| Next changeset 1:76c040c8b9fc (2017-08-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c |
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added:
macros.xml normalize_by_copynumber.xml test-data/16S_13_5_precalculated_minimal.tab test-data/categorize_biom.hdf5 test-data/closed_picked_otus.biom test-data/closed_picked_otus.tab test-data/cog_predicted_metagenomes.L2.biom test-data/custom_trait_table.tab test-data/normalized_otus.biom test-data/normalized_otus.classic test-data/observation_table.biom test-data/otu_table_for_custom_trait_table.biom test-data/predicted_metagenomes.L3.biom test-data/tempout.table tool-data/picrust_precalculated.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 6273e2721fa3 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -0,0 +1,90 @@ +<macros> + <token name="@WRAPPER_VERSION@">1.0.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.0.1">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="json" selected="true">JSON</option> + <option value="hdf5">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="json"/> + <when input="output_type" value="tsv" format="tabular"/> + <when input="output_type" value="hdf5" format="hdf5"/> + </change_format> + </data> + </xml> + + <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[ + #if $output_type == "json": + && biom convert -i tempbiom -o '$out_biom' --to-json + #elif $output_type == "tsv": + && biom convert -i tempbiom -o '$out_biom' --to-tsv + #else + && biom convert -i tempbiom -o '$out_biom' --to-hdf5 + #end if + ]]></token> + + <token name="@PICRUST_OVERVIEW@"> +<![CDATA[ +**PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States** + +The PICRUSt project aims to support prediction of the unobserved character states in a community of +organisms from phylogenetic information about the organisms in that community. The primary application +is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only +marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative +bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs. + +For more information please visit: + +- Picrust Documentation: https://picrust.github.io/picrust/ +- Picrust GitHub: http://picrust.github.com/ +- Picrust Support: https://groups.google.com/d/forum/picrust-users + +**Reference Data** + +Precalculated files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/ + +]]> + </token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.2676</citation> + <yield/> + </citations> + </xml> + +</macros> |
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| diff -r 000000000000 -r 6273e2721fa3 normalize_by_copynumber.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalize_by_copynumber.xml Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -0,0 +1,61 @@ +<tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0"> + <description>OTUs by copy number</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + normalize_by_copy_number.py + -i '$input_data' + -o tempbiom + -c '$gg.precalc' + + @OUTPUT_CONVERSION_COMMANDS@ + ]]></command> + <inputs> + <param name="input_data" type="data" format="tabular,biom1" label="Input file" help="biom file or legacy QIIME OTU table"/> + <expand macro="otu-reference-precalculated"/> + <expand macro="biom_format_select"/> + </inputs> + <outputs> + <expand macro="biom_output"/> + </outputs> + <tests> + <test> <!-- test with biom input --> + <param name="input_data" value="closed_picked_otus.biom"/> + <param name="source" value="hist"/> + <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/> + <param name="output_type" value="json"/> + <output name="out_biom" ftype="json"> + <assert_contents> + <has_text text="Biological Observation Matrix"/> + <has_text text="generated_by"/> + </assert_contents> + </output> + </test> + <test> <!-- test with QIIME input and classic output --> + <param name="input_data" value="closed_picked_otus.tab"/> + <param name="source" value="hist"/> + <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/> + <param name="output_type" value="tsv"/> + <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/> + </test> + </tests> + <help> +<![CDATA[ +@PICRUST_OVERVIEW@ + +**Command Documenation** + +This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU. + +Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_. +A sample file can be downloaded here_ + +.. _guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html +.. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab +]]> + </help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/16S_13_5_precalculated_minimal.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/16S_13_5_precalculated_minimal.tab Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/categorize_biom.hdf5 |
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| Binary file test-data/categorize_biom.hdf5 has changed |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/closed_picked_otus.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closed_picked_otus.biom Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/closed_picked_otus.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closed_picked_otus.tab Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/cog_predicted_metagenomes.L2.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cog_predicted_metagenomes.L2.biom Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/custom_trait_table.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trait_table.tab Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/normalized_otus.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/normalized_otus.biom Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/normalized_otus.classic --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/normalized_otus.classic Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/observation_table.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/observation_table.biom Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/otu_table_for_custom_trait_table.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/otu_table_for_custom_trait_table.biom Thu Dec 08 06:28:17 2016 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 6273e2721fa3 test-data/predicted_metagenomes.L3.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/predicted_metagenomes.L3.biom Thu Dec 08 06:28:17 2016 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"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": [[0,0,4.0],[0,1,520.0],[1,0,11253380.0],[1,1,14766313.0],[3,0,40038.0],[3,1,207872.0],[4,0,8251.0],[4,1,7424.0],[5,0,2629787.0],[5,1,3843593.0],[7,0,273619.0],[7,1,349797.0],[8,0,782585.0],[8,1,1617459.0],[9,0,3877219.0],[9,1,5825383.0],[10,0,3487288.0],[10,1,4801487.0],[11,0,3208588.0],[11,1,4558273.0],[12,0,810978.0],[12,1,1433244.0],[13,0,31993.0],[13,1,62805.0],[14,0,139406.0],[14,1,291752.0],[15,0,10913.0],[15,1,27859.0],[16,0,37461.0],[16,1,18670.0],[17,0,191152.0],[17,1,224917.0],[18,0,3230253.0],[18,1,5657091.0],[20,0,408582.0],[20,1,543762.0],[21,0,260597.0],[21,1,398834.0],[23,0,705213.0],[23,1,740153.0],[24,0,30921.0],[24,1,11673.0],[25,0,1469523.0],[25,1,2186655.0],[26,0,1736700.0],[26,1,2233662.0],[27,0,247913.0],[27,1,477448.0],[28,0,2365.0],[28,1,9296.0],[29,0,1304315.0],[29,1,1830933.0],[30,0,957684.0],[30,1,2017640.0],[31,0,4.0],[31,1,2.0],[32,0,73103.0],[32,1,56023.0],[33,0,117478.0],[33,1,247280.0],[35,0,144022.0],[35,1,234998.0],[36,0,189245.0],[36,1,154809.0],[37,0,1410.0],[37,1,2666.0],[39,0,460516.0],[39,1,1004204.0],[40,0,58390.0],[40,1,149415.0],[41,0,351690.0],[41,1,543670.0],[42,0,266238.0],[42,1,377057.0],[43,0,15305.0],[43,1,55903.0],[44,0,2544556.0],[44,1,3874762.0],[45,0,116850.0],[45,1,157739.0],[46,0,1111533.0],[46,1,1439049.0],[47,0,62.0],[47,1,57.0],[48,0,2508.0],[48,1,85400.0],[49,0,36.0],[49,1,36.0],[50,0,233621.0],[50,1,887598.0],[51,0,42238.0],[51,1,46679.0],[52,0,426106.0],[52,1,672681.0],[53,0,1564477.0],[53,1,2069862.0],[54,0,3423917.0],[54,1,5415852.0],[55,0,27563.0],[55,1,109603.0],[56,0,207772.0],[56,1,319028.0],[58,0,170.0],[58,1,16.0],[59,0,1215970.0],[59,1,1657997.0],[61,0,146237.0],[61,1,241917.0],[62,0,307968.0],[62,1,608632.0],[63,0,119063.0],[63,1,246046.0],[64,0,6818.0],[64,1,4746.0],[65,0,2096405.0],[65,1,3376677.0],[66,0,1019609.0],[66,1,1117023.0],[67,0,58307.0],[67,1,179414.0],[69,0,3929087.0],[69,1,5661716.0],[72,0,2512.0],[72,1,85417.0],[73,0,2787766.0],[73,1,3646434.0],[74,0,1408.0],[74,1,2666.0],[75,0,18666.0],[75,1,2000.0],[76,0,6169.0],[76,1,658.0],[77,0,429275.0],[77,1,710029.0],[78,0,2700365.0],[78,1,3443871.0],[79,0,1.0],[82,0,447622.0],[82,1,1002838.0],[84,0,652223.0],[84,1,623437.0],[85,0,78674.0],[85,1,55663.0],[86,0,366805.0],[86,1,559930.0],[87,0,7983105.0],[87,1,10379144.0],[88,0,1879891.0],[88,1,2390086.0],[89,0,3255430.0],[89,1,3917884.0],[91,0,176058.0],[91,1,163412.0],[92,0,543218.0],[92,1,662487.0],[93,0,841415.0],[93,1,1197648.0],[94,0,26.0],[94,1,21.0],[95,0,86670.0],[95,1,105638.0],[96,0,1.0],[96,1,2.0],[97,0,6171.0],[97,1,658.0],[98,0,1339496.0],[98,1,2028140.0],[99,0,211712.0],[99,1,323256.0],[101,0,11525.0],[101,1,11642.0],[102,0,256598.0],[102,1,477181.0],[104,0,1807371.0],[104,1,2216964.0],[105,0,20326.0],[105,1,100307.0],[106,0,1419270.0],[106,1,2825371.0],[108,0,6170.0],[108,1,658.0],[109,0,709835.0],[109,1,395878.0],[110,0,6750.0],[110,1,10854.0],[111,0,20472.0],[111,1,96330.0],[112,0,36705.0],[112,1,118595.0],[113,0,26.0],[113,1,21.0],[114,0,1735901.0],[114,1,2251484.0],[115,0,2469292.0],[115,1,3037468.0],[116,0,4687776.0],[116,1,6566679.0],[119,0,1677847.0],[119,1,1937822.0],[121,0,11928288.0],[121,1,16604102.0],[122,0,336947.0],[122,1,1168819.0],[123,0,5706.0],[123,1,8734.0],[125,0,174485.0],[125,1,291743.0],[126,0,932339.0],[126,1,1175246.0],[128,0,72026.0],[128,1,63015.0],[129,0,1457117.0],[129,1,1817000.0],[130,0,1758852.0],[130,1,2144456.0],[131,0,2894248.0],[131,1,3765864.0],[132,0,4587003.0],[132,1,5451627.0],[135,0,20867.0],[135,1,133848.0],[136,0,11417.0],[136,1,105441.0],[137,0,22269.0],[137,1,140299.0],[140,0,1300662.0],[140,1,1516986.0],[141,0,1673703.0],[141,1,2550245.0],[142,0,6170.0],[142,1,658.0],[145,0,170.0]'..b's", "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}]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 6273e2721fa3 test-data/tempout.table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tempout.table Thu Dec 08 06:28:17 2016 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 6273e2721fa3 tool-data/picrust_precalculated.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/picrust_precalculated.loc.sample Thu Dec 08 06:28:17 2016 -0500 |
| b |
| @@ -0,0 +1,10 @@ +#This is a sample file distributed with Galaxy. +# +# PICRUSt supplied files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/ +# +# 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 |
| b |
| diff -r 000000000000 -r 6273e2721fa3 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Dec 08 06:28:17 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="picrust_precalculated" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/picrust_precalculated.loc" /> + </table> +</tables> |