputs> + <data name="output_biom_fp" format="biom1" label="${tool.name} on ${on_string}: Collapsed biom table"/> + <data name="output_mapping_fp" format="tabular" label="${tool.name} on ${on_string}: Collapsed mapping file"/> + </outputs> + <tests> + <!-- Qiime collapse_samples.py generates a binary file (Collapsed biom file) that can't be directly compared to the sample biom file using diff --> + <!-- The following tests on output biom files are then based on a comparison of file sizes with a maximum delta of 0 bytes instead of the classic diff-based comparison --> + <test> + <param name="input_biom_fp" value="collapse_samples/table.biom" /> + <param name="mapping_fp" value="collapse_samples/map.txt" /> + <param name="collapse_mode" value="sum" /> + <repeat name="collapse_fields_repeat"> + <param name="collapse_fields" value="SampleType" /> + </repeat> + <output name="output_biom_fp" file="collapse_samples/collapsed_sum_SampleType_table.biom" compare="sim_size"/> + <output name="output_mapping_fp" file="collapse_samples/collapsed_sum_SampleType_map.txt" ftype="tabular" /> + </test> + <test> + <param name="input_biom_fp" value="collapse_samples/table.biom" /> + <param name="mapping_fp" value="collapse_samples/map.txt" /> + <param name="collapse_mode" value="first" /> + <param name="normalize" value="True" /> + <repeat name="collapse_fields_repeat"> + <param name="collapse_fields" value="subject" /> + </repeat> + <repeat name="collapse_fields_repeat"> + <param name="collapse_fields" value="year" /> + </repeat> + <output name="output_biom_fp" file="collapse_samples/collapsed_first_2fields_table.biom" compare="sim_size"/> + <output name="output_mapping_fp" file="collapse_samples/collapsed_first_2fields_map.txt" ftype="tabular" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +The script `collapse_samples.py <http://qiime.org/scripts/collapse_samples.html>`_ collapse samples in a BIOM table and mapping file. + +The values in the BIOM table are collapsed in one of several different ways (see possible values of the --collapse_mode parameter). + +The values in the mapping file are collapsed by grouping the values if they differ for the grouped samples, and by providing the single value if they don’t differ for the grouped samples. + +The output of `collapse_samples.py <http://qiime.org/scripts/collapse_samples.html>`_ are a collapsed `biom file <http://biom-format.org/>`_ and a collapsed mapping file. + +More information about this tool is available on +`QIIME documentation <http://qiime.org/scripts/collapse_samples.html>`_. + ]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_test_data.sh Mon Jul 10 16:38:55 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 16:38:55 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/test-data/collapse_samples/collapsed_first_2fields_map.txt Mon Jul 10 16:38:55 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 16:38:55 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 16:38:55 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 16:38:55 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 16:38:55 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 16:38:55 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 16:38:55 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 16:38:55 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 16:38:55 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 16:38:55 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 16:38:55 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