Mercurial > repos > iuc > picrust_compare_biom
changeset 0:43244ad9e7ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,34 @@ +## PICRUSt Galaxy Wrapper + +This page is for anyone interested in installing [PICRUSt](http://picrust.github.io/picrust/) in a [galaxy instance](https://galaxyproject.org/).The below descriptions should clarify the most confusing part of the installation. + +The most important steps are that you need to go to the Galaxy IUC tool shed and install the 4 wrapper scripts there along with PICRUSt itself. If you install PICRUSt through this interface the precalculated files will not also be installed, you will need to download them separately (see below). + +Once these scripts are installed sections like the one below should be added to *galaxy/config/shed_tool_data_table_conf.xml* automatically. They will point to different *picrust_precalculated.loc* files; you only need to edit one of them since all of these files will be checked. + +``` +<tables> + <table name="picrust_precalculated" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/picrust_precalculated.loc" /> + </table> +</tables> +``` + +You should download the precalculated files from http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/. + +Most users only use the below two files (however you can also download the precalculated COG and RFAM abundances): +``` +16S_13_5_precalculated.tab.gz +ko_13_5_precalculated.tab.gz +``` + +Once you download these files we just need to point to them in a *picrust_precalculated.loc* file. + +An example file is shown below. Note that tabs should separate the two columns and that in the below command "16S 13_5" (separated by one space) is one example dbname. + +``` +<dbname> <file_base> +16S 13_5 /path/to/16S_13_5_precalculated.tab.gz +ko 13_5 /path/to/ko_13_5_precalculated.tab.gz +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compare_biom.xml Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,130 @@ +<tool id="picrust_compare_biom" name="Compare BIOM tables" version="@WRAPPER_VERSION@.0"> + <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ + compare_biom.py + -e '$expected' + -o '$outfile' + $not_relative_abundance_scores + $advanced.normalize + $advanced.limit_to_observed_observations + $advanced.limit_to_expected_observations + $advanced.shuffle_samples + + '$observed' + ]]></command> + <inputs> + <param name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/> + <param name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/> + <param argument="not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?" + help="Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN"/> + <section name="advanced" title="Advanced parameters" expanded="false"> + <param argument="compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations" + help="Calculate accuracy values by comparing between observations (instead of between samples)."/> + <param argument="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?" + help="Convert both expected and observed tables to relative abundances (instead of observations)."/> + <param argument="limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?" + help="Ignore observations that are not in the observed table."/> + <param argument="limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?" + help="Ignore observations that are not in the expected table."/> + <param argument="shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?" + help="Shuffle samples ids randomly before measuring accuracy."/> + </section> + </inputs> + <outputs> + <data format="tabular" name="outfile" label="${tool.name} on ${on_string} Comparison summary"/> + </outputs> + <tests> + <test><!-- relative abundance test --> + <param name="observed" value="observed_ra.biom" ftype="biom1"/> + <param name="expected" value="expected_ra.biom" ftype="biom1"/> + <output name="outfile" ftype="tabular"> + <assert_contents> + <has_text_matching expression="file\tlabel\taccuracy"/> + <has_text text="sample1"/> + <has_text text="sample3"/> + <has_text text="sample2"/> + </assert_contents> + </output> + </test> + <test><!-- real counts test --> + <param name="observed" value="observed.biom" ftype="biom1"/> + <param name="expected" value="expected.biom" ftype="biom1"/> + <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/> + <output name="outfile" ftype="tabular"> + <assert_contents> + <has_text_matching expression="file\tlabel\taccuracy"/> + <has_text text="sample1"/> + <has_text text="sample3"/> + <has_text text="sample2"/> + </assert_contents> + </output> + </test> + <test><!-- all other switches test --> + <param name="observed" value="observed.biom" ftype="biom1"/> + <param name="expected" value="expected.biom" ftype="biom1"/> + <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/> + <param name="compare_observations" value="--compare_observations"/> + <param name="normalize" value="--normalize"/> + <param name="limit_to_observed_observations" value="--limit_to_observed_observations"/> + <param name="shuffle_samples" value="--shuffle_samples"/> + <output name="outfile" ftype="tabular"> + <assert_contents> + <has_text_matching expression="file\tlabel\taccuracy"/> + <has_text text="sample1"/> + <has_text text="sample3"/> + <has_text text="sample2"/> + </assert_contents> + </output> + </test> + </tests> + <help> +<![CDATA[ +@PICRUST_OVERVIEW@ + +**Command Documentation** + +Compare an observed table to an expected table using either relative abundance or real counts. + +**Input files:** + +**Observed table:** A table of observed relative abundances or real counts in .biom format. + +**Expected table:** The expected table of relative abundances or real counts in .biom format. + +**Output file:** Tab delimited file with various accuracy metrics. + +**Optional Parameters:** + +*compare observations* + + Calculate accuracy values by comparing between observations (instead of between samples) [default: False] + +*normalize* + + Convert both expected and observed tables to relative abundances (instead of observations) [default: False] + +*limit to expected observations* + + Ignore observations that are not in the expected table[default: False] + +*limit to observed observations* + + Ignore observations that are not in the observed table[default: False] + +*shuffle samples* + + Shuffle samples ids randomly before measuring accuracy[default: False] + +*not relative abundance scores* + + Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN [default: False] + +]]> + </help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,97 @@ +<macros> + <token name="@WRAPPER_VERSION@">1.1.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.1.1">picrust</requirement> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command> + </xml> + + <xml name="otu-reference-precalculated"> + <!-- selection of "gg" picrust parameter reference data file --> + <conditional name="gg"> + <param name="source" type="select" label="Select precalculated file from" help=""> + <option value="ref">Cached Reference</option> + <option value="hist">History</option> + </param> + <when value="ref"> + <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis"> + <options from_data_table="picrust_precalculated"/> + </param> + </when> + <when value="hist"> + <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis" + help="files may be downloaded from PICRUSt website (see tool help below)" /> + </when> + </conditional> + </xml> + + <xml name="biom_format_select"> + <param name="output_type" type="select" label="Format of the output BIOM file"> + <option value="hdf5" selected="true">HDF5</option> + <option value="json">JSON</option> + <option value="tsv">Classic (tab-separated text)</option> + </param> + </xml> + + <xml name="biom_format_select_no_json"> + <param name="output_type" type="select" label="Format of the output BIOM file"> + <option value="hdf5" selected="true">HDF5</option> + <option value="tsv">Classic (tab-separated text)</option> + </param> + </xml> + + <xml name="biom_output"> + <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs"> + <change_format> + <when input="output_type" value="json" format="biom1"/> + <when input="output_type" value="tsv" format="tabular"/> + <when input="output_type" value="hdf5" format="h5"/> + </change_format> + </data> + </xml> + + <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[ + #if $output_type == "hdf5": + && mv tempbiom '$out_biom' + #elif $output_type == "tsv": + && biom convert -i tempbiom -o '$out_biom' --to-tsv + #else: + && biom convert -i tempbiom -o '$out_biom' --to-json + #end if + ]]></token> + + <token name="@PICRUST_OVERVIEW@"> +<![CDATA[ +**PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States** + +The PICRUSt project aims to support prediction of the unobserved character states in a community of +organisms from phylogenetic information about the organisms in that community. The primary application +is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only +marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative +bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs. + +For more information please visit: + +- PICRUSt Documentation: https://picrust.github.io/picrust/ +- PICRUSt GitHub: http://picrust.github.com/ +- PICRUSt Support: https://groups.google.com/d/forum/picrust-users + +**Reference Data** + +Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/ + +]]> + </token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.2676</citation> + <yield/> + </citations> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/16S_13_5_precalculated_minimal.tab Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,5 @@ +#OTU_IDs 16S_rRNA_Count +290426 10.0 +265267 5.0 +248563 4.0 +61102 4.0 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closed_picked_otus.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2-dev","date": "2013-08-20T16:13:50.386985","matrix_type": "sparse","matrix_element_type": "float","shape": [4, 2],"data": [[0,0,1.0],[1,0,2.0],[2,1,2.0],[3,0,1.0],[3,1,1.0]],"rows": [{"id": "290426", "metadata": null},{"id": "265267", "metadata": null},{"id": "248563", "metadata": null},{"id": "61102", "metadata": null}],"columns": [{"id": "sample1", "metadata": null},{"id": "sample2", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closed_picked_otus.tab Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,6 @@ +# Constructed from biom file +#OTU ID sample1 sample2 +290426 1 0 +265267 2 0 +248563 0 2 +61102 1 1 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cog_predicted_metagenomes.L2.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "Gene table","generated_by": "picrust 1.0.0-dev - categorize_by_function","date": "2013-10-10T12:55:15.589322","matrix_type": "sparse","matrix_element_type": "float","shape": [25, 2],"data": [[1,0,2.0],[1,1,2.0],[2,0,275.0],[2,1,128.0],[3,0,74.0],[3,1,18.0],[4,0,577.0],[4,1,233.0],[5,0,231.0],[5,1,50.0],[6,0,540.0],[6,1,144.0],[7,0,218.0],[7,1,93.0],[8,0,196.0],[8,1,96.0],[9,0,473.0],[9,1,142.0],[10,0,566.0],[10,1,216.0],[11,0,368.0],[11,1,110.0],[12,0,353.0],[12,1,121.0],[13,0,103.0],[13,1,72.0],[14,0,213.0],[14,1,73.0],[15,0,323.0],[15,1,111.0],[16,0,100.0],[16,1,55.0],[17,0,747.0],[17,1,251.0],[18,0,500.0],[18,1,95.0],[19,0,326.0],[19,1,166.0],[20,0,134.0],[20,1,58.0],[21,0,154.0],[21,1,34.0]],"rows": [{"id": "[A] RNA processing and modification", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[A] RNA processing and modification"]}},{"id": "[B] Chromatin structure and dynamics", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[B] Chromatin structure and dynamics"]}},{"id": "[C] Energy production and conversion", "metadata": {"COG_Category": ["METABOLISM", "[C] Energy production and conversion"]}},{"id": "[D] Cell cycle control, cell division, chromosome partitioning", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[D] Cell cycle control, cell division, chromosome partitioning"]}},{"id": "[E] Amino acid transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[E] Amino acid transport and metabolism"]}},{"id": "[F] Nucleotide transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[F] Nucleotide transport and metabolism"]}},{"id": "[G] Carbohydrate transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[G] Carbohydrate transport and metabolism"]}},{"id": "[H] Coenzyme transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[H] Coenzyme transport and metabolism"]}},{"id": "[I] Lipid transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[I] Lipid transport and metabolism"]}},{"id": "[J] Translation, ribosomal structure and biogenesis", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[J] Translation, ribosomal structure and biogenesis"]}},{"id": "[K] Transcription", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[K] Transcription"]}},{"id": "[L] Replication, recombination and repair", "metadata": {"COG_Category": ["INFORMATION STORAGE AND PROCESSING", "[L] Replication, recombination and repair"]}},{"id": "[M] Cell wall/membrane/envelope biogenesis", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[M] Cell wall/membrane/envelope biogenesis"]}},{"id": "[N] Cell motility", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[N] Cell motility"]}},{"id": "[O] Post-translational modification, protein turnover, and chaperones", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[O] Post-translational modification, protein turnover, and chaperones"]}},{"id": "[P] Inorganic ion transport and metabolism", "metadata": {"COG_Category": ["METABOLISM", "[P] Inorganic ion transport and metabolism"]}},{"id": "[Q] Secondary metabolites biosynthesis, transport, and catabolism", "metadata": {"COG_Category": ["METABOLISM", "[Q] Secondary metabolites biosynthesis, transport, and catabolism"]}},{"id": "[R] General function prediction only", "metadata": {"COG_Category": ["POORLY CHARACTERIZED", "[R] General function prediction only"]}},{"id": "[S] Function unknown", "metadata": {"COG_Category": ["POORLY CHARACTERIZED", "[S] Function unknown"]}},{"id": "[T] Signal transduction mechanisms", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[T] Signal transduction mechanisms"]}},{"id": "[U] Intracellular trafficking, secretion, and vesicular transport", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[U] Intracellular trafficking, secretion, and vesicular transport"]}},{"id": "[V] Defense mechanisms", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[V] Defense mechanisms"]}},{"id": "[W] Extracellular structures", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[W] Extracellular structures"]}},{"id": "[Y] Nuclear structure", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[Y] Nuclear structure"]}},{"id": "[Z] Cytoskeleton", "metadata": {"COG_Category": ["CELLULAR PROCESSES AND SIGNALING", "[Z] Cytoskeleton"]}}],"columns": [{"id": "staggered", "metadata": null},{"id": "even", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trait_table.tab Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,5 @@ +#OTU_IDs trait1 trait2 metadata_NSTI +A 1.0 2.0 0.0 +C 1.0 1.0 0.0 +B 1.0 0.0 0.0 +D 1.0 1.0 0.7 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2","date": "2013-04-16T14:39:16.483909","matrix_type": "sparse","matrix_element_type": "float","shape": [5, 3],"data": [[0,0,5.0],[0,1,4.0],[0,2,3.0],[2,0,1.0],[2,1,2.0],[2,2,3.0],[3,0,7.0],[3,1,7.0],[3,2,7.0],[4,0,2.0],[4,1,2.0],[4,2,2.0]],"rows": [{"id": "K00001", "metadata": null},{"id": "K00002", "metadata": null},{"id": "K00003", "metadata": null},{"id": "K00004", "metadata": null},{"id": "K00005", "metadata": null}],"columns": [{"id": "sample1", "metadata": null},{"id": "sample2", "metadata": null},{"id": "sample3", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected_ra.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2","date": "2013-04-16T14:42:26.823100","matrix_type": "sparse","matrix_element_type": "float","shape": [5, 3],"data": [[0,0,0.5],[0,1,0.40000000000000002],[0,2,0.29999999999999999],[2,0,1.0],[2,1,1.0],[2,2,1.0],[3,0,0.29999999999999999],[3,1,0.5],[3,2,0.69999999999999996],[4,0,1.0],[4,1,1.0],[4,2,1.0]],"rows": [{"id": "K00001", "metadata": null},{"id": "K00002", "metadata": null},{"id": "K00003", "metadata": null},{"id": "K00004", "metadata": null},{"id": "K00005", "metadata": null}],"columns": [{"id": "sample1", "metadata": null},{"id": "sample2", "metadata": null},{"id": "sample3", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/normalized_otus.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2-dev","date": "2013-08-19T13:58:00.733870","matrix_type": "sparse","matrix_element_type": "float","shape": [4, 2],"data": [[0,0,0.090909090909100002],[1,0,2.5],[2,1,0.083333333333299994],[3,0,0.5],[3,1,0.5]],"rows": [{"id": "290426", "metadata": null},{"id": "265267", "metadata": null},{"id": "248563", "metadata": null},{"id": "61102", "metadata": null}],"columns": [{"id": "staggered", "metadata": null},{"id": "even", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/normalized_otus.classic Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,6 @@ +# Constructed from biom file +#OTU ID sample1 sample2 +290426 0.1 0.0 +265267 0.4 0.0 +248563 0.0 0.5 +61102 0.25 0.25
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/observation_table.biom Sat Jan 20 03:31:34 2018 -0500 @@ -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","date": "2013-05-16T01:50:26.488550","matrix_type": "sparse","matrix_element_type": "int","shape": [4, 3],"data": [[0,0,1],[1,1,1],[2,2,1],[3,0,1]],"rows": [{"id": "651338519", "metadata": {"taxonomy": ["None"]}},{"id": "644273636", "metadata": {"taxonomy": ["Environmental Information Processing", " Membrane Transport", " Transporters", " K09686"]}},{"id": "644269307", "metadata": {"taxonomy": ["None"]}},{"id": "644228691", "metadata": {"taxonomy": ["None"]}}],"columns": [{"id": "121.PD", "metadata": null},{"id": "124.PD", "metadata": null},{"id": "123.PD", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/observed.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2","date": "2013-04-16T14:39:11.550319","matrix_type": "sparse","matrix_element_type": "float","shape": [5, 3],"data": [[0,0,3.0],[0,1,3.0],[0,2,1.0],[1,2,1.0],[2,0,1.0],[2,1,2.0],[2,2,2.0],[3,0,2.0],[3,1,10.0],[3,2,7.0],[4,0,2.0],[4,1,1.0],[4,2,2.0]],"rows": [{"id": "K00001", "metadata": null},{"id": "K00002", "metadata": null},{"id": "K00003", "metadata": null},{"id": "K00004", "metadata": null},{"id": "K00005", "metadata": null}],"columns": [{"id": "sample1", "metadata": null},{"id": "sample2", "metadata": null},{"id": "sample3", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/observed_ra.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "BIOM-Format 1.1.2","date": "2013-04-16T14:42:20.632211","matrix_type": "sparse","matrix_element_type": "float","shape": [5, 3],"data": [[0,0,0.5],[0,1,0.20000000000000001],[1,2,0.10000000000000001],[2,0,0.25],[2,1,1.0],[2,2,1.0],[3,0,0.29999999999999999],[3,1,0.5],[3,2,0.69999999999999996],[4,1,1.0],[4,2,0.80000000000000004]],"rows": [{"id": "K00001", "metadata": null},{"id": "K00002", "metadata": null},{"id": "K00003", "metadata": null},{"id": "K00004", "metadata": null},{"id": "K00005", "metadata": null}],"columns": [{"id": "sample1", "metadata": null},{"id": "sample2", "metadata": null},{"id": "sample3", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/otu_table_for_custom_trait_table.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "picrust","date": "2015-03-07T11:40:42.151151","type": "OTU table","matrix_element_type": "float","shape": [3, 4],"data": [[0,0,1.0],[0,1,2.0],[0,2,3.0],[0,3,5.0],[1,0,5.0],[1,1,1.0],[1,3,2.0],[2,2,1.0],[2,3,4.0]],"rows": [{"id": "A", "metadata": null},{"id": "B", "metadata": null},{"id": "C", "metadata": null}],"columns": [{"id": "Sample1", "metadata": {"pH": 7.0}},{"id": "Sample2", "metadata": {"pH": 8.0}},{"id": "Sample3", "metadata": {"pH": 7.0}},{"id": "Sample4", "metadata": {"pH": NaN}}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/predicted_metagenomes.L3.biom Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "Gene table","generated_by": "picrust 0.9.1-dev - categorize_by_function","date": "2013-05-27T13:45:53.337575","matrix_type": "sparse","matrix_element_type": "float","shape": [333, 2],"data": 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metabolites", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Biosynthesis and biodegradation of secondary metabolites"]}},{"id": "Biosynthesis of 12-, 14- and 16-membered macrolides", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Biosynthesis of 12-, 14- and 16-membered macrolides"]}},{"id": "Biosynthesis of ansamycins", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Biosynthesis of ansamycins"]}},{"id": "Biosynthesis of siderophore group nonribosomal peptides", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Biosynthesis of siderophore group nonribosomal peptides"]}},{"id": "Biosynthesis of type II polyketide backbone", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Biosynthesis of type II polyketide backbone"]}},{"id": "Biosynthesis of type II polyketide products", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Biosynthesis of type II polyketide products"]}},{"id": "Biosynthesis of unsaturated fatty acids", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Biosynthesis of unsaturated fatty acids"]}},{"id": "Biosynthesis of vancomycin group antibiotics", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Biosynthesis of vancomycin group antibiotics"]}},{"id": "Biotin metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Biotin metabolism"]}},{"id": "Bisphenol degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Bisphenol degradation"]}},{"id": "Bladder cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Bladder cancer"]}},{"id": "Butanoate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Butanoate metabolism"]}},{"id": "Butirosin and neomycin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Butirosin and neomycin biosynthesis"]}},{"id": "C5-Branched dibasic acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "C5-Branched dibasic acid metabolism"]}},{"id": "CAM ligands", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "CAM ligands"]}},{"id": "Caffeine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Caffeine metabolism"]}},{"id": "Calcium signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Calcium signaling pathway"]}},{"id": "Caprolactam degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Caprolactam degradation"]}},{"id": "Carbohydrate digestion and absorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Carbohydrate digestion and absorption"]}},{"id": "Carbohydrate metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Carbohydrate metabolism"]}},{"id": "Carbon fixation in photosynthetic organisms", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Carbon fixation in photosynthetic organisms"]}},{"id": "Carbon fixation pathways in prokaryotes", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Carbon fixation pathways in prokaryotes"]}},{"id": "Cardiac muscle contraction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Circulatory System", "Cardiac muscle contraction"]}},{"id": "Carotenoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Carotenoid biosynthesis"]}},{"id": "Cell adhesion molecules (CAMs)", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Cell adhesion molecules (CAMs)"]}},{"id": "Cell cycle", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Cell cycle"]}},{"id": "Cell cycle - Caulobacter", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Cell cycle - Caulobacter"]}},{"id": "Cell cycle - yeast", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Cell cycle - yeast"]}},{"id": "Cell division", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Cell division"]}},{"id": "Cell motility and secretion", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Cell motility and secretion"]}},{"id": "Cellular antigens", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Cellular antigens"]}},{"id": "Chagas disease (American trypanosomiasis)", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Chagas disease (American trypanosomiasis)"]}},{"id": "Chaperones and folding catalysts", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Chaperones and folding catalysts"]}},{"id": "Chloroalkane and chloroalkene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Chloroalkane and chloroalkene degradation"]}},{"id": "Chlorocyclohexane and chlorobenzene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Chlorocyclohexane and chlorobenzene degradation"]}},{"id": "Cholinergic synapse", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Cholinergic synapse"]}},{"id": "Chromosome", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Chromosome"]}},{"id": "Chronic myeloid leukemia", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Chronic myeloid leukemia"]}},{"id": "Circadian rhythm - mammal", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Environmental Adaptation", "Circadian rhythm - mammal"]}},{"id": "Circadian rhythm - plant", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Environmental Adaptation", "Circadian rhythm - plant"]}},{"id": "Citrate cycle (TCA cycle)", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Citrate cycle (TCA cycle)"]}},{"id": "Clavulanic acid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Clavulanic acid biosynthesis"]}},{"id": "Colorectal cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Colorectal cancer"]}},{"id": "Complement and coagulation cascades", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Complement and coagulation cascades"]}},{"id": "Cyanoamino acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Cyanoamino acid metabolism"]}},{"id": "Cysteine and methionine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Cysteine and methionine metabolism"]}},{"id": "Cytochrome P450", "metadata": {"KEGG_Pathways": ["Metabolism", "Enzyme Families", "Cytochrome P450"]}},{"id": "Cytokine receptors", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Cytokine receptors"]}},{"id": "Cytokine-cytokine receptor interaction", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Cytokine-cytokine receptor interaction"]}},{"id": "Cytoskeleton proteins", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Motility", "Cytoskeleton proteins"]}},{"id": "Cytosolic DNA-sensing pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Cytosolic DNA-sensing pathway"]}},{"id": "D-Alanine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "D-Alanine metabolism"]}},{"id": "D-Arginine and D-ornithine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "D-Arginine and D-ornithine metabolism"]}},{"id": "D-Glutamine and D-glutamate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "D-Glutamine and D-glutamate metabolism"]}},{"id": "DNA repair and recombination proteins", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "DNA repair and recombination proteins"]}},{"id": "DNA replication", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "DNA replication"]}},{"id": "DNA replication proteins", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "DNA replication proteins"]}},{"id": "Dilated cardiomyopathy (DCM)", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cardiovascular Diseases", "Dilated cardiomyopathy (DCM)"]}},{"id": "Dioxin degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Dioxin degradation"]}},{"id": "Drug metabolism - cytochrome P450", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Drug metabolism - cytochrome P450"]}},{"id": "Drug metabolism - other enzymes", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Drug metabolism - other enzymes"]}},{"id": "ECM-receptor interaction", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "ECM-receptor interaction"]}},{"id": "Electron transfer carriers", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Electron transfer carriers"]}},{"id": "Endocrine and other factor-regulated calcium reabsorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Excretory System", "Endocrine and other factor-regulated calcium reabsorption"]}},{"id": "Endocytosis", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Transport and Catabolism", "Endocytosis"]}},{"id": "Energy metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Energy metabolism"]}},{"id": "Epithelial cell signaling in Helicobacter pylori infection", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Epithelial cell signaling in Helicobacter pylori infection"]}},{"id": "ErbB signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "ErbB signaling pathway"]}},{"id": "Ether lipid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Ether lipid metabolism"]}},{"id": "Ethylbenzene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Ethylbenzene degradation"]}},{"id": "Fat digestion and absorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Fat digestion and absorption"]}},{"id": "Fatty acid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Fatty acid biosynthesis"]}},{"id": "Fatty acid elongation in mitochondria", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Fatty acid elongation in mitochondria"]}},{"id": "Fatty acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Fatty acid metabolism"]}},{"id": "Fc epsilon RI signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Fc epsilon RI signaling pathway"]}},{"id": "Fc gamma R-mediated phagocytosis", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Fc gamma R-mediated phagocytosis"]}},{"id": "Flagellar assembly", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Motility", "Flagellar assembly"]}},{"id": "Flavone and flavonol biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Flavone and flavonol biosynthesis"]}},{"id": "Flavonoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Flavonoid biosynthesis"]}},{"id": "Fluorobenzoate degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Fluorobenzoate degradation"]}},{"id": "Focal adhesion", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Communication", "Focal adhesion"]}},{"id": "Folate biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Folate biosynthesis"]}},{"id": "Fructose and mannose metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Fructose and mannose metabolism"]}},{"id": "Function unknown", "metadata": {"KEGG_Pathways": ["Unclassified", "Poorly Characterized", "Function unknown"]}},{"id": "G protein-coupled receptors", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "G protein-coupled receptors"]}},{"id": "GTP-binding proteins", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "GTP-binding proteins"]}},{"id": "Galactose metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Galactose metabolism"]}},{"id": "Gastric acid secretion", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Gastric acid secretion"]}},{"id": "General function prediction only", "metadata": {"KEGG_Pathways": ["Unclassified", "Poorly Characterized", "General function prediction only"]}},{"id": "Geraniol degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Geraniol degradation"]}},{"id": "Germination", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Germination"]}},{"id": "Glioma", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Glioma"]}},{"id": "Glutamatergic synapse", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Glutamatergic synapse"]}},{"id": "Glutathione metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Glutathione metabolism"]}},{"id": "Glycan bindng proteins", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Glycan bindng proteins"]}},{"id": "Glycan biosynthesis and metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Glycan biosynthesis and metabolism"]}},{"id": "Glycerolipid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Glycerolipid metabolism"]}},{"id": "Glycerophospholipid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Glycerophospholipid metabolism"]}},{"id": "Glycine, serine and threonine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Glycine, serine and threonine metabolism"]}},{"id": "Glycolysis / Gluconeogenesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Glycolysis / Gluconeogenesis"]}},{"id": "Glycosaminoglycan biosynthesis - chondroitin sulfate", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosaminoglycan biosynthesis - chondroitin sulfate"]}},{"id": "Glycosaminoglycan biosynthesis - heparan sulfate", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosaminoglycan biosynthesis - heparan sulfate"]}},{"id": "Glycosaminoglycan degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosaminoglycan degradation"]}},{"id": "Glycosphingolipid biosynthesis - ganglio series", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosphingolipid biosynthesis - ganglio series"]}},{"id": "Glycosphingolipid biosynthesis - globo series", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosphingolipid biosynthesis - globo series"]}},{"id": "Glycosphingolipid biosynthesis - lacto and neolacto series", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosphingolipid biosynthesis - lacto and neolacto series"]}},{"id": "Glycosylphosphatidylinositol(GPI)-anchor biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosylphosphatidylinositol(GPI)-anchor biosynthesis"]}},{"id": "Glycosyltransferases", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Glycosyltransferases"]}},{"id": "Glyoxylate and dicarboxylate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Glyoxylate and dicarboxylate metabolism"]}},{"id": "GnRH signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "GnRH signaling pathway"]}},{"id": "Hedgehog signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Hedgehog signaling pathway"]}},{"id": "Hematopoietic cell lineage", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Hematopoietic cell lineage"]}},{"id": "Hepatitis C", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Hepatitis C"]}},{"id": "Histidine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Histidine metabolism"]}},{"id": "Homologous recombination", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Homologous recombination"]}},{"id": "Huntington's disease", "metadata": {"KEGG_Pathways": ["Human Diseases", "Neurodegenerative Diseases", "Huntington's disease"]}},{"id": "Hypertrophic cardiomyopathy (HCM)", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cardiovascular Diseases", "Hypertrophic cardiomyopathy (HCM)"]}},{"id": "Indole alkaloid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Indole alkaloid biosynthesis"]}},{"id": "Influenza A", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Influenza A"]}},{"id": "Inorganic ion transport and metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Inorganic ion transport and metabolism"]}},{"id": "Inositol phosphate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Inositol phosphate metabolism"]}},{"id": "Insulin signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "Insulin signaling pathway"]}},{"id": "Ion channels", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Ion channels"]}},{"id": "Isoflavonoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Isoflavonoid biosynthesis"]}},{"id": "Isoquinoline alkaloid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Isoquinoline alkaloid biosynthesis"]}},{"id": "Leishmaniasis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Leishmaniasis"]}},{"id": "Leukocyte transendothelial migration", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "Leukocyte transendothelial migration"]}},{"id": "Limonene and pinene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Limonene and pinene degradation"]}},{"id": "Linoleic acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Linoleic acid metabolism"]}},{"id": "Lipid biosynthesis proteins", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Lipid biosynthesis proteins"]}},{"id": "Lipid metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Lipid metabolism"]}},{"id": "Lipoic acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Lipoic acid metabolism"]}},{"id": "Lipopolysaccharide biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Lipopolysaccharide biosynthesis"]}},{"id": "Lipopolysaccharide biosynthesis proteins", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Lipopolysaccharide biosynthesis proteins"]}},{"id": "Long-term depression", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Long-term depression"]}},{"id": "Long-term potentiation", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Long-term potentiation"]}},{"id": "Lysine biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Lysine biosynthesis"]}},{"id": "Lysine degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Lysine degradation"]}},{"id": "Lysosome", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Transport and Catabolism", "Lysosome"]}},{"id": "MAPK signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "MAPK signaling pathway"]}},{"id": "MAPK signaling pathway - yeast", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "MAPK signaling pathway - yeast"]}},{"id": "Measles", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Measles"]}},{"id": "Meiosis - yeast", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Meiosis - yeast"]}},{"id": "Melanogenesis", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "Melanogenesis"]}},{"id": "Membrane and intracellular structural molecules", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Membrane and intracellular structural molecules"]}},{"id": "Metabolism of cofactors and vitamins", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Metabolism of cofactors and vitamins"]}},{"id": "Metabolism of xenobiotics by cytochrome P450", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Metabolism of xenobiotics by cytochrome P450"]}},{"id": "Methane metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Methane metabolism"]}},{"id": "Mineral absorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Mineral absorption"]}},{"id": "Mismatch repair", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Mismatch repair"]}},{"id": "N-Glycan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "N-Glycan biosynthesis"]}},{"id": "NOD-like receptor signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "NOD-like receptor signaling pathway"]}},{"id": "Naphthalene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Naphthalene degradation"]}},{"id": "Neuroactive ligand-receptor interaction", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signaling Molecules and Interaction", "Neuroactive ligand-receptor interaction"]}},{"id": "Neurotrophin signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Nervous System", "Neurotrophin signaling pathway"]}},{"id": "Nicotinate and nicotinamide metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Nicotinate and nicotinamide metabolism"]}},{"id": "Nitrogen metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Nitrogen metabolism"]}},{"id": "Nitrotoluene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Nitrotoluene degradation"]}},{"id": "Non-coding RNAs", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "RNA family", "Non-coding RNAs"]}},{"id": "Non-homologous end-joining", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Non-homologous end-joining"]}},{"id": "Notch signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Notch signaling pathway"]}},{"id": "Novobiocin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Novobiocin biosynthesis"]}},{"id": "Nucleotide excision repair", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Replication and Repair", "Nucleotide excision repair"]}},{"id": "Nucleotide metabolism", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Nucleotide metabolism"]}},{"id": "Olfactory transduction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Sensory System", "Olfactory transduction"]}},{"id": "One carbon pool by folate", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "One carbon pool by folate"]}},{"id": "Oocyte meiosis", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "Oocyte meiosis"]}},{"id": "Other glycan degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Other glycan degradation"]}},{"id": "Other ion-coupled transporters", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Other ion-coupled transporters"]}},{"id": "Other transporters", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Other transporters"]}},{"id": "Other types of O-glycan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Other types of O-glycan biosynthesis"]}},{"id": "Others", "metadata": {"KEGG_Pathways": ["Unclassified", "Metabolism", "Others"]}},{"id": "Oxidative phosphorylation", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Oxidative phosphorylation"]}},{"id": "PPAR signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "PPAR signaling pathway"]}},{"id": "Pancreatic cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Pancreatic cancer"]}},{"id": "Pancreatic secretion", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Pancreatic secretion"]}},{"id": "Pantothenate and CoA biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Pantothenate and CoA biosynthesis"]}},{"id": "Parkinson's disease", "metadata": {"KEGG_Pathways": ["Human Diseases", "Neurodegenerative Diseases", "Parkinson's disease"]}},{"id": "Pathogenic Escherichia coli infection", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Pathogenic Escherichia coli infection"]}},{"id": "Pathways in cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Pathways in cancer"]}},{"id": "Penicillin and cephalosporin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Penicillin and cephalosporin biosynthesis"]}},{"id": "Pentose and glucuronate interconversions", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Pentose and glucuronate interconversions"]}},{"id": "Pentose phosphate pathway", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Pentose phosphate pathway"]}},{"id": "Peptidases", "metadata": {"KEGG_Pathways": ["Metabolism", "Enzyme Families", "Peptidases"]}},{"id": "Peptidoglycan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Peptidoglycan biosynthesis"]}},{"id": "Peroxisome", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Transport and Catabolism", "Peroxisome"]}},{"id": "Pertussis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Pertussis"]}},{"id": "Phagosome", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Transport and Catabolism", "Phagosome"]}},{"id": "Phenylalanine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Phenylalanine metabolism"]}},{"id": "Phenylalanine, tyrosine and tryptophan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Phenylalanine, tyrosine and tryptophan biosynthesis"]}},{"id": "Phenylpropanoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Phenylpropanoid biosynthesis"]}},{"id": "Phosphatidylinositol signaling system", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Phosphatidylinositol signaling system"]}},{"id": "Phosphonate and phosphinate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Phosphonate and phosphinate metabolism"]}},{"id": "Phosphotransferase system (PTS)", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Membrane Transport", "Phosphotransferase system (PTS)"]}},{"id": "Photosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Photosynthesis"]}},{"id": "Photosynthesis - antenna proteins", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Photosynthesis - antenna proteins"]}},{"id": "Photosynthesis proteins", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Photosynthesis proteins"]}},{"id": "Phototransduction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Sensory System", "Phototransduction"]}},{"id": "Phototransduction - fly", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Sensory System", "Phototransduction - fly"]}},{"id": "Plant-pathogen interaction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Environmental Adaptation", "Plant-pathogen interaction"]}},{"id": "Polycyclic aromatic hydrocarbon degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Polycyclic aromatic hydrocarbon degradation"]}},{"id": "Polyketide sugar unit biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Polyketide sugar unit biosynthesis"]}},{"id": "Pores ion channels", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Pores ion channels"]}},{"id": "Porphyrin and chlorophyll metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Porphyrin and chlorophyll metabolism"]}},{"id": "Prenyltransferases", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Prenyltransferases"]}},{"id": "Primary bile acid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Primary bile acid biosynthesis"]}},{"id": "Primary immunodeficiency", "metadata": {"KEGG_Pathways": ["Human Diseases", "Immune System Diseases", "Primary immunodeficiency"]}},{"id": "Prion diseases", "metadata": {"KEGG_Pathways": ["Human Diseases", "Neurodegenerative Diseases", "Prion diseases"]}},{"id": "Progesterone-mediated oocyte maturation", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "Progesterone-mediated oocyte maturation"]}},{"id": "Propanoate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Propanoate metabolism"]}},{"id": "Prostate cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Prostate cancer"]}},{"id": "Proteasome", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Proteasome"]}},{"id": "Protein digestion and absorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Protein digestion and absorption"]}},{"id": "Protein export", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Protein export"]}},{"id": "Protein folding and associated processing", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Protein folding and associated processing"]}},{"id": "Protein kinases", "metadata": {"KEGG_Pathways": ["Metabolism", "Enzyme Families", "Protein kinases"]}},{"id": "Protein processing in endoplasmic reticulum", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Protein processing in endoplasmic reticulum"]}},{"id": "Proximal tubule bicarbonate reclamation", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Excretory System", "Proximal tubule bicarbonate reclamation"]}},{"id": "Purine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Nucleotide Metabolism", "Purine metabolism"]}},{"id": "Pyrimidine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Nucleotide Metabolism", "Pyrimidine metabolism"]}},{"id": "Pyruvate metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Pyruvate metabolism"]}},{"id": "RIG-I-like receptor signaling pathway", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Immune System", "RIG-I-like receptor signaling pathway"]}},{"id": "RNA degradation", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "RNA degradation"]}},{"id": "RNA polymerase", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Transcription", "RNA polymerase"]}},{"id": "RNA transport", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "RNA transport"]}},{"id": "Regulation of actin cytoskeleton", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Motility", "Regulation of actin cytoskeleton"]}},{"id": "Renal cell carcinoma", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Renal cell carcinoma"]}},{"id": "Renin-angiotensin system", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Endocrine System", "Renin-angiotensin system"]}},{"id": "Replication, recombination and repair proteins", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Replication, recombination and repair proteins"]}},{"id": "Restriction enzyme", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Restriction enzyme"]}},{"id": "Retinol metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Retinol metabolism"]}},{"id": "Rheumatoid arthritis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Immune System Diseases", "Rheumatoid arthritis"]}},{"id": "Riboflavin metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Riboflavin metabolism"]}},{"id": "Ribosome", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "Ribosome"]}},{"id": "Ribosome Biogenesis", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "Ribosome Biogenesis"]}},{"id": "Ribosome biogenesis in eukaryotes", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "Ribosome biogenesis in eukaryotes"]}},{"id": "Salivary secretion", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Digestive System", "Salivary secretion"]}},{"id": "Secondary bile acid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Secondary bile acid biosynthesis"]}},{"id": "Secretion system", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Membrane Transport", "Secretion system"]}},{"id": "Selenocompound metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Selenocompound metabolism"]}},{"id": "Sesquiterpenoid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Sesquiterpenoid biosynthesis"]}},{"id": "Shigellosis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Shigellosis"]}},{"id": "Signal transduction mechanisms", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Signal transduction mechanisms"]}},{"id": "Small cell lung cancer", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cancers", "Small cell lung cancer"]}},{"id": "Sphingolipid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Sphingolipid metabolism"]}},{"id": "Spliceosome", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Transcription", "Spliceosome"]}},{"id": "Sporulation", "metadata": {"KEGG_Pathways": ["Unclassified", "Cellular Processes and Signaling", "Sporulation"]}},{"id": "Staphylococcus aureus infection", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Staphylococcus aureus infection"]}},{"id": "Starch and sucrose metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Carbohydrate Metabolism", "Starch and sucrose metabolism"]}},{"id": "Steroid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Steroid biosynthesis"]}},{"id": "Steroid hormone biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Steroid hormone biosynthesis"]}},{"id": "Stilbenoid, diarylheptanoid and gingerol biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Stilbenoid, diarylheptanoid and gingerol biosynthesis"]}},{"id": "Streptomycin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Streptomycin biosynthesis"]}},{"id": "Styrene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Styrene degradation"]}},{"id": "Sulfur metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Energy Metabolism", "Sulfur metabolism"]}},{"id": "Sulfur relay system", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Sulfur relay system"]}},{"id": "Synthesis and degradation of ketone bodies", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "Synthesis and degradation of ketone bodies"]}},{"id": "Systemic lupus erythematosus", "metadata": {"KEGG_Pathways": ["Human Diseases", "Immune System Diseases", "Systemic lupus erythematosus"]}},{"id": "TGF-beta signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "TGF-beta signaling pathway"]}},{"id": "Taurine and hypotaurine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "Taurine and hypotaurine metabolism"]}},{"id": "Terpenoid backbone biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Terpenoid backbone biosynthesis"]}},{"id": "Tetracycline biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Tetracycline biosynthesis"]}},{"id": "Thiamine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Thiamine metabolism"]}},{"id": "Tight junction", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Communication", "Tight junction"]}},{"id": "Toluene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Toluene degradation"]}},{"id": "Toxoplasmosis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Toxoplasmosis"]}},{"id": "Transcription factors", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Transcription", "Transcription factors"]}},{"id": "Transcription machinery", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Transcription", "Transcription machinery"]}},{"id": "Transcription related proteins", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Transcription related proteins"]}},{"id": "Translation factors", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "Translation factors"]}},{"id": "Translation proteins", "metadata": {"KEGG_Pathways": ["Unclassified", "Genetic Information Processing", "Translation proteins"]}},{"id": "Transporters", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Membrane Transport", "Transporters"]}},{"id": "Tropane, piperidine and pyridine alkaloid biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "Tropane, piperidine and pyridine alkaloid biosynthesis"]}},{"id": "Tryptophan metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Tryptophan metabolism"]}},{"id": "Tuberculosis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Tuberculosis"]}},{"id": "Two-component system", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Two-component system"]}},{"id": "Type I diabetes mellitus", "metadata": {"KEGG_Pathways": ["Human Diseases", "Metabolic Diseases", "Type I diabetes mellitus"]}},{"id": "Type II diabetes mellitus", "metadata": {"KEGG_Pathways": ["Human Diseases", "Metabolic Diseases", "Type II diabetes mellitus"]}},{"id": "Tyrosine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Tyrosine metabolism"]}},{"id": "Ubiquinone and other terpenoid-quinone biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Ubiquinone and other terpenoid-quinone biosynthesis"]}},{"id": "Ubiquitin system", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Folding, Sorting and Degradation", "Ubiquitin system"]}},{"id": "VEGF signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "VEGF signaling pathway"]}},{"id": "Valine, leucine and isoleucine biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Valine, leucine and isoleucine biosynthesis"]}},{"id": "Valine, leucine and isoleucine degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Amino Acid Metabolism", "Valine, leucine and isoleucine degradation"]}},{"id": "Various types of N-glycan biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Glycan Biosynthesis and Metabolism", "Various types of N-glycan biosynthesis"]}},{"id": "Vascular smooth muscle contraction", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Circulatory System", "Vascular smooth muscle contraction"]}},{"id": "Vasopressin-regulated water reabsorption", "metadata": {"KEGG_Pathways": ["Organismal Systems", "Excretory System", "Vasopressin-regulated water reabsorption"]}},{"id": "Vibrio cholerae infection", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Vibrio cholerae infection"]}},{"id": "Vibrio cholerae pathogenic cycle", "metadata": {"KEGG_Pathways": ["Human Diseases", "Infectious Diseases", "Vibrio cholerae pathogenic cycle"]}},{"id": "Viral myocarditis", "metadata": {"KEGG_Pathways": ["Human Diseases", "Cardiovascular Diseases", "Viral myocarditis"]}},{"id": "Vitamin B6 metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Cofactors and Vitamins", "Vitamin B6 metabolism"]}},{"id": "Wnt signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "Wnt signaling pathway"]}},{"id": "Xylene degradation", "metadata": {"KEGG_Pathways": ["Metabolism", "Xenobiotics Biodegradation and Metabolism", "Xylene degradation"]}},{"id": "Zeatin biosynthesis", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Terpenoids and Polyketides", "Zeatin biosynthesis"]}},{"id": "alpha-Linolenic acid metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Lipid Metabolism", "alpha-Linolenic acid metabolism"]}},{"id": "beta-Alanine metabolism", "metadata": {"KEGG_Pathways": ["Metabolism", "Metabolism of Other Amino Acids", "beta-Alanine metabolism"]}},{"id": "beta-Lactam resistance", "metadata": {"KEGG_Pathways": ["Metabolism", "Biosynthesis of Other Secondary Metabolites", "beta-Lactam resistance"]}},{"id": "mRNA surveillance pathway", "metadata": {"KEGG_Pathways": ["Genetic Information Processing", "Translation", "mRNA surveillance pathway"]}},{"id": "mTOR signaling pathway", "metadata": {"KEGG_Pathways": ["Environmental Information Processing", "Signal Transduction", "mTOR signaling pathway"]}},{"id": "p53 signaling pathway", "metadata": {"KEGG_Pathways": ["Cellular Processes", "Cell Growth and Death", "p53 signaling pathway"]}}],"columns": [{"id": "staggered", "metadata": null},{"id": "even", "metadata": null}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tempout.table Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,45 @@ +# Constructed from biom file +#OTU ID staggered even KEGG_Pathways +Amino Acid Metabolism 28955185.0 45374765.0 Metabolism; Amino Acid Metabolism +Biosynthesis of Other Secondary Metabolites 1737365.0 2923945.0 Metabolism; Biosynthesis of Other Secondary Metabolites +Cancers 282088.0 393993.0 Human Diseases; Cancers +Carbohydrate Metabolism 33779735.0 44900117.0 Metabolism; Carbohydrate Metabolism +Cardiovascular Diseases 18668.0 2002.0 Human Diseases; Cardiovascular Diseases +Cell Communication 26.0 21.0 Cellular Processes; Cell Communication +Cell Growth and Death 1340246.0 1728222.0 Cellular Processes; Cell Growth and Death +Cell Motility 3332193.0 4325524.0 Cellular Processes; Cell Motility +Cellular Processes and Signaling 12376427.0 16085447.0 Unclassified; Cellular Processes and Signaling +Circulatory System 27563.0 109603.0 Organismal Systems; Circulatory System +Development 0.0 0.0 Organismal Systems; Development +Digestive System 205590.0 268235.0 Organismal Systems; Digestive System +Endocrine System 311963.0 901422.0 Organismal Systems; Endocrine System +Energy Metabolism 16483126.0 22914670.0 Metabolism; Energy Metabolism +Environmental Adaptation 263572.0 488829.0 Organismal Systems; Environmental Adaptation +Enzyme Families 5457311.0 7759696.0 Metabolism; Enzyme Families +Excretory System 36303.0 100424.0 Organismal Systems; Excretory System +Folding, Sorting and Degradation 6690470.0 9464060.0 Genetic Information Processing; Folding, Sorting and Degradation +Genetic Information Processing 7466411.0 10678653.0 Unclassified; Genetic Information Processing +Glycan Biosynthesis and Metabolism 5153604.0 6993096.0 Metabolism; Glycan Biosynthesis and Metabolism +Immune System 38800.0 75125.0 Organismal Systems; Immune System +Immune System Diseases 141292.0 225122.0 Human Diseases; Immune System Diseases +Infectious Diseases 1734917.0 1799045.0 Human Diseases; Infectious Diseases +Lipid Metabolism 9430513.0 14243639.0 Metabolism; Lipid Metabolism +Membrane Transport 40619910.0 51257841.0 Environmental Information Processing; Membrane Transport +Metabolic Diseases 245399.0 327300.0 Human Diseases; Metabolic Diseases +Metabolism 7818926.0 11548413.0 Unclassified; Metabolism +Metabolism of Cofactors and Vitamins 13332788.0 18431813.0 Metabolism; Metabolism of Cofactors and Vitamins +Metabolism of Other Amino Acids 5175074.0 6958034.0 Metabolism; Metabolism of Other Amino Acids +Metabolism of Terpenoids and Polyketides 5806434.0 9500869.0 Metabolism; Metabolism of Terpenoids and Polyketides +Nervous System 174485.0 291743.0 Organismal Systems; Nervous System +Neurodegenerative Diseases 660119.0 1222484.0 Human Diseases; Neurodegenerative Diseases +Nucleotide Metabolism 11770630.0 16309025.0 Metabolism; Nucleotide Metabolism +Poorly Characterized 16616064.0 23170781.0 Unclassified; Poorly Characterized +RNA family 0.0 0.0 Genetic Information Processing; RNA family +Replication and Repair 23845775.0 31340489.0 Genetic Information Processing; Replication and Repair +Sensory System 0.0 0.0 Organismal Systems; Sensory System +Signal Transduction 6054447.0 7820067.0 Environmental Information Processing; Signal Transduction +Signaling Molecules and Interaction 503602.0 917661.0 Environmental Information Processing; Signaling Molecules and Interaction +Transcription 7071835.0 8709955.0 Genetic Information Processing; Transcription +Translation 14940935.0 19978123.0 Genetic Information Processing; Translation +Transport and Catabolism 585366.0 1330052.0 Cellular Processes; Transport and Catabolism +Xenobiotics Biodegradation and Metabolism 7799254.0 12542712.0 Metabolism; Xenobiotics Biodegradation and Metabolism \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/picrust_precalculated.loc.sample Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,11 @@ +#This is a sample file distributed with Galaxy. +# +# PICRUSt supplied files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/ +# +# files may be in gzipped format or unzipped +# +#<dbname> <file_base> +#16S 13_5 /path/to/file/16S_13_5_precalculated.tab.gz +#cog 13_5 /path/to/file/cog_13_5_precalculated.tab +#ko 13_5 /path/to/file/ko_13_5_precalculated.tab.gz +#rfam 13_5 /path/to/file/rfam_13_5_precalculated.tab.gz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,6 @@ +<tables> + <table name="picrust_precalculated" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/picrust_precalculated.loc" /> + </table> +</tables>