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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647 |
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README.md RELEASE_NOTE.md affiliation_OTU.xml affiliation_postprocess.xml affiliations_stat.xml biom_to_stdBiom.xml biom_to_tsv.xml clustering.xml clusters_stat.xml demultiplex.xml filters.xml galaxy_project_logo_square.png itsx.xml normalisation.xml preprocess.xml r_alpha_diversity.xml r_beta_diversity.xml r_clustering.xml r_composition.xml r_import_data.xml r_manova.xml r_structure.xml remove_chimera.xml static/images/frogs_images/FROGS_affiliation_combined_percent_id.png static/images/frogs_images/FROGS_affiliation_overlapped_percent_id.png static/images/frogs_images/FROGS_affiliation_percent_id_formula.png static/images/frogs_images/FROGS_affiliation_stat_alignment.png static/images/frogs_images/FROGS_affiliation_stat_bootstrap.png static/images/frogs_images/FROGS_affiliation_stat_rarefaction.png static/images/frogs_images/FROGS_affiliation_stat_sunburst.png static/images/frogs_images/FROGS_affiliation_stat_taxonomies.png static/images/frogs_images/FROGS_affiliation_summary.png static/images/frogs_images/FROGS_cluster_stat_clusterDistrib1.png static/images/frogs_images/FROGS_cluster_stat_clusterDistrib2.png static/images/frogs_images/FROGS_cluster_stat_sample_dist1.png static/images/frogs_images/FROGS_cluster_stat_sample_dist2.png static/images/frogs_images/FROGS_cluster_stat_seq_dist.png static/images/frogs_images/FROGS_cluster_swarm.png static/images/frogs_images/FROGS_logo.png static/images/frogs_images/FROGS_preprocess_ampliconSize_multimodal_v3.png static/images/frogs_images/FROGS_preprocess_ampliconSize_unimodal_v3.png static/images/frogs_images/FROGS_preprocess_combined_sequence1.png static/images/frogs_images/FROGS_preprocess_combined_sequence2.png static/images/frogs_images/FROGS_preprocess_lengthsSamples.png static/images/frogs_images/FROGS_preprocess_lengthsSamples_v3.png static/images/frogs_images/FROGS_preprocess_overlapped_sequence.png static/images/frogs_images/FROGS_preprocess_summary_v3.png static/images/frogs_images/biomfile.png static/images/frogs_images/demultiplex_barcode.png static/images/frogs_images/demultiplex_fastq_ex.png static/images/frogs_images/frogs_tree_otufile.png static/images/frogs_images/nwk_treefile.png static/images/frogs_images/phyloseq_alpha_diversity_table.png static/images/frogs_images/phyloseq_bar_plot.png static/images/frogs_images/phyloseq_beta_diversity.png static/images/frogs_images/phyloseq_beta_diversity_matrix.png static/images/frogs_images/phyloseq_clustering_ward.png static/images/frogs_images/phyloseq_composition_plot.png static/images/frogs_images/phyloseq_import_data_html.png static/images/frogs_images/phyloseq_manova.png static/images/frogs_images/phyloseq_plot_heatmap_red.png static/images/frogs_images/phyloseq_plot_richness.png static/images/frogs_images/phyloseq_plot_richness_box.png static/images/frogs_images/phyloseq_plot_sample_ellipse.png static/images/frogs_images/phyloseq_rarefaction_curves.png static/images/frogs_images/phyloseq_samplefile.png test-data/databases/HVL_db.loc test-data/databases/HVL_db_data/Unite_extract_ITS1.fasta test-data/databases/frogs_db.loc test-data/databases/frogs_db_data/ITS1.rdp.fasta test-data/databases/frogs_db_data/ITS1.rdp.fasta.nhr test-data/databases/frogs_db_data/ITS1.rdp.fasta.nin test-data/databases/frogs_db_data/ITS1.rdp.fasta.nsq test-data/databases/frogs_db_data/ITS1.rdp.fasta.properties test-data/databases/frogs_db_data/ITS1.rdp.tax test-data/databases/frogs_db_data/bergeyTrainingTree.xml test-data/databases/frogs_db_data/genus_wordConditionalProbList.txt test-data/databases/frogs_db_data/logWordPrior.txt test-data/databases/frogs_db_data/wordConditionalProbIndexArr.txt test-data/databases/phiX_db.loc test-data/databases/phiX_db_data/phi.fa test-data/databases/phiX_db_data/phi.fa.nhr test-data/databases/phiX_db_data/phi.fa.nin test-data/databases/phiX_db_data/phi.fa.nsq test-data/input/chaillou.biom test-data/input/demultiplex_barcode.txt test-data/input/demultiplex_summary.txt test-data/input/demultiplex_test2_R1.fq test-data/input/demultiplex_test2_R2.fq test-data/input/sample_metadata.tsv test-data/input/test_dataset.tar.gz test-data/input/tree.nwk test-data/references/01-prepro-flash.fasta test-data/references/01-prepro-flash.html test-data/references/01-prepro-flash.log test-data/references/01-prepro-flash.tsv test-data/references/01-prepro-vsearch.fasta test-data/references/01-prepro-vsearch.html test-data/references/01-prepro-vsearch.log test-data/references/01-prepro-vsearch.tsv test-data/references/02-clustering.biom test-data/references/02-clustering.fasta test-data/references/02-clustering.log test-data/references/02-clustering_compo.tsv test-data/references/03-chimera.biom test-data/references/03-chimera.fasta test-data/references/03-chimera.log test-data/references/04-filters.biom test-data/references/04-filters.excluded test-data/references/04-filters.fasta test-data/references/04-filters.log test-data/references/05-itsx.html test-data/references/05-itsx.log test-data/references/06-affiliation.biom test-data/references/06-affiliation.html test-data/references/06-affiliation.log test-data/references/07-affiliation_postprocessed.compo.tsv test-data/references/07-affiliation_postprocessed.log test-data/references/08-clustersStat.html test-data/references/08-clustersStat.log test-data/references/09-affiliationsStat.html test-data/references/09-affiliationsStat.log test-data/references/10-biom2tsv-affiliation_multihit.tsv test-data/references/10-biom2tsv.log test-data/references/10-biom2tsv.tsv test-data/references/11-affiliation_multihit.tsv test-data/references/11-affiliation_std.biom test-data/references/11-biom2stdbiom.log test-data/references/12-tsv2biom.biom test-data/references/12-tsv2biom.fasta test-data/references/12-tsv2biom.log test-data/references/13-tree-mafft.log test-data/references/14-phylo_import.Rdata test-data/references/14-phylo_import.log test-data/references/15-phylo_composition.log test-data/references/16-phylo_alpha_div.log test-data/references/16-phylo_alpha_div.tsv test-data/references/17-phylo_beta_div.log test-data/references/18-phylo_structure.log test-data/references/19-phylo_clustering.log test-data/references/20-phylo_manova.log test-data/references/Unifrac.tsv test-data/references/normalisation.log test-data/references/normalisation_report.html tool-data/HVL_db.loc.sample tool-data/frogs_db.loc.sample tool-data/phiX_db.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test tree.xml tsv_to_biom.xml |
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| diff -r 000000000000 -r 59bc96331073 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Feb 28 10:14:49 2019 -0500 |
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| b'@@ -0,0 +1,331 @@\n+\xe2\x80\x8b\t\t\t\t\t<img src="static/images/frogs_images/FROGS_logo.png" width="20%" style="display: block; margin: auto;"/>\t\t\t\t\t<img src="galaxy_project_logo_square.png" width="20%" style="display: block; margin: auto;"/> \n+\n+\n+\n+Visit our web site : http://frogs.toulouse.inra.fr/\n+\n+[](https://github.com/geraldinepascal/FROGS-wrappers/releases)[<img src="https://www.podcastscience.fm/wp-content/uploads/2017/12/deezer.png" width="5%" style="display: block; margin: auto;"/>](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web)\n+\n+\n+\n+# Description\n+\n+FROGS is a workflow designed to produce an OTU count matrix from high depth sequencing amplicon data.\n+\n+FROGS-wrapper allow to add FROGS on a Galaxy instance.\n+\n+# Table of content\n+\n+* [Installing FROGS\\-wrappers](#installing-frogs-wrappers)\n+ * [Simplest way](#simplest-way)\n+ * [From sources](#from-sources)\n+ * [Prerequisites](#prerequisites)\n+ * [FROGS\\-wrappers installation](#frogs-wrappers-installation)\n+* [Use PEAR as reads merge software in preprocess](#use-pear-as-reads-merge-software-in-preprocess)\n+* [Upload and configure the databanks](#upload-and-configure-the-databanks)\n+* [Galaxy configuration](#galaxy-configuration)\n+ * [Setup Galaxy environment variables](#setup-galaxy-environment-variables)\n+ * [Install python packages inside virtual env](#install-python-packages-inside-virtual-env)\n+ * [Avoid FROGS HTML report sanitization](#avoid-FROGS-HTML-report-sanitization)\n+ * [Set memory and parallelisation settings](#set-memory-and-parallelisation-settings)\n+* [License](#license)\n+* [Copyright](#copyright)\n+* [Citation](#citation)\n+* [Contact](#contact)\n+\n+# Installing FROGS-wrappers\n+\n+## Simplest way\n+\n+FROGS is available on the Toolshed : https://toolshed.g2.bx.psu.edu/repository?repository_id=525e78406276b403&changeset_revision=76c750c5f0d1\n+\n+It will install FROGS thanks to [conda](https://anaconda.org/bioconda/frogs), download all these XML tools and well configure them in your Galaxy.\n+\n+The 22 FROGS tools will be in random order in your tools panel. We propose to control that order by modifying the `integrated_tool_panel.xml `. \n+\n+We suppose that you installed FROGS in a sp\xc3\xa9cific section named `FROGS` (update the FROGS version if necessary).\n+\n+```\n+<section id="FROGS" name="FROGS" version="">\n+\n+ <label text="OTUs reconstruction" id="FROGS_OTU" />\n+\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_demultiplex/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_preprocess/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_clustering/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_remove_chimera/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_filters/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_itsx/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliation_OTU/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliation_postprocess/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_normalisation/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_Tree/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_clusters_stat/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliations_stat/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_biom_to_stdBiom/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_biom_to_tsv/3.1" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_tsv_to_biom/3.1" />\n+\n+ <label text="OTUs structure and composition analysis" id="'..b'eq_Sample_Clustering\n+FROGSSTAT_Phyloseq_Structure_Visualisation\n+FROGS_Tree\n+FROGS_affiliation_OTU\n+FROGS_affiliations_stat\n+FROGS_clustering\n+FROGS_clusters_stat\n+FROGS_filters\n+FROGS_itsx\n+FROGS_normalisation\n+FROGS_preprocess\n+FROGS_remove_chimera\n+```\n+\n+## Set memory and parallelisation settings\n+\n+If you have more than one CPU, it is recommended to increase the number of CPUs used by tools.\n+\n+All CPUs must be on the same computer/node.\n+\n+\n+ * Specifications\n+\n+ | Tool | RAM per CPU | Minimal RAM | Configuration example |\n+ | :-------------------: | :---------: | :---------: | :-------------------: |\n+ | preprocess | 8Gb | - | 12 CPUs and 96 GB |\n+ | clustering | - | 10 Gb | 16 CPUs and 60 GB |\n+ | ITSx / remove_chimera | 3Gb | 5Gb | 12 CPUs and 36 GB |\n+ | affiliation_OTU | - | 20 Gb | 30 CPUs and 300 GB |\n+\n+ * Galaxy configuration\n+\n+ You need to add `destiantion` sections (one per tool) in the `<Galaxy-Dir>/config/job_conf.xml` \n+ Example for SGE scheduler:\n+\n+\n+```\n+<destinations>\n+\t...\n+\t<destination id="FROGS_preprocess_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=5G -l h_vmem=13G -pe parallel_smp 12</param>\n+\t</destination>\n+\t<destination id="FROGS_clustering_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=10G -pe parallel_smp 16</param>\n+\t</destination>\n+\t<destination id="FROGS_remove_chimera_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12</param>\n+\t</destination>\n+\t<destination id="FROGS_itsx_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12</param>\n+\t</destination>\n+\t<destination id="FROGS_affiliation_OTU_job" runner="drmaa">\n+\t\t<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>\n+\t\t<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>\n+\t\t<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>\n+\t\t<param id="nativeSpecification">-clear -q galaxyq -l mem=7G -l h_vmem=10G -pe parallel_smp 30</param>\n+\t</destination>\n+</destinations>\n+<tools>\n+...\n+\t<tool id="FROGS_preprocess" destination="FROGS_preprocess_job"/> \n+\t<tool id="FROGS_clustering" destination="FROGS_clustering_job"/> \n+\t<tool id="FROGS_remove_chimera" destination="FROGS_remove_chimera_job"/> \n+\t<tool id="FROGS_itsx" destination="FROGS_itsx_job"/> \n+\t<tool id="FROGS_affiliation_OTU" destination="FROGS_affiliation_OTU_job"/>\n+</tools>\n+```\n+\n+# License\n+ GNU GPL v3\n+\n+# Copyright\n+ 2018 INRA\n+\n+# Citation\n+ Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*\n+\n+# Contact\n+ frogs@inra.fr\n+\n' |
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| diff -r 000000000000 -r 59bc96331073 RELEASE_NOTE.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RELEASE_NOTE.md Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,20 @@ +# v3.1 [2018-02-12] + +This release corresponds to the FROGS 3.1.0 release. + +* ### Tools added: + + - ITSx : tool available for selecting and trimming ITS sequences based on ITSx tool + - Affiliation Postprocess : resolve ambiguities due to inclusiv ITS, and aggregated OTU based on + taxonomic affiliations + +* ### Modifications: + + - use tool data table instead of simple loc files for filters, affiliation_OTU and affiliation_postprocess + - Tree do no longer support Pynast alignment thanks to a template file + +# v2.0.0 [2018-12-11] + + First package. + +This release corresponds to the FROGS 2.0.0 release |
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| diff -r 000000000000 -r 59bc96331073 affiliation_OTU.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/affiliation_OTU.xml Thu Feb 28 10:14:49 2019 -0500 |
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| b'@@ -0,0 +1,198 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="3.1">\n+\t<description>Taxonomic affiliation of each OTU\'s seed by RDPtools and BLAST</description>\n+ \t<requirements>\n+ <requirement type="package" version="3.1.0">frogs</requirement>\n+ </requirements>\n+ \t<stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\t<command>\n+\t\t#set $reference_filename = str( $ref_file.fields.path )\n+\t\taffiliation_OTU.py \n+\t\t --reference "${reference_filename}"\n+\t\t --input-biom $biom_abundance \n+\t\t --input-fasta $fasta_sequences\n+\t\t --output-biom $biom_affiliation \n+\t\t --summary $summary \n+\t\t --nb-cpus \\${GALAXY_SLOTS:-1}\n+\t\t --java-mem $mem \n+\t\t #if $rdp\n+\t\t \t\t--rdp\n+\t\t \t#end if\n+\t</command>\n+\t<inputs>\n+\t\t<!-- JOB Parameter -->\n+\t\t<param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param>\n+\t\t<!-- Database Choice -->\n+\t\t<param name="ref_file" type="select" label="Using reference database" help="Select reference from the list">\n+\t \t\t<options from_data_table="frogs_db"></options>\n+\t\t\t<validator type="no_options" message="A built-in database is not available" />\n+\t\t</param> \n+ \t\t<param name="rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allow you to perform it also with RDP classifier (default No)" />\n+\t <!-- Files -->\n+\t <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/>\n+\t <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="OTU abundances (format: BIOM)."/>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation.biom" from_work_dir="affiliation.biom" />\n+\t\t<data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/>\n+\t</outputs>\n+ <tests>\n+ <test>\n+ <param name="ref_file" value="ITS1_test"/>\n+ <param name="fasta_sequences" value="references/04-filters.fasta"/>\n+ <param name="biom_abundance" value="references/04-filters.biom"/>\n+ <!-- <param name="fasta_sequences" value="swarm.fasta"/>\n+ <param name="biom_abundance" value="swarm.biom"/> -->\n+ <output name="biom_affiliation" file="references/06-affiliation.biom"/>\n+ <output name="summary" file="references/06-affiliation.html" compare="sim_size" delta="0" />\n+ </test>\n+ </tests>\n+\n+ \t<help>\n+\n+.. image:: static/images/frogs_images/FROGS_logo.png \n+ :height: 144\n+ :width: 110\n+\n+\n+.. class:: infomark page-header h2\n+\n+What it does\n+\n+Add taxonomic affiliation in abundance file.\n+\n+\n+.. class:: infomark page-header h2\n+\n+Inputs/outputs\n+\n+.. class:: h3\n+\n+Inputs\n+\n+**Sequence file**:\n+\n+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_'..b'oulouse.inra.fr/frogs_databanks/assignation/readme.txt\n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+.. csv-table:: \n+ :header: "Steps", "Description"\n+ :widths: 5, 150\n+ :class: table table-striped\n+\n+ "1", "`RDPClassifier <https://rdp.cme.msu.edu/tutorials/classifier/RDPtutorial_RDP_classifier.html>`_ may be used with database to associate to each OTU a taxonomy and a bootstrap (example: *Bacteria;(1.0);Firmicutes;(1.0);Clostridia;(1.0);Clostridiales;(1.0);Clostridiaceae 1;(1.0);Clostridium sensu stricto;(1.0);*)."\n+ "2", "`blastn+ <http://blast.ncbi.nlm.nih.gov/>`_ or `needlall <http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html>`_ is used to find alignment between each OTU and the database. Only the bests hits with the same score are reported. blastn+ is used for merged read pair, and needall is used for artificially combined sequence. For each alignment returned, several metrics are computed: identity percentage, coverage percentage, and alignment length"\n+ "3", "For each OTU with several blastn+/needlall alignment results a consensus is determined on each taxonomic level. If all the taxa in a taxonomic rank are identical the taxon name is reported otherwise *Multi-affiliation* is reported. By example, if you have an OTU with two corresponding sequences, the first is a *Bacteria;Proteobacteria;Gamma Proteobacteria;Enterobacteriales*, the second is a *Bacteria;Proteobacteria;Beta Proteobacteria;Methylophilales*, the consensus will be *Bacteria;Proteobacteria;Multi-affiliation;Multi-affiliation*."\n+\n+.. class:: infomark page-header h2\n+\n+Alignment metrics details on identity percentage calculation\n+\n+With classicala %id computation method, we will obtain for overlapped amplicon sequence and for artificially combined amplicon sequence :\n+\n+* **Case 1: a sequencing of overlapping sequences i.e. 16S V3-V4 amplicon MiSeq sequencing**\n+\n+.. image:: static/images/frogs_images/FROGS_affiliation_overlapped_percent_id.png\n+ :height: 325\n+ :width: 807\n+\n+* **Case 2 : a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**\n+\n+.. image:: static/images/frogs_images/FROGS_affiliation_combined_percent_id.png\n+ :height: 310\n+ :width: 887\n+\n+* **Finally, how percentage identity is computed ?**\n+\n+With the classical method of %id calculation, filtering on %id will systematically removed \xe2\x80\x9cFROGS combined\xe2\x80\x9d OTUs. So, we proposed to replace the classical %id by a %id computed on the sequenced bases only.\n+\n+.. image:: static/images/frogs_images/FROGS_affiliation_percent_id_formula.png\n+ :height: 36\n+ :width: 637\n+\n+For the precedent use cases we will obtain:\n+\n+* Case 1: 16S V3V4 overlapped sequence\n+\t% sequenced bases identity = 400 matches / 400 bp = 100%\n+\n+* Case 2: very large ITS1 \xe2\x80\x9cFROGS combined\xe2\x80\x9d shorter than the real sequence\n+\t% sequenced bases identity = (250 + 250 ) / (600 - 100) = 100%\n+\n+This calculation allows to return 100% of identity on sequenced bases for \xe2\x80\x9cFROGS combined\xe2\x80\x9d shorter or longer than reality in case of perfect sequencing, and a smaller percentage of identity in the case of small overlap repeat kept in FROGS combined sequence. \n+\n+.. class:: infomark page-header h2\n+\n+\n+Advices\n+\n+This tool can take large time. It is recommended to filter your abundance and your sequence file before this tool (see **FROGS Filters**).\n+\n+As you can see the affiliation of each OTU is not human readable in outputed abundance file. We provide a tools to convert these BIOM file in tabulated file, see the **FROGS BIOM to TSV** tool.\n+\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs@inra.fr\n+\n+Repository: https://github.com/geraldinepascal/FROGS\n+website: http://frogs.toulouse.inra.fr/\n+\n+Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*\n+\n+\t</help>\n+\t<citations>\n+\t\t<citation type="doi">10.1093/bioinformatics/btx791</citation>\n+\t</citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 59bc96331073 affiliation_postprocess.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/affiliation_postprocess.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,154 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="3.1"> + <description>Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + affiliation_postprocess.py + #if $is_HVL.HVL_amplicon + #set $reference_filename = str( $is_HVL.ref_file.fields.path ) + --reference "${reference_filename}" + #end if + --identity $identity + --coverage $coverage + --input-biom $biom_in + --input-fasta $fasta_in + --output-biom $biom_out + --output-fasta $fasta_out + --output-compo $compo_out + </command> + <inputs> + <!-- Files --> + <param format="biom1" name="biom_in" type="data" label="Abundance file of affiliated OTUs" help="Abundances of affiliated OTUs (format: BIOM)."/> + <param format="fasta" name="fasta_in" type="data" label="OTU seed sequences" help="OTU sequences (format: fasta)."/> + <conditional name="is_HVL"> + <param name="HVL_amplicon" type="boolean" label="Is this an hyper variable in length amplicon ?" help="Multi-affiliation tag may be resolved by selecting the shortest amplicon reference. For this you need the reference fasta file of your kind of amplicon."/> + <when value="true"> + <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> + <options from_data_table="HVL_db"></options> + <validator type="no_options" message="A built-in database is not available" /> + <!--column name="name" index="0"/> + <column name="value" index="1"/--> + </param> + </when> + <when value="false"/> + </conditional> + + <param name="identity" type="float" min="0.0" max="100.0" value="99.0" label="minimum identity for aggregation" help="OTUs will be aggregated if they share the same taxonomy with at least X% identity." /> + <param name="coverage" type="float" min="0.0" max="100.0" value="99.0" label="minimum coverage for aggregation" help="OTUs will be aggregated if they share the same taxonomy with at least X% alignment coverage." /> + </inputs> + <outputs> + <data format="biom1" name="biom_out" label="${tool.name}: affiliation.biom" from_work_dir="affiliation.biom" /> + <data format="fasta" name="fasta_out" label="${tool.name}: sequences.fasta" from_work_dir="sequences.fasta" /> + <data format="tabular" name="compo_out" label="${tool.name}: aggregation_composition.txt" from_work_dir="aggregation_composition.txt" /> + </outputs> + <tests> + <test> + <param name="biom_in" value="references/06-affiliation.biom"/> + <param name="fasta_in" value="references/04-filters.fasta"/> + <conditional name="is_HVL"> + <param name="HVL_amplicon" value="true"/> + <param name="ref_file" value="Unite_extract_ITS1_test"/> + </conditional> + <output name="compo_out" file="references/07-affiliation_postprocessed.compo.tsv"/> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +Resolves multi-hit ambiguities if exact amplicon length are available and aggregrated OTUs sharing same taxonomy based on alignment metrics thresholds + + +.. class:: infomark page-header h2 + +Inputs/outputs + +.. class:: h3 + +Inputs + +**Abundance file**: + +The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_) with taxonomic affiliations metadata. + +**Sequence file**: + +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_) of each OTU seed. + +**Reference file** (optionnal): + +The exact amplicon reference sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + + +.. class:: h3 + +Outputs + +**Abundance file**: + + The abundance file of OTUs and aggregated OTUs, with their affiliation (format `BIOM <http://biom-format.org/>`_) and with potentially less ambiguities. + +**Sequence file**: + +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_) of each aggregated OTU seed. + +**Composition file**: + +The aggregation composition file (format text) describing the composition of each resulting OTU. + +.. class:: infomark page-header h2 + +How it works + +If a reference fasta file is provided, for each OTU with multiaffiliation, among the different possible affiliations, we only keep the affiliation of the sequence with the shorter length. The aim is to resolve ambiguities due to potential inclusive sequences such as ITS. + +Second step is the OTUs aggregation that share the same taxonomy inferred on alignment metrics. +We start with the most abundant OTU. If an OTU shares at least one affiliation with another OTU with at least I% of identity and C% of alignment coverage, so the OTUs are aggregated together (The different affiliations, which then generate the multi-affiliation tag, are merged, abundance counts are summed). The seed of the most abundant OTU is kept. +---- + +**Contact** + +Support: please contact first your galaxy support team. + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 affiliations_stat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/affiliations_stat.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,175 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="3.1"> + <description>Process some metrics on taxonomies.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + affiliations_stat.py + --input-biom $biom + --output-file $summary_file + --rarefaction-ranks $rarefaction_ranks + #if $affiliation.affiliation_type == "FROGS_blast" + --taxonomic-ranks Domain Phylum Class Order Family Genus Species + --multiple-tag "blast_affiliations" + --tax-consensus-tag "blast_taxonomy" + --identity-tag "perc_identity" + --coverage-tag "perc_query_coverage" + #else if $affiliation.affiliation_type == "FROGS_rdp" + --taxonomic-ranks Domain Phylum Class Order Family Genus Species + --taxonomy-tag "rdp_taxonomy" + --bootstrap-tag "rdp_bootstrap" + #else + --taxonomic-ranks $affiliation.taxonomic_ranks + --taxonomy-tag "$affiliation.taxonomy_tag" + #if $affiliation.bootstrap_tag + --bootstrap-tag "$affiliation.bootstrap_tag" + #end if + #if $affiliation.identity_tag and $affiliation.coverage_tag + --identity-tag "$affiliation.identity_tag" + --coverage-tag "$affiliation.coverage_tag" + #end if + #end if + </command> + <inputs> + <!-- Files --> + <param format="biom1" name="biom" type="data" label="Abundance file" help="OTUs abundances and affiliations (format: BIOM)." optional="false" /> + <!-- Parameters --> + <param name="rarefaction_ranks" type="text" label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space." optional="false" value="Class Order Family Genus Species" size="80" /> + <conditional name="affiliation"> + <param name="affiliation_type" type="select" label="Affiliation processed" help="Select the type of affiliation processed. If your affiliation has been processed with an external tool: use 'Custom'."> + <option value="FROGS_blast" selected="true">FROGS blast</option> + <option value="FROGS_rdp">FROGS rdp</option> + <option value="custom">Custom</option> + </param> + <when value="FROGS_blast"></when> + <when value="FROGS_rdp"></when> + <when value="custom"> + <param name="taxonomic_ranks" type="text" label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space." optional="false" value="Domain Phylum Class Order Family Genus Species" size="80" /> + <param name="taxonomy_tag" type="text" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy." optional="false" value="taxonomy" size="20" /> + <param name="bootstrap_tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap." value="" size="20" /> + <param name="identity_tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity." value="" size="20" /> + <param name="coverage_tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment OTUs coverage." value="" size="20" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="biom" value="references/06-affiliation.biom" /> + <param name="rarefaction_ranks" value="Family Genus Species" /> + <conditional name="affiliation"> + <param name="affiliation_type" value="FROGS_blast" /> + <param name="taxonomic_ranks" value="Domain Phylum Class Order Family Genus Species" /> + <param name="taxonomy_tag" value="blast_taxonomy" /> + <param name="identity_tag" value="perc_identity" /> + <param name="coverage_tag" value="perc_query_coverage" /> + <!-- pas de parametre dans le formulaire pour multiple-tag, uniquement une option dans la ligne de commande --> + </conditional> + <output name="summary_file" file="references/09-affiliationsStat.html" compare="sim_size" delta="0" /> + <!-- log-file option presente dans la ligne de commande dans le test.sh n'apparait pas du tout ici --> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +FROGS Affiliations stat computes several metrics and generates a HTML file describing OTUs based on their taxonomies and the quality of the affiliations. + + +.. class:: infomark page-header h2 + +Input/output + +.. class:: h3 + +Input + +**Abundance file**: + +The abundance and affiliation of each OTUs in each sample (format `BIOM <http://biom-format.org/>`_). This file can be produced by FROGS Affiliation OTU. + +The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format. + +.. class:: h3 + +Output + +**Summary file** (summary.html): + + OTUs taxonomies and affiliations metrics (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + + *-Taxonomy distribution*: display the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_taxonomies.png + :height: 380 + :width: 650 + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_rarefaction.png + :height: 380 + :width: 550 + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_sunburst.png + :height: 380 + :width: 430 + + -Bootstrap distribution: display for affiliation methods with bootstrap the bootstrap on each taxonomic rank + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_bootstrap.png + :height: 380 + :width: 650 + + -Alignment distribution: display for affiliation methods with alignment the distribution of identity/covrage + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_alignment.png + :height: 380 + :width: 650 + + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 biom_to_stdBiom.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biom_to_stdBiom.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,108 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="3.1"> + <description>Converts a FROGS BIOM in fully compatible BIOM.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + biom_to_stdBiom.py + --input-biom $input_biom + --output-biom $output_biom + --output-metadata $output_blast_details + </command> + <inputs> + <!-- Files --> + <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The FROGS BIOM file to convert (format: BIOM)." optional="false" /> + </inputs> + <outputs> + <data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom"/> + <data format="tabular" name="output_blast_details" label="${tool.name}: blast_details.tsv" from_work_dir="blast_details.tsv" /> + </outputs> + <tests> + <test> + <param name="input_biom" value="references/06-affiliation.biom"/> + <output name="output_biom" value="references/11-affiliation_std.biom"/> + <output name="output_blast_details" value="references/11-affiliation_multihit.tsv"/> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +Converts a BIOM generated by FROGS in generic BIOM. + +The detailed blast affiliations can trigger problem with tools like Qiime. This tool extracts the blast details in a second file and writes a BIOM usable in every tools using BIOM. + +.. class:: h3 + +Inputs + +**Abundance file**: + +The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). + +.. class:: h3 + +Outputs + +**Abundance file**: + + The abundance without the ambiguous blast details (format `BIOM <http://biom-format.org/>`_). + +**Blast details file**: + + The details for each alignment on clusters (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). + + +.. class:: infomark page-header h2 + +How it works + +FROGS BIOM to std BIOM extracts the blast alignment details in a second file, write a BIOM usable in every tools using BIOM and defined the consensus taxonomy provided by blast as main taxonomy. + + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 biom_to_tsv.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biom_to_tsv.xml Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,130 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="3.1"> + <description>Converts a BIOM file in TSV file.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + biom_to_tsv.py + --input-biom $biom_file + #if $sequence_file + --input-fasta $sequence_file + #end if + --output-tsv $tsv_file + #if $extract_multi_align + --output-multi-affi $multi_affi_file + #end if + </command> + <inputs> + <!-- Files --> + <param format="biom1" name="biom_file" type="data" label="Abundance file" help="The BIOM file to convert (format: BIOM)." optional="false" /> + <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta). If you use this option the sequences will be add in TSV." optional="true" /> + <!-- Parameters --> + <param name="extract_multi_align" type="boolean" label="Extract multi-alignments" help="If you have used FROGS affiliation on your data, you can extract information about multiple alignements in a second TSV." checked="true"/> + </inputs> + <outputs> + <data format="tabular" name="tsv_file" label="${tool.name}: abundance.tsv" from_work_dir="abundance.tsv"/> + <data format="tabular" name="multi_affi_file" label="${tool.name}: multi_hits.tsv" from_work_dir="multi_hits.tsv" > + <filter>extract_multi_align</filter> + </data> + </outputs> + <tests> + <test> + <param name="biom_file" value="references/06-affiliation.biom"/> + <param name="sequence_file" value="references/04-filters.fasta"/> + <param name="extract_multi_align" value="true"/> + <output name="tsv_file" value="references/10-biom2tsv.tsv"/> + <output name="multi_affi_file" value="references/10-biom2tsv-affiliation_multihit.tsv"/> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +Converts a BIOM file in TSV file. + +.. class:: h3 + +Inputs + +**Abundance file**: + +The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). + +**Sequence file [optional]**: + +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + +.. class:: h3 + +Outputs + +**Abundance file**: + + The abundance of each cluster in each sample and theirs metadata (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). + + If you add the sequences file, this information is added for each cluster. + +**Multiple affiliation file**: + + If you have used *FROGS affiliation* on your data, each OTU can have several affiliations: several alignments with same score on reference database. The multiple affiliation file contains details on these possibles affiliations (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). + + +.. class:: infomark page-header h2 + +How it works + +FROGS Biom to Tsv will search if any metadata are available, and the OTU sequence if fasta file is precised. Then it will extract the OTU name, sum the abundance, and extract the detailed abundance for each sample. Finally it will write all these fields separated by tabulation in the TSV file. + + +.. class:: infomark page-header h2 + +Advices + +This output tsv file is easily readable in any spreadsheet software. Be aware that these software have a number of line limit (1 048 576 for Excel and LibreOffice calc ate least). If you have more OTU, use **FROGS Filters** to extract for example the most abundant OTU before converting your BIOM abundance table in TSV file. + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 clustering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustering.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,178 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_clustering" name="FROGS Clustering swarm" version="3.1"> + <description>Single-linkage clustering on sequences</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + clustering.py + --nb-cpus \${GALAXY_SLOTS:-1} + --distance $maximal_distance + --input-fasta $sequence_file + --input-count $count_file + --output-biom $abundance_biom + --output-fasta $seed_file + --output-compo $swarms_composition + $denoising + </command> + <inputs> + <!-- Files --> + <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" /> + <param format="tabular" name="count_file" type="data" label="Count file" help="It contains the count by sample for each sequence (format: TSV)." optional="false" /> + <!-- Parameters --> + <param name="maximal_distance" type="integer" label="Aggregation distance" help="Maximum number of differences between sequences in each aggregation step." value="3" min="1" max="15" optional="false" /> + <param name="denoising" type="boolean" checked="true" truevalue="--denoising" falsevalue="" label="Performe denoising clustering step?" help="If checked, clustering will be perform in two steps, first with distance = 1 and then with your input distance"/> + </inputs> + <outputs> + <data format="fasta" name="seed_file" label="${tool.name}: seed_sequences.fasta" from_work_dir="seeds.fasta"/> + <data format="biom1" name="abundance_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" /> + <data format="tabular" name="swarms_composition" label="${tool.name}: swarms_composition.tsv" from_work_dir="swarms.tsv"/> + </outputs> + <tests> + <test> + <param name="sequence_file" value="references/01-prepro-vsearch.fasta"/> + <param name="count_file" value="references/01-prepro-vsearch.tsv"/> + <param name="maximal_distance" value="3"/> + <param name="denoising" value="true"/> + <output name="seed_file" file="references/02-clustering.fasta" compare="sim_size" delta="0" /> + <!-- output name="abundance_biom" file="references/02-clustering.biom" --> + <!-- Voila deux autres facon de comparer: (Mais ca ne marche pas dans ce cas car les fichiers générés par planemo sont vraiments différents comparé à nos test manuels (cf. /tmp/frogs-test-result-olivier /tmp/frogs-test-result-olivier2) --> + <!-- cf. https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests-test-output --> + <!--output name="abundance_biom" file="references/02-clustering.biom" compare="sim_size" delta="10"/--> + <!--output name="abundance_biom" file="references/02-clustering.biom" compare="diff" lines_diff="1"/--> + <output name="swarms_composition" file="references/02-clustering_compo.tsv" compare="sim_size" delta="0" /> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +Single-linkage clustering on sequences. + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Inputs + +**Sequences file**: + +The sequence file with all samples sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). These sequences are dereplicated: strictly identical sequence are represented only one and the initial count is kept in count file. + +The sequence ID must be "sequenceID;size=X" with X equal to the total abundance among all samples. + +*It corresponds to one output of FROGS Pre-process tools.* + +**Count file**: + +This file contains the count of all uniq sequences in each sample (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). + +Example:: + + #id splA splB + seq1 1289 2901 + seq2 3415 0 + + +.. class:: h3 + +Outputs + +**Abundance file** (abundance.biom): + + The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). This format is widely used in metagenomic softwares. + + +**Clusters seeds** (seed_sequences.fasta): + + The clusters representative sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + + +**Clusters composition** (swarms_composition.tsv): + + A text file representing the read composition of each cluster (format txt). Each line represents one cluster and is composed of read identifier separated by space. + + +.. class:: infomark page-header h2 + +How it works + +.. csv-table:: + :header: "Steps", "With denoising", "Without denoising" + :widths: 5, 150, 150 + :class: table table-striped + + "1", "Sorting the reads by their abundance", "Sorting the reads by their abundance" + "2", "Clusters the reads (`Swarm <https://github.com/torognes/swarm>`_). The distance parameter is 1", "/" + "3", "Sorting the pre-clusters by their abundance", "/" + "4", "Clusters the pre-clusters (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specify", "Clusters the reads (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specify" + +**Swarm focus** + +Swarm use an iterative growth process and the use of sequence abundance values to delineate OTUs. + +.. image:: static/images/frogs_images/FROGS_cluster_swarm.png + :height: 223 + :width: 666 + +In each groth step the sequence of the previous step is used to find the others sequences with a number of differences inferior or equal to the "Aggregation distance". + +After agregation Swarm refines the clusters by looking at the abundancies along the connections. Theoritically the abundances must decrease when you are going away from the seed (which is often the most abundant sequence). If this abundance raises again it means that two different clusters are connected by some poorly abundant sequences, so swarm cut the connection. + + +.. class:: infomark page-header h2 + +Advices + +The denoising step allows to build very fine clusters with minimal differences. In this case, the number of differences is equal at 1 between sequences of each crowns. This first clustering is extremly quick. After the denoising, a second swarm is run with an aggregation distance >1 as you have configured, between seeds from this first clustering. + +To have some metrics on your clusters, you can use the tool **FROGS Clusters Stat**. + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
| b |
| diff -r 000000000000 -r 59bc96331073 clusters_stat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clusters_stat.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,128 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="3.1"> + <description>Process some metrics on clusters.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + clusters_stat.py + --input-biom $biom + --output-file $summary_file + </command> + <inputs> + <param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)." optional="false" /> + </inputs> + <outputs> + <data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="biom" value="references/06-affiliation.biom"/> + <output name="summary_file" value="references/08-clustersStat.html" compare="sim_size" delta="0"/> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +FROGS Clusters stat computes several metrics and generates a HTML file describing clusters based on abundances, samples, ... + + +.. class:: infomark page-header h2 + +Input/output + +.. class:: h3 + +Input + +**Abundance file**: + +The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). + +The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format. + +.. class:: h3 + +Output + +**Summary file** (summary.html): + + Clusters metrics (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + + *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables + + .. image:: static/images/frogs_images/FROGS_cluster_stat_clusterDistrib1.png + :height: 426 + :width: 520 + + .. image:: static/images/frogs_images/FROGS_cluster_stat_clusterDistrib2.png + :height: 300 + :width: 460 + + *Sequences distributions* : describes the sequences distribution among clusters + + .. image:: static/images/frogs_images/FROGS_cluster_stat_seq_dist.png + :height: 326 + :width: 473 + + *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering <http://en.wikipedia.org/wiki/Hierarchical_clustering>`_ on samples abundance profile (distance method = `braycurtis <http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis>`_, linkage method = average) + + .. image:: static/images/frogs_images/FROGS_cluster_stat_sample_dist1.png + :height: 400 + :width: 700 + + .. image:: static/images/frogs_images/FROGS_cluster_stat_sample_dist2.png + :height: 350 + :width: 610 + +.. class:: infomark page-header h2 + +Advices + +This is a very usefull tool to see the evolution of your OTU. Do not hesitate to run this tool after each FROGS step beginning at the clustering step. + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 59bc96331073 demultiplex.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/demultiplex.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,213 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_demultiplex" name="FROGS Demultiplex reads" version="3.1">\n+\t<description>Attribute reads to samples in function of inner barcode.</description>\n+ <requirements>\n+ <requirement type="binary">perl</requirement>\n+ <requirement type="package" version="3.1.0">frogs</requirement>\n+ <requirement type="package" version="1.10">perl-io-zlib</requirement>\n+ <requirement type="package" version="0.20">perl-io-gzip</requirement>\n+ <!--requirement type="package">perl</requirement-->\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\t<command>\n+\t\tdemultiplex.py\n+\t\t#if str( $fastq_input.fastq_input_selector ) == "paired":\n+\t\t --input-R1 "${fastq_input.fastq_input1}" \n+\t\t --input-R2 "${fastq_input.fastq_input2}"\n+\t\t#else:\n+\t\t --input-R1 "${fastq_input.fastq_input1}"\n+\t\t#end if \n+\t\t --input-barcode $barcode_file\n+\t\t --mismatches $mismatches\n+\t\t --end $end\n+\t\t --summary $summary\n+\t\t --output-demultiplexed $demultiplexed_archive\n+\t\t --output-excluded $undemultiplexed_archive\n+\t</command>\n+\t<inputs>\n+\t\t<!-- Input file -->\n+\t\t<param format="tabular" name="barcode_file" type="data" label="Barcode file" help="This file describes barcodes and samples (one line by sample tabulated separated from barcode sequence(s)). See Help section" optional="false" />\n+\t\t\n+\t\t<conditional name="fastq_input">\n+\t \t<param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single-end data">\n+\t \t\t<option value="single">Single</option>\n+\t \t<option value="paired">Paired</option>\n+\t </param>\n+\t \t<when value="paired">\n+\t \t<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" help="Specify dataset of your forward reads"/>\n+\t \t<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" help="Specify dataset of your reverse reads"/>\n+\t </when>\n+\t <when value="single">\n+\t \t<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" help="Specify dataset of your single end reads"/>\n+\t \t</when>\n+\t \t</conditional>\n+\n+\t\t<!-- Option -->\n+\t\t<param name="mismatches" type="integer" label="Barcode mismatches" help="Number of mismatches allowed in barcode" value="0" optional="false" />\n+\t\t<param name="end" type="select" label="Barcode on which end ?" help="The barcode is placed either at the beginning of the forward end or of the reverse end or both?">\n+\t\t\t<option value="bol" selected="true">Forward</option>\n+\t\t\t<option value="eol">Reverse</option>\n+\t\t\t<option value="both">Both ends</option>\n+\t\t</param>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data name="demultiplexed_archive" format="tar" label="${tool.name}: demultiplexed.tar.gz" from_work_dir="demultiplexed.tar.gz"/>\n+\t\t<data name="undemultiplexed_archive" format="tar" label="${tool.name}: undemultiplexed.tar.gz" from_work_dir="undemultiplexed.tar.gz"/>\n+\t\t<data name="summary" format="tabular" label="${tool.name}: report" from_work_dir="report.tsv"/>\n+\t</outputs>\n+ <tests>\n'..b'+ "-e/--end END", "To which end must the barcode be found : forward (begin of the (first) read), reverse (end of the (second) read) or both"\n+\n+.. csv-table:: Outputs\n+ :header: "Output name", "Meaning"\n+ :widths: 20, 80\n+ :class: table table-striped\n+\n+ "TXT_SUMMARY_OUTPUT", "A tabulated text file which summarises the number of sequences (single or paired) for each sample"\n+ "TARGZ_DEMULT_ARCHIVE_OUTPUT", "A TAR.GZ archive that contains all fastq files for each sample"\n+ "TARGZ_UNDEMULT_ARCHIVE_OUTPUT", "A TAR.GZ archive that contains all fastq files for undemultiplexed reads"\n+\n+.. class:: h3\n+\n+Format\n+\n+BARCODE_FILE :\n+ This file is expected to be tabulated\n+\t\t\n+ -first column corresponds to the sample name\n+ \n+ -second column corresponds to the sequence barcode used\n+ \n+ -third column (optional) corresponds to the reverse sequence barcode\n+ \n+.. class:: warningmark\n+\n+Take care to indicate sequence barcode in the strand of the read, so you may need to reverse complement the reverse barcode sequence\n+\n+.. class:: warningmark\n+\n+All barcode sequences must have the same length\n+ \n+Example of barcode file: Here the sample is multiplexed by both fragment ends.\n+\n+.. image:: static/images/frogs_images/demultiplex_barcode.png\n+ :height: 18\n+ :width: 286\n+\n+FASTQ : \n+ Text file describing biological sequences in a 4 line format: \n+\t\t\n+ -first line starts by "@" corresponds to the sequence identifier and optionally the sequence description\n+ \n+ -second line is the sequence itself\n+ \n+ -third line is a "+" following by the sequence identifier or not depending on the version\n+ \n+ -fourth line is the quality sequence, one code per base. The code depends on its version and the sequencer\n+ \n+`Click here for more details on the fastq format <https://en.wikipedia.org/wiki/FASTQ_format>`_\n+\n+Example of fastq read corresponding to the previous barcode file \n+\n+.. image:: static/images/frogs_images/demultiplex_fastq_ex.png\n+ :height: 57\n+ :width: 420\n+\n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+For each sequence or sequence pair, the sequence fragment at the beginning (forward multiplexing) of the (first) read or at the end (reverse multiplexing) of the (second) read will be compared to all barcodes of the barecode file.\n+\n+If this fragment is found once and only once (regarding the mismatch threshold), the fragment is trimmed and the sequence will be attributed to the corresponding sample.\n+\n+Finally fastq files (or pair of fastq files) for each sample are included in an archive and a report, describing how many sequences are attributed for each sample, is created.\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices\n+\n+Do not forget to indicate barcode sequence as they really are in the fastq sequence file, especially if you have multiplexed data via the reverse strand.\n+\n+For the mismatch threshold, we advised to let the threshold to 0. Then if you are not satisfied by the result try with 1. The number of mismatches depends on the length of the barcode, but frequently this sequences are very short so 1 mismatch is already more than the sequencing error rate.\n+\n+If you have different barcode lengths, you must demultiplex your data in several steps, beginning by the longest barcode set. Then to trim the barcodes with smaller lengths, you use the "unmatched" or "ambiguous" sequence file with smaller barcodes and so on.\n+\n+If you have Roche 454 sequences in sff format, you must convert them with some programs like `sff2fastq <https://github.com/indraniel/sff2fastq>`_ or sff_to_fastq (installable in Galaxy)\n+\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs@inra.fr\n+\n+Repository: https://github.com/geraldinepascal/FROGS\n+website: http://frogs.toulouse.inra.fr/\n+\n+Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*\n+\n+\t</help>\n+\t<citations>\n+\t\t<citation type="doi">10.1093/bioinformatics/btx791</citation>\n+\t</citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 filters.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filters.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,282 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_filters" name="FROGS Filters" version="3.1">\n+\t<description>Filters OTUs on several criteria.</description>\n+ <requirements>\n+ <requirement type="package" version="3.1.0">frogs</requirement>\n+ </requirements>\n+ <stdio> \n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\n+\t<command>\n+\n+\t\tfilters.py\n+\t\t\t--nb-cpus \\${GALAXY_SLOTS:-1} \n+\t\t\t--input-biom $input_biom \n+\t\t\t--input-fasta $input_fasta\n+\t\t\t--output-fasta $output_fasta\n+\t\t\t--output-biom $output_biom\n+\t\t\t--excluded $output_excluded\n+\t\t\t--summary $output_summary\n+\t\t\t#if $contaminations_filter.contaminations_filter_isApplied == "yes"\n+ \t\t#set $contaminants_filename = str( $contaminations_filter.contaminants_db.fields.path )\n+\t\t\t\t--contaminant $contaminants_filename\n+\t\t\t#end if\t \n+\t\t\t\n+\t\t\t#if $abundance_filters.abundance_filters_areApplied == "yes"\n+\t\t\t\t#if $abundance_filters.min_sample_presence\n+\t\t\t\t\t--min-sample-presence $abundance_filters.min_sample_presence\n+\t\t\t\t#end if\n+\t\t\t\t#if $abundance_filters.min_abundance\n+\t\t\t\t\t--min-abundance $abundance_filters.min_abundance\n+\t\t\t\t#end if\n+\t\t\t\t#if $abundance_filters.nb_biggest_otu\n+\t\t\t\t\t--nb-biggest-otu $abundance_filters.nb_biggest_otu\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\n+\t\t\t#if $RDP_filters.RDP_filters_areApplied == "yes"\n+\t\t\t\t--min-rdp-bootstrap $RDP_filters.rdp_rank:$RDP_filters.rdp_bootstrap\n+\t\t\t#end if\n+\t\t\n+\t\t\t#if $blast_filters.blast_filters_areApplied == "yes"\n+\t\t\t\t#if $blast_filters.min_blast_length\n+\t\t\t\t\t--min-blast-length $blast_filters.min_blast_length\n+\t\t\t\t#end if\n+\t\t\t\t#if $blast_filters.max_blast_evalue\n+\t\t\t\t\t--max-blast-evalue $blast_filters.max_blast_evalue\n+\t\t\t\t#end if\n+\t\t\t\t#if $blast_filters.min_blast_identity\n+\t\t\t\t\t--min-blast-identity $blast_filters.min_blast_identity\n+\t\t\t\t#end if\n+\t\t\t\t#if $blast_filters.min_blast_coverage\n+\t\t\t\t\t--min-blast-coverage $blast_filters.min_blast_coverage\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\t</command>\n+\t<inputs>\n+\t\t<!-- Files -->\n+\t\t<param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." />\n+\t\t<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." />\n+\t\t\n+\t\t<conditional name="abundance_filters">\n+\t\t\t<param name="abundance_filters_areApplied" type="select" label=" *** THE FILTERS ON OTUS IN SAMPLES, OTUS SIZE and SEQUENCE PERCENTAGE" help="If you want to filter OTUs on their abundance and occurrence." >\n+\t\t\t\t<option value="no">No filters</option>\n+\t\t\t\t<option value="yes">Apply filters</option>\n+\t\t\t</param>\n+\t\t\t<when value="no"></when>\n+\t\t\t<when value="yes">\n+\t\t\t\t<param name="min_sample_presence" type="integer" optional="true" label="Minimum number of samples" size="5" help="Fill the field only if you want this treatment. Keep OTU present in at least this number of samples." />\n+\t\t\t\t<param name="min_abundance" type="text" optional="true" label="Minimum proportion/number of sequences to keep OTU" size="5" help="Fill the field only if you want this treatment. Use decimal notation for proportion (example: 0.01 for keep OTU with at least 1% of all sequences) ; Use integer notation for number of sequence (example: 2 for keep OTU'..b'ces/03-chimera.biom" /> \n+\t\t <conditional name="abundance_filters">\n+\t \t \t<param name="abundance_filters_areApplied" value="yes" />\n+\t\t\t\t<param name="min_abundance" value="0.00005" />\t\n+\t\t\t\t<param name="min_sample_presence" value="3" />\n+\t\t </conditional>\n+\t\t <conditional name="contaminations_filter">\n+\t <param name="contaminations_filter_isApplied" value="yes" />\n+\t\t\t\t<param name="contaminants_db" value="phiX_test" />\t\n+\t\t </conditional>\n+\t \t <output name="output_fasta" file="references/04-filters.fasta" />\n+\t\t <output name="output_excluded" file="references/04-filters.excluded" />\n+\t </test>\n+\t</tests>\n+\t<help>\n+\n+.. image:: static/images/frogs_images/FROGS_logo.png\n+ :height: 144\n+ :width: 110\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+What it does\n+\n+Filter the OTUs of an abundance table according :\n+\n+ -The abundance and the occurence of OTUs: presence in samples, OTU size and maximum number of OTUs.\n+\n+ -The taxonomic affiliation produced by RDP: rank and bootstrap.\n+\n+ -The taxonomic affiliation produced by Blast: e-value, percentage of identity, percentage of coverage and alignment length.\n+ \n+ -Contamination: phiX a control added in Illumina sequencing technologies.\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+Inputs/outputs\n+\n+\n+.. class:: h3\n+\n+Inputs\n+\n+**Sequence file**:\n+\n+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n+\n+**Abundance file**:\n+\n+The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_).\n+\n+\n+.. class:: h3\n+\n+Outputs\n+\n+**Sequence file** (sequences.fasta):\n+\n+ The sequences after filtering (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n+\n+**Abundance file** (abundance.biom):\n+\n+ The abundance after filtering (format `BIOM <http://biom-format.org/>`_).\n+\n+**Excluded file** (excluded.txt):\n+\n+ The list of the OTUs deleted by filters (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_).\n+\n+**Summary file** (report.html):\n+\n+ The filters and the number of removed sequences (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+How it works\n+\n+\n+\n+\n+The OTUs kept are the ones that satisfy into the BIOM input file the thresholds specified by the user.\n+\n+The BIOM abundance table and the fasta file are written again according to the OTUs kept.\n+\n+The OTUs discarded are listed in the excluded file.\n+\n+.. csv-table:: \n+ :header: "Steps", "description"\n+ :widths: 5, 150\n+ :class: table table-striped\n+\n+ "1", "Except the filter to select the n most abundant OTUs, all the selected filters are run independently. For each filters an list of the OTUs to remove is generated."\n+ "2", "All the OTUs tagged to remove by at least one filter are removed."\n+ "3", "If the filter to select the N most abundant OTUs is filled it is applied."\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices\n+\n+Please check that the input fasta file and the input BIOM file correspond to the same OTUs.\n+\n+Examples for the filters on abundance and occurence of the OTUs : \n+\n+-To keep the filters that are present in 5 samples, fill the corresponding field with "5".\n+\n+-To display the 20 biggest OTU, fill the corresponding field with "20".\n+\n+-To filter on abundance, we advise you to specify 0.005%. It seems to be the optimal threshold (`Bokulich *et al*, 2013 <http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html>`_ ).\n+\n+If you use "FROGS Filters" before "FROGS Affiliation", the filters on RDP and Blast are useless.\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs@inra.fr\n+\n+Repository: https://github.com/geraldinepascal/FROGS\n+website: http://frogs.toulouse.inra.fr/\n+\n+Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*\n+\n+\t</help>\n+\t<citations>\n+\t\t<citation type="doi">10.1093/bioinformatics/btx791</citation>\n+\t</citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 59bc96331073 itsx.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/itsx.xml Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,154 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_itsx" name="FROGS ITSx" version="3.1"> + <description>Extract the highly variable ITS1 and ITS2 subregions from ITS sequences.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + itsx.py + --nb-cpus \${GALAXY_SLOTS:-1} + --region $region + --input-fasta $input_fasta + --input-biom $input_biom + --out-fasta $out_fasta + --out-abundance $out_abundance_biom + --out-removed $out_excluded + --summary $summary_file + $check_only + + </command> + <inputs> + <!-- Files --> + <param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." /> + <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." /> + <param name="region" type="select" label="ITS region" help="Which fungal ITS region is targeted: either ITS1 or ITS2" > + <option value="ITS1">ITS1</option> + <option value="ITS2">ITS2</option> + </param> + <param name="check_only" type="boolean" checked="false" truevalue="--check-its-only" falsevalue="" label="Check only if sequence detected as ITS ?" help="If Yes, sequences with ITS signature will be kept without trimming SSU, LSU or 5.8S regions."/> + </inputs> + <outputs> + <data format="fasta" name="out_fasta" label="${tool.name}: itsx.fasta" from_work_dir="itsx.fasta"/> + <data format="biom1" name="out_abundance_biom" label="${tool.name}: itsx.biom" from_work_dir="itsx.biom"/> + <data format="fasta" name="out_excluded" label="${tool.name}: out_removed.fasta" from_work_dir="out_removed.fasta"/> + <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/> + </outputs> + <tests> + <test> + <param name="input_fasta" value="references/04-filters.fasta"/> + <param name="input_biom" value="references/04-filters.biom"/> + <param name="region" value="ITS1"/> + <param name="check_only" value="false"/> + <output name="summary_file" file="references/05-itsx.html"/> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. + +.. class:: infomark page-header h2 + +Context + +The ITSx software identifies and extracts only ITS regions. It then excludes the highly conserved neighbouring sequences SSU, 5S and ARNr LSU. These sequences can lead to misleading results if they are conserved. +If the ITS1 or ITS2 region is not detected, the observation is discarded. + +You can choose to only check if the sequence is detected as an ITS. The sequence is not trimmed, only sequences not detected as ITS are discarded (contaminants by example). + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Inputs + +**Sequence file**: + +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + +**Abundance file**: + + The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). + + +.. class:: h3 + +Outputs + +**Sequence file** (itsx.fasta): + + The sequence file with only ITS1 or ITS2 part, or with the original sequence if check-its-only is choosen (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + +**Abundance file** (itsx.biom): + + The abundance file with only ITS sequences (format `BIOM <http://biom-format.org/>`_). + +**Discarded file** (out_removed.fasta) + + The sequence file with discarded sequences. + +**Summary file** (report.html): + + This file presents the summary of process (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). + + +.. class:: infomark page-header h2 + +How it works + +.. csv-table:: + :header: "Steps", "Description" + :widths: 10, 90 + :class: table table-striped + + "1", "Predicts positions of the ribosomal genes in the sequences (`ITSx <http://microbiology.se/software/itsx/>`_)." + "2", "Removes the sequences without prediction of the targeted ITS region (ITS1 or ITS2)." + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 normalisation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalisation.xml Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,122 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="3.1"> + <description>Normalize OTUs abundance.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + normalisation.py + --input-biom $input_biom + --input-fasta $input_fasta + --num-reads $num_reads + --output-biom $output_biom + --output-fasta $output_fasta + --summary-file $summary_file + </command> + <inputs> + <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalize (format: fasta)." /> + <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalize (format: BIOM)." /> + <param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." /> + </inputs> + <outputs> + <data format="fasta" name="output_fasta" label="${tool.name}: normalized.fasta" from_work_dir="normalized.fasta" /> + <data format="biom1" name="output_biom" label="${tool.name}: normalized.biom" from_work_dir="normalized.biom" /> + <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" /> + </outputs> + <tests> + <test> + <param name="input_fasta" value="references/04-filters.fasta"/> + <param name="input_biom" value="references/06-affiliation.biom"/> + <param name="num_reads" value="100"/> + <output name="summary_file" file="references/normalisation_report.html" compare="sim_size" delta="0" /> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +This tool keeps, in each sample, the same number of elements by random sampling. + +.. class:: infomark page-header h2 + +Inputs/outputs + +.. class:: h3 + +Inputs + +**Sequence file**: + +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + +**Abundance file**: + +The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_). + +.. class:: h3 + +Outputs + +**Sequence file** (normalised_seed.fasta): + + The normalised sequences file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + +**Abundance file** (normalised_abundance.biom): + + The normalised abundance file (format `BIOM <http://biom-format.org/>`_). + +**Summary file** (report.html): + + Information about discarded data (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). + + +.. class:: infomark page-header h2 + +Advices + +The number specified in "Number of reads" must be smaller than each total number of sequences by sample. + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 59bc96331073 preprocess.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/preprocess.xml Thu Feb 28 10:14:49 2019 -0500 |
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| b'@@ -0,0 +1,501 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_preprocess" name="FROGS Pre-process" version="3.1">\n+\t<description>merging, denoising and dereplication.</description>\n+ <requirements>\n+ <requirement type="package" version="3.1.0">frogs</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\t<command>\n+\t\tpreprocess.py $sequencer_type.sequencer_selected\n+\t\t--output-dereplicated $dereplicated_file --output-count $count_file --summary $summary_file \n+\t\t--nb-cpus \\${GALAXY_SLOTS:-1}\n+\t\t--min-amplicon-size $sequencer_type.min_amplicon_size --max-amplicon-size $sequencer_type.max_amplicon_size \n+\t\t\n+\t\t#if $sequencer_type.sequencer_selected == "illumina"\n+\t\t #if $sequencer_type.sequencing_protocol.sequencing_protocol_selected == "standard"\n+\t\t --five-prim-primer $sequencer_type.sequencing_protocol.five_prim_primer --three-prim-primer $sequencer_type.sequencing_protocol.three_prim_primer \n+\t\t #else\n+\t\t --without-primers\n+\t\t #end if\n+\t\t#else\n+\t\t --five-prim-primer $sequencer_type.five_prim_primer --three-prim-primer $sequencer_type.three_prim_primer \n+\t\t#end if\n+\t\t\n+\t\t#if $sequencer_type.input_type.input_type_selected == "archive" \n+\t\t --input-archive $sequencer_type.input_type.archive_file\n+\t\t #if $sequencer_type.sequencer_selected == "illumina" and $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged"\n+\t\t\t --already-contiged\n+\t\t #elif $sequencer_type.sequencer_selected == "illumina"\n+\t --R1-size $sequencer_type.input_type.archive_type.R1_size --R2-size $sequencer_type.input_type.archive_type.R2_size \n+\t \t--mismatch-rate $sequencer_type.input_type.archive_type.mm_rate\n+\t \t--merge-software $sequencer_type.input_type.archive_type.merge_software_type.merge_software_selected\n+\t \t#if $sequencer_type.input_type.archive_type.merge_software_type.merge_software_selected == "flash"\n+\t\t\t\t\t--expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size\n+\t\t\t#end if\n+\t \t#if $sequencer_type.input_type.archive_type.keep_unmerged\n+\t \t\t--keep-unmerged\n+\t \t#end if\n+\t\t #end if\n+\t\t#else\n+\t\t #set $sep = \' \'\n+\t\t #if $sequencer_type.sequencer_selected == "illumina"\n+\t --samples-names \n+\t #for $current in $sequencer_type.input_type.files_by_samples_type.samples \n+\t $sep"${current.name.strip()}"\n+\t #end for\n+\t\t --input-R1 \n+\t\t #for $current in $sequencer_type.input_type.files_by_samples_type.samples \n+\t\t $sep${current.R1_file}\n+\t\t #end for\n+\t\t #if $sequencer_type.input_type.files_by_samples_type.files_by_samples_type_selected == "already_merged"\n+\t\t --already-contiged\n+\t\t #else\n+\t\t --input-R2\n+\t\t #for $current in $sequencer_type.input_type.files_by_samples_type.samples \n+\t\t $sep${current.R2_file}\n+\t\t #end for\n+\t\t --R1-size $sequencer_type.input_type.files_by_samples_type.R1_size --R2-size $sequencer_type.input_type.files_by_samples_type.R2_size \n+\t\t --mismatch-rate $sequencer_type.input_type.files_by_samples_t'..b'n size - primer length\' and \'Maximum amplicon size - primer length\'", "the tool removes sequences with at least one homopolymer with more than seven nucleotides and with a distance of less than or equal to 10 nucleo-tides between two poor quality positions, i.e. with a Phred quality score lesser than 10" \n+ "4", "Dereplicates sequences", "Dereplicates sequences"\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices/details on parameters\n+\n+.. class:: h3\n+\n+What is the differency between overlapped sequences and combined sequences?\n+\n+- **Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing**\n+\n+.. image:: static/images/frogs_images/FROGS_preprocess_overlapped_sequence.png\n+ :height: 261\n+ :width: 531\n+\n+- **Case of a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**\n+\n+.. image:: static/images/frogs_images/FROGS_preprocess_combined_sequence1.png\n+ :height: 279\n+ :width: 797\n+\n+.. class:: warningmark\n+\n+**\xe2\x80\x9cFROGS combined\xe2\x80\x9d warning points**\n+\n+Reads pair are not merged because:\n+\n+\t- the real amplicon length is greater than de number of base sequences (500 bp for MiSeq 2x250bp)\n+\t- the overlapped region is smaller than 10 (fixed parameter in FROGS).\n+\n+Thus, \xe2\x80\x9cFROGS combined\xe2\x80\x9d sequences are artificial and present particular features especially on size.\n+Imagine a MiSeq sequencing of 2x250pb with sequences that cannot overlap, the resulting \xe2\x80\x9cFROGS combined\xe2\x80\x9d sequences length will be 600 bp.\n+\n+.. image:: static/images/frogs_images/FROGS_preprocess_combined_sequence2.png\n+ :height: 357\n+ :width: 798\n+\n+.. class:: h3\n+\n+Keeping or not un-merged paired reads\n+\n+This option is usefull when and only when, targeted amplicon is longer than the sequencing technology can provide (ITS amplicon for example). In other case, carefully, you will only keep noise in your analysis.\n+\n+\n+.. class:: h3\n+\n+Primers parameters\n+\n+The (`Kozich et al. 2013 <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/>`_ ) protocol uses custom sequencing primers which are also the PCR primers. In this case the reads do not contain the PCR primers.\n+\n+In case of Illumina standard protocol, the primers must be provided in 5\' to 3\' orientation. \n+\n+.. role:: alert-info\n+\n+Example:\n+\n+ 5\' :alert-info:`ATGCCC` GTCGTCGTAAAATGC :alert-info:`ATTTCAG` 3\'\n+ \n+ Value for parameter 5\' primer: ATGCCC\n+ \n+ Value for parameter 3\' primer: ATTTCAG\n+\n+.. class:: h3\n+\n+FLASH : Amplicons sizes parameters\n+\n+ The two following images show two examples of perfect values fors sizes parameters.\n+\n+ .. image:: static/images/frogs_images/FROGS_preprocess_ampliconSize_unimodal_v3.png\n+ :height: 415\n+ :width: 676\n+ \n+ .. image:: static/images/frogs_images/FROGS_preprocess_ampliconSize_multimodal_v3.png\n+ :height: 415\n+ :width: 676\n+\n+ Don\'t worry the "Expected amplicon size" does not need to be very accurate, and only necessary for sequences merging with FLASH.\n+\n+.. class:: h3\n+\n+If the filter \'merged\' reduce drasticaly the number of sequences:\n+\n+ In un-merged Illumina data, the reduction of dataset by the merged filter is classicaly inferior than 20%. A loss of more than 20% in all samples can highlight a quality problem.\n+ \n+ If the overlap between R1 and R2 is superior to 50 nucleotides and the quality of the end of the sequences is poor (see `FastQC <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_) you can try to cut the end of your sequences and relaunch the preprocess tool. You can either raise the mismatch percent in the overlapped region, but not too much!\n+\n+----\n+\n+**Contact**\n+\n+Contacts: frogs@inra.fr\n+\n+Repository: https://github.com/geraldinepascal/FROGS\n+website: http://frogs.toulouse.inra.fr/\n+\n+Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*\n+\n+\t</help>\n+\t<citations>\n+\t\t<citation type="doi">10.1093/bioinformatics/btx791</citation>\n+\t</citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 59bc96331073 r_alpha_diversity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_alpha_diversity.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,127 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.1"> + <description>with richness plot</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_alpha_diversity.py + --rdata $data + --varExp $varExp + --alpha-measures $measures + --alpha-out $alphaD + --html $html + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This file is the result of FROGS Phyloseq Import Data tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="measures" type="select" label="The alpha diversity indices to compute" multiple="true" display="checkboxes"> + <option value="Observed" selected="True">Observed</option> + <option value="Chao1" selected="True">Chao1</option> + <option value="Shannon" selected="True">Shannon</option> + <option value="InvSimpson" selected="True">InvSimpson</option> + <option value="Simpson">Simpson</option> + <option value="ACE">ACE</option> + <option value="Fisher">Fisher</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/> + <data format="html" name="html" label="${tool.name}: alpha_diversity.html" from_work_dir="alpha_diversity.html"/> + </outputs> + <tests> + <test> + <param name="data" value="references/14-phylo_import.Rdata" /> + <param name="varExp" value="EnvType" /> + <param name="measures" value="Observed,Chao1,Shannon" /> + <output name="alphaD" file="references/16-phylo_alpha_div.tsv" compare="diff" lines_diff="0" /> + </test> + </tests> +<help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool constructs richness plots to visualise sample alpha diversity. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**Data file** (format RData): +One phyloseq object containing OTU abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata. +This file is the result of "FROGS Phyloseq Import Data tool". + +.. class:: h3 + +Output + +**Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): the review of richness plots and rarefaction curves. + +.. image:: static/images/frogs_images/phyloseq_plot_richness.png + :height: 400 + :width: 525 + +.. image:: static/images/frogs_images/phyloseq_plot_richness_box.png + :height: 400 + :width: 499 + +.. image:: static/images/frogs_images/phyloseq_rarefaction_curves.png + :height: 400 + :width: 498 + +**Alpha diversity table** (alpha_diversity.tsv): +The data file containing table of alpha diversity indices. + +.. image:: static/images/frogs_images/phyloseq_alpha_diversity_table.png + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 59bc96331073 r_beta_diversity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_beta_diversity.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,145 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool name="FROGSSTAT Phyloseq Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.1"> + <description>distance matrix</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_beta_diversity.py + --rdata $data + --varExp $varExp + #if $methods != "None" + #if $other_method != "" + --distance-methods $methods,$other_method + #else + --distance-methods $methods + #end if + #else + #if $other_method != "" + --distance-methods $other_method + #end if + #end if + --matrix-outdir BetaMatrix + --html $html + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="methods" type="select" label="The methods of beta diversity" help="N.B. if the tree is not available in your RData, you cannot choose Unifrac or Weighted Unifrac" multiple="true" display="checkboxes"> + <option value="unifrac" selected="False">Unifrac</option> + <option value="wunifrac" selected="False">Weighted Unifrac</option> + <option value="bray" selected="False">Bray-Curtis</option> + <option value="cc" selected="False">Jaccard</option> + </param> + <param type="text" name="other_method" label="Other method" help="The other methods of beta diversity that you want to use (comma separated value). c.f. details below." optional="false" value="" size="40"/> + </inputs> + <outputs> + <data format="html" name="html" label="${tool.name}: beta_diversity" from_work_dir="beta_diversity.html"> + <discover_datasets pattern="__designation__" ext="tabular" directory="BetaMatrix" visible="true"/> + </data> + </outputs> + <tests> + <test> + <param name="data" value="references/14-phylo_import.Rdata" /> + <param name="varExp" value="EnvType" /> + <param name="methods" value="cc,unifrac" /> + <!--output name="html" file="references/17-phylo_beta_div.html" compare="sim_size" delta="0" /--> + <output name="html"> + <assert_contents> + <has_text_matching expression="html\sxmlns=.*" /> + <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" /> + </assert_contents> + </output> + </test> + </tests> + + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool compute beta distance matrix and display them in a heatmap + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format RData): +One phyloseq object containing OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. +This file is the result of "FROGS Phyloseq Import Data tool". + +**distance methods** : +The list of Phyloseq distanceMethodList is available here `distanceMethodList <https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf>`_ . +You have to copy the exact name as in this list in the parameter window "Other Method". +To use several methods, separate them by a space. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + +The review of beta diversity with heatmap plots: + +.. image:: static/images/frogs_images/phyloseq_beta_diversity.png + :height: 609 + :width: 800 + + +**beta diversity matrix** (format tabular): +The distance matrix of beta diversity. + + .. image:: static/images/frogs_images/phyloseq_beta_diversity_matrix.png + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
| b |
| diff -r 000000000000 -r 59bc96331073 r_clustering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_clustering.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,121 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.1"> + <description>of samples using different linkage methods</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_clustering.py + --html $html + --rdata $data + --varExp $varExp + --distance-matrix $method + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40"> + <validator type="empty_field" message="This parameter is required." /> + </param> + </inputs> + <outputs> + <data format="html" name="html" label="${tool.name}: clustering.html" from_work_dir="clustering.html"/> + </outputs> + <tests> + <test> + <param name="data" value="references/14-phylo_import.Rdata"/> + <param name="varExp" value="EnvType"/> + <param name="method" value="references/Unifrac.tsv"/> + <!--output name="html" file="references/19-phylo_structure.html" compare="sim_size" delta="0" /--> + <output name="html"> + <assert_contents> + <has_text_matching expression="html\sxmlns=.*" /> + <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" /> + </assert_contents> + </output> + + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool contructs the clustering plot for cluster analysis with different linkage methods. + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format RData): +The informations of data in one phyloseq object. +This is the result of FROGS Phyloseq Import Data tool. + +**distance file** (format tabular): +The data file containing beta diversity distance matrix. +This file is the result of FROGS Phyloseq Beta Diversity tool. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + +.. container:: row + + .. image:: static/images/frogs_images/phyloseq_clustering_ward.png + :height: 576 + :width: 768 + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 r_composition.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_composition.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,147 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="3.1"> + <description>with bar plot and composition plot</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_composition.py + --rdata $data + --varExp $varExp + --taxaRank1 $taxaRank1 + --taxaSet1 $taxaSet1 + --taxaRank2 $taxaRank2 + --numberOfTaxa $numberOfTaxa + --html $html + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="taxaRank1" type="text" label="Taxonomic level to filter your data" help="ex: Kingdom, Phylum, Class, Order, Family, Genus, Species" value="Kingdom" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="taxaSet1" type="text" label="Taxa (at the above taxonomic level) to keep in the dataset" help="ex: Bacteria (when filtering at the Kingdom level), Firmicutes (when filtering at the Phylum level). Multiple taxa (separated by a space) can be specified, i.e. Firmicutes Proteobacteria" value="Bacteria" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="taxaRank2" type="text" label="Taxonomic level used for aggregation" help="ex: Family (when filtering at the Phylum level). The aggregation level must be below the filtering level." value="Phylum" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="numberOfTaxa" type="text" label="Number of most abundant taxa to keep" help="ex: 9, i.e. Tool keeps the 9 most abundant taxa and the remaining taxa are aggregated in a group 'Other'" value="9" size="20"> + <validator type="empty_field" message="This parameter is required." /> + </param> + </inputs> + <outputs> + <data format="html" name="html" label="${tool.name}: composition.html" from_work_dir="composition.html"/> + </outputs> + <tests> + <test> + <param name="data" value="references/14-phylo_import.Rdata" /> + <param name="varExp" value="EnvType" /> + <param name="taxaRank1" value="Kingdom" /> + <param name="taxaSet1" value="Bacteria" /> + <param name="taxaRank2" value="Phylum" /> + <param name="numberOfTaxa" value="9" /> + <!--output name="html" file="references/15-phylo_composition.html" compare="sim_size" delta="0" /--> + <output name="html"> + <assert_contents> + <has_text_matching expression="html\sxmlns=.*" /> + <has_text_matching expression="application/json.*Sample: BHT0.LOT01" /> + </assert_contents> + </output> + </test> + </tests> + <help> +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and custom R function, this tool constructs two plots to visualise the sample composition: one at the OTU level and another one at the specified aggregation level (*e.g.* Phylum) after keeping only a subset of taxa (*e.g.* Bacteria at the level Kingdom). It helps answer the question: "What is the composition at the Phylum level within Bacteria?". By default, the plot exhibits only the abundance of the 9 most abundant taxa (as specified). In general, the representation of more than 10 taxa is hard to read on plots. + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format rdata): +One phyloseq object containing the OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. +this file is the result of FROGS Phyloseq Import Data tool. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): data composition plots. + +Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" : + + .. image:: static/images/frogs_images/phyloseq_bar_plot.png + :height: 646 + :width: 800 + +Composition plot: plot the most abundant sub taxonomic level among a selection of OTUs. + +- Selection of OTUs: + + - Taxonomic level name to subset: Kingdom + - Taxon name: Bacteria + +- Aggregation of OTUs : + + - Taxonomic level used to agglomerate: Phylum + +- Number of the most abundant taxa to keep: 5 + + .. image:: static/images/frogs_images/phyloseq_composition_plot.png + :height: 644 + :width: 800 + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 r_import_data.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_import_data.xml Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,138 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.1"> + <description>from 3 files: biomfile, samplefile, treefile </description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_import_data.py --biomfile $biomfile + + --samplefile $samplefile + #if $treefile + --treefile $treefile + #end if + --ranks "$ranks" + #if $normalization + --normalization + #end if + --html $html + --rdata $data + </command> + <inputs> + <!-- Files --> + <param format="biom1" name="biomfile" type="data" label="Standard biom file" help="The file contains the OTU informations (format: biom1)." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + + <param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + + <param format="nhx" name="treefile" type="data" label="Tree file" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" /> + + <!-- Parameters --> + <param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space." value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/> + <param name="normalization" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before analysis." optional="false" /> + </inputs> + <outputs> + <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/> + <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="biomfile" value="input/chaillou.biom"/> + <param name="samplefile" value="input/sample_metadata.tsv"/> + <param name="treefile" value="input/tree.nwk"/> + <output name="data" value="references/14-phylo_import.Rdata" compare="sim_size" delta="10"/> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq <https://joey711.github.io/phyloseq/>`_ object. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**OTU biom file**: + +The OTU biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). +This file is the result of FROGS BIOM to std BIOM. +The example of biom file: + + .. image:: static/images/frogs_images/biomfile.png + :height: 30 + :width: 733 + +**Newick file** (tree.nwk): + +Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree: + + .. image:: static/images/frogs_images/nwk_treefile.png + +**Sample file**: +The file contains the conditions of experiment with sample ID in the first column: + + .. image:: static/images/frogs_images/phyloseq_samplefile.png + :height: 115 + :width: 369 + +.. class:: h3 + +Output + +**Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. + + .. image:: static/images/frogs_images/phyloseq_import_data_html.png + +**Data file** (format rdata): The informations of data in one phyloseq object. + + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 r_manova.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_manova.xml Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,115 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="3.1"> + <description>perform Multivariate Analysis of Variance (MANOVA)</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_manova.py + --rdata $data + --varExp "$varExp" + --distance-matrix $method + --html $html + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40"> + <validator type="empty_field" message="This parameter is required." /> + </param> + </inputs> + <outputs> + <data format="html" name="html" label="${tool.name}: manova.html" from_work_dir="manova.html"/> + </outputs> + <tests> + <test> + <param name="data" value="references/14-phylo_import.Rdata"/> + <param name="varExp" value="EnvType"/> + <param name="method" value="references/Unifrac.tsv"/> + <!--output name="html" file="references/20-phylo_structure.html" compare="sim_size" delta="0" /--> + <output name="html"> + <assert_contents> + <has_text_matching expression="html\sxmlns=.*" /> + <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" /> + </assert_contents> + </output> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and `vegan <https://cran.r-project.org/web/packages/vegan/index.html>`_ functions to perform Multivariate Analysis of Variance (MANOVA) + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format RData): +The informations of data in one phyloseq object. +This is the result of FROGS Phyloseq Import Data tool. + +**distance file** (format tabular): +The data file containing beta diversity distance matrix. +This file is the result of FROGS Phyloseq Beta Diversity tool. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The review of Manova test. + +.. image:: static/images/frogs_images/phyloseq_manova.png + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 r_structure.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_structure.xml Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,131 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool name="FROGSSTAT Phyloseq Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="3.1"> + <description>with heatmap plot and ordination plot</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>r_structure.py + --html $html + --rdata $data + --varExp $varExp + --ordination-method $method + --distance-matrix $distance + </command> + <inputs> + <!-- Files --> + <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data Tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="distance" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity tool." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <!-- Parameters --> + <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param name="method" type="select" label="Ordination method"> + <option value="MDS" >MDS/PCoA</option> + <option value="NMDS" >NMDS</option> + <option value="DPCoA" >DPCoA</option> + </param> + </inputs> + <outputs> + <data format="html" name="html" label="${tool.name}: structure.html" from_work_dir="structure.html"/> + </outputs> + <tests> + <test> + <param name="data" value="references/14-phylo_import.Rdata" /> + <param name="varExp" value="EnvType" /> + <param name="method" value="MDS" /> + <param name="distance" value="references/Unifrac.tsv" /> + <!--output name="html" file="references/18-phylo_structure.html" compare="sim_size" delta="10" /--> + <output name="html"> + <assert_contents> + <has_text_matching expression="html\sxmlns=.*" /> + <has_text_matching expression="application/json.*DesLardons" /> + </assert_contents> + </output> + + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool constructs heatmap plot and ordination plot with the `ordination methods <https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods>`_ to visualise data structure. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format rdata): +The informations of data in one phyloseq object. +This file is the result of "FROGS Phyloseq Import Data tool". + +**distance file** (format tabular): +The data file containing beta diversity distance matrix. +This file is the result of "FROGS Phyloseq Beta Diversity tool". + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + +The review of data structure with an ordination plot and with an heatmap plot: + +.. image:: static/images/frogs_images/phyloseq_plot_sample_ellipse.png + :height: 343 + :width: 450 + +.. image:: static/images/frogs_images/phyloseq_plot_heatmap_red.png + :height: 343 + :width: 450 + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 remove_chimera.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/remove_chimera.xml Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,174 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="3.1"> + <description>Remove PCR chimera in each sample.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + remove_chimera.py + --nb-cpus \${GALAXY_SLOTS:-1} + --input-fasta $sequence_file --non-chimera $non_chimera_fasta + --summary $summary_file + #if $abundance_type.abundance_type_selected == "biom" + --input-biom $abundance_biom + --out-abundance $out_abundance_biom + #else + --input-count $abundance_count + --out-abundance $out_abundance_count + #end if + </command> + <inputs> + <!-- Files --> + <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" /> + <conditional name="abundance_type"> + <param name="abundance_type_selected" type="select" label="Abundance type" help="Select the type of file where the abundance of each sequence by sample is stored."> + <option value="biom" selected="true">BIOM file</option> + <option value="count">TSV file</option> + </param> + <when value="biom"> + <param format="biom1" name="abundance_biom" type="data" label="Abundance file" help="It contains the count by sample for each sequence." optional="false" /> + </when> + <when value="count"> + <param format="tabular" name="abundance_count" type="data" label="Count file" help="It contains the count by sample for each sequence (see below)." optional="false" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="fasta" name="non_chimera_fasta" label="${tool.name}: non_chimera.fasta" from_work_dir="non_chimera.fasta"/> + <data format="biom1" name="out_abundance_biom" label="${tool.name}: non_chimera_abundance.biom" from_work_dir="non_chimera_abundance.biom"> + <filter>abundance_type['abundance_type_selected'] == "biom"</filter> + </data> + <data format="tabular" name="out_abundance_count" label="${tool.name}: non_chimera_abundance.tsv" from_work_dir="non_chimera_abundance.tsv"> + <filter>abundance_type['abundance_type_selected'] == "count"</filter> + </data> + <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/> + </outputs> + <tests> + <test> + <param name="sequence_file" value="references/02-clustering.fasta"/> + <conditional name="abundance_type"> + <param name="abundance_type_selected" value="biom"/> + <param name="abundance_biom" value="references/02-clustering.biom" /> + </conditional> + <output name="non_chimera_fasta" file="references/03-chimera.fasta"/> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +Remove chimeric sequences by sample. + + +.. class:: infomark page-header h2 + +Context + +Chimeras are sequences formed from two or more biological sequences joined together. + +The majority of these anomalous sequences are formed from an incomplete extension during a PCR cycle. During subsequent cycles, a partially extended strand can bind to a template derived from a different but similar sequence. + +This phenomena is particularly common in amplicon sequencing where closely related sequences are amplified. + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Inputs + +**Sequence file**: + +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + +**Abundance file**: + + The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). + +OR + + The abundance of each sequence in each sample (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). This type of file is produced by *FROGS pre-process*. + + Example:: + + #id splA splB + seq1 1289 2901 + seq2 3415 0 + +.. class:: h3 + +Outputs + +**Sequence file** (non_chimera.fasta): + + The sequence file with only non-chimera (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + +**Abundance file** (non_chimera.biom or non_chimera.tsv): + + The abundance file with only non-chimera (format the same of the abundance input). + +**Summary file** (report.html): + + This file presents the number of removed elements (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). + + +.. class:: infomark page-header h2 + +How it works + +.. csv-table:: + :header: "Steps", "Description" + :widths: 10, 90 + :class: table table-striped + + "1", "Split input data by sample (classicaly the PCR is realised by sample)." + "2", "Find chimera in each sample (`vsearch <https://github.com/torognes/vsearch>`_)." + "3", "Remove the sequences identify as chimera in all samples where they are present." + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r 59bc96331073 test-data/databases/HVL_db.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/HVL_db.loc Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,34 @@ +# Copyright (C) 2014 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_affiliations_postprocess to solve +#inclusive amplicon sequence by selecting the smallest reference among multihit +#You will need to create or download exact amplicon sequence reference fasta file +#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL_reference +#Finally you will need to create HVL_db.loc file similar to this one in your galaxy +#tool-data directory.The HVL_db.loc file has this format (longer white space characters are +#TAB characters): +# +#<unique_database_name> <name> <file_path> +# +#First column will be the visible name in galaxy. +#So, for example, if you have UNITE 7.1 ITS1 (only!) stored +#in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta +#then the HVL_db.loc entry would look like this: +# +# +# EXAMPLE FOR TEST : +Unite_extract_ITS1_test Unite_extract_ITS1_test ${__HERE__}/HVL_db_data/Unite_extract_ITS1.fasta |
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| diff -r 000000000000 -r 59bc96331073 test-data/databases/HVL_db_data/Unite_extract_ITS1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/HVL_db_data/Unite_extract_ITS1.fasta Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,497 @@\n+>AB594796_SH278638.07FU_refs\n+GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGC\n+AGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTAC\n+CCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCG\n+TCTTATTTTAATAAGTCA\n+>AB747657_SH134902.07FU_refs\n+CTGAGTATTTGTCTTTTAAAGACATCTCTCTATCCATACACTCTTTTTTTTAAAAAGACA\n+TGATTTATACAGTTAGTCTGAATGATTTTTTAAAATCTTCA\n+>AF033454_SH086742.07FU_refs_singleton\n+AAGGATCATTACCGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATCGTACC\n+TCGTTGCTTCGGCGGGCCCGCCGCAAGGCCGCCGGGGGGCTTCTGCCCCCGGGCCCGTGC\n+CCGCCGAAGACACCATTGAACGCTGTCTGAAGATTGCAGTCTGAGCAATTAGCTAAATAA\n+GTTA\n+>AF033476_SH407699.07FU_refs\n+AAGGATCATTACCGAGTGAGGGCCCTTTGGGTCCAACCTCCCACCCGTGTTTATTTTACC\n+TTGTTGCTTCGGCGGGCCCGCCTTTACTGGCCGCCGGGGGGCTTCACGCCCCCGGGCCCG\n+CGCCCGCCGAAGACACCCTCGAACTCTGTCTGAAGATTGAAGTCTGAGTGAAAATATAAA\n+TTATTTA\n+>AF033486_SH207156.07FU_refs\n+AAGGATCATTACTGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTGTACC\n+TTGTTGCTTCGGCGGGCCCGCCCTAGTGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCG\n+CCCGCCGAAGACACCCTCGAACTCTGTCTGAAGATTGTAGTCTGAGTGGAATTATAAATT\n+ATTTA\n+>AF054858_SH194959.07FU_refs\n+CCGAGTTTACAACTCCCAAACCCCATGTGAACCTACCACTACGTTGCTTCGGCGGGATGC\n+CCCGGGCGCGGGCCGCAAGGCCTCAGCCCCGGAACCAGGCGCCCGCCGGAGGCCCAAACC\n+AAACTCTTGTTTTTATAGAATCTTCTGAGTGGCCTTTTAGGCAACAAATGAATCA\n+>AF118139_SH214931.07FU_refs\n+GAACCAGCGGAGGGATCATTAACGAGTTTCGTACTCCAAACCCTTTGTGAACATACCTGT\n+TTTCGTTGCTTCGGCAGGTGAAGGCGGAGGGCCTCCGGGCCTGAAGCCGCCGCCGGGCGG\n+ACCCCTCGCGGGGCGCTGCCGGGTGGGCCTGCCGGAGGGCACAGACTCTGTATTACAACG\n+TACCTCTCTGAGTTATATTTTACAAACAAGTAA\n+>AF456924_SH097201.07FU_refs\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATC\n+TCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAAC\n+TCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCG\n+TAGGCGTTTCGAAAATGAATCA\n+>AJ786644_SH470265.07FU_refs_singleton\n+CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCT\n+TTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGG\n+TGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAA\n+AACCTAATTATTA\n+>AY373856_SH207595.07FU_refs\n+CTGAGTGAGGGTCCCTCGGGGCCCAACCTCCCACCCGTGTATACCGTACCTTGTTGCTTC\n+GGCGAGCCCGCCCCCTTTTTCTTTTAGGGGGCACAGCGCTCGCCGGAGACACCAACGTGA\n+ACACTGTCTGAAGTTTTGTCGTCTGAGTCGATTGTATCGCAATCAGTTA\n+>AY443470_SH407688.07FU_refs\n+CGAGCGAGAATTCTCTGAATTCAACCTCCCACCCGTGTTTATTGTACCTTGTTGCTTCGG\n+CGGGCCCGCCTCACGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCCCGCCGAAGACA\n+CCTTGAACTCTGTATGAAAATTGCAGTCTGAGTCTAAATATAAATTATTTA\n+>AY615141_SH195460.07FU_refs\n+GGAAGGATCATTACCGAGTTGACTCGAGCTCCGGCTCGACTCTCCCACCCTATGTGTACC\n+TACCTCTGTTGCTTTGGCGGGCCGCGGTCCTCCGCACCGGCCCCCTTTGGGGGCTGGCCA\n+GCGCCCGCCAGAGGACCACAAAACTCCAGTCAGTAAACGTTGCAGTCTGAAAACCAAGTT\n+AATAAACTA\n+>AY616689_SH196294.07FU_refs\n+GAGGAATACCCAAAACCTCCCAACCCCTGTGAACTTACCACTGTTTCCTCGGCGTGCGCA\n+CCTGGTTGCCCGCGGGGGATCCGAGCCTACCCTGTAGCTACCCTGTAGCTACCCTGTAGA\n+CCCGGGTCCTCAGCACACGGCGCCGCTCAAGGTCCCGCCGAAGTACCCTGAACTCTGTTT\n+AACGTGGAATTCTGAATGCTTCAACTAAATAAGTTA\n+>AY737760_SH296378.07FU_refs\n+CTGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACT\n+GTTGCCTCGGCGGGATCTCTGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCG\n+GAGGAAAAAACAACCAAAACTCTTTTTGTATACCCCCTCGCGGGTTTTTTACTTCTGAGA\n+ACTTCTCGGCGCCCCTTTGCGGGCGTTTCGAAAATGAATCA\n+>AY953383_SH113362.07FU_refs\n+TACTGAGTTTTTGTACTCTATAAACCATGTGTGAACGTACCTATCTTGTAGTGAGATGAA\n+TGCTGTTTTGGTGGTAGGGCCCTTCTGAAGAGAGGGCACCGCTGCCAGCAGTATAGTCTC\n+ACCACTATAAAACTCTTTTATTATTTTCTAGATTTTTCATTGCTGAGTGGCATAACTATA\n+AAAAAGTTA\n+>DQ267916_SH386829.07FU_refs\n+CCGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTATACCTTGTTGCTTCG\n+GCGGGCCCGCCGTATGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCCCGCCGAAGAC\n+ATCTCGAACTCTGTCTGAAGATTGTAGTCTGAGTCAAAATATAAATTATTTA\n+>DQ317630_SH187202.07FU_refs\n+TGGGTTTTCCACTCTGTGGTAACCCTCACTACAATACACCAACATCCATATACACCTGTG\n+CACCGTTGGCTAGATGTGGCTCATTCGTGAGTCTTCGTCTGCTGACAACAATTTATAAAC\n+TCTGAGTTATAATGAATGTTAATTGTATCTTGCCATTTGGCAGAAACTAAATA\n+>DQ898183_SH216206.07FU_refs\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCAT\n+GTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTT\n+TGGGGAAGGGCCAGTTATTAAACCTTTATACCAATT'..b'SH188638.07FU_refs\n+TTGAAATAAACCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCAT\n+CTTTATATCTCCACCTGTGCACTTTTTGTAGACCTTTCAGGTCTATGTTTTCTCATTTTA\n+CCCCAATGTATGTCGATAGAATGTTGTGCCTTTATAATGTATA\n+>KP170652_SH495686.07FU_refs_singleton\n+CACTCAGTAGTTTACTACTGTTAAAGAGGCTGTTAGTCTGTATAGCTTTACCGCTGACGA\n+GCAGCTTGCCTCTTTTCTCTACCCTTGTCTTTTGCGTACCCATGTTTCCTCGGCAGGCCT\n+GCCTGCCGATAGGACCCTTCTACAACCTTTATTATTTCAATCAGCGTCTGAAAAACTTAA\n+TAATTA\n+>KP744516_SH528288.07FU_refs\n+CCGAGTGAGGGTCTTCAAAGGCTCAACCTCCCAAACCCCTTGTATATCACCGAGAGTTTT\n+ATTGTTGCTTCGGTGGGTCCACAGTGCCCACCGAAGACCCACCAAAAATCCTAGTAAGAG\n+TGTCGTCTGAGTAATTAAAAAATAATCA\n+>KT716464_SH554678.07FU_refs_singleton\n+CATTACAGAGTTGCAAAACTCCCAAACCCATTGCGTACATACCATGTCGTTGCTTCGGCG\n+GGCTGCCGTCCTCCCCCAGGGGAGGCGGACCCGGCCCCTCGGGGAGCCCGCCGGAGGTAT\n+AAACTCTTATCTTTATAGAAAAGCCTTCTGAGTATCTTGAAAAATCAAGTAA\n+>UDB000320_SH220111.07FU_refs\n+TCGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGG\n+AGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCC\n+TTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAA\n+AGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATA\n+>UDB001086_SH222381.07FU_refs\n+CTGCGGAAGGATCATTATTGAAATAAATCTGATGAGTTGCTGCTGGTTCTCTTAGGGAGC\n+ATGTGCACACTTGTCATCTTTATATTCTCCACCTTGTGCACCTTTTGTAGACCTGGATAT\n+CTCTCTGAGTGCTTTTAGCACTCAGGTTTGGAGGATTGACTTTTCTGTCTTTCCTTACCT\n+TTCCCGGCCTATGTTTCTTCAAATACCCAATGTGTATGTCATTAGAATGTAATAAATGGG\n+CTTTTGTGCCTTATAAATCTATA\n+>UDB001581_SH219736.07FU_refs\n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCAT\n+CTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCG\n+GTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATAC\n+ACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATA\n+>UDB002317_SH221025.07FU_refs\n+CTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGC\n+TGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGA\n+GGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATT\n+TTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTA\n+AATGATAAAATA\n+>UDB003291_SH182302.07FU_refs\n+GGACTGCGGAGGACATTAATGAAATCGACGTTTCGGGAAAGGTTGTTGCTGGCCCCACGG\n+CATGTGCACGCCTTTACCGGATGTATTCGTCCTTTCTTTACACCTGTGCACGATCTGTAG\n+CTAGGGATGATCACGGAGCCTGTCGGTTCCGAATGCCCTGGCTATGAACGTTTTTATACC\n+CTCTTATAAAGTTTTTTTTGAATGTTTGTCCTGCGTGTAACAGCGCGAATGAAATA\n+>UDB006042_SH184945.07FU_refs\n+CCGAGTTTACACAACTCCCAAACCCACTGTGAACCTTACCGAATCGTTGCTTCGGCGGGA\n+ACGCCCCGGGCCCCGTCGCCCGGACCCAGGCGCCCGCCGGAGGCCCGAAAAAACTCTCGT\n+GTTTCTCCCAGCGGAATCAAGTCTGAGTGGCCCACAGCGGCAAGAAAATGAATCA\n+>UDB009021_SH177627.07FU_refs\n+CATTATTGAAATCCAAGGTGCAGAGGGGGACCGGAGAAATCCATTCCTCTGAAGCCCTTT\n+TACCTCTTTCACACCTGTGTGCACCCACATTCGCAAAGTCCTTCGGGACCTGCGCTTTCT\n+ATCTCGAACTCGCATGTCTACAGAATGTCGCTAGCGTTTGAAATGAAATA\n+>UDB011541_SH194446.07FU_refs\n+GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCT\n+TTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCT\n+GTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAA\n+ATAAATAAATA\n+>UDB011569_SH190415.07FU_refs\n+GTGACTGCGGAGGATCATTATTGAAATAAAGCTTGGTTAGGTTGTTGCTGGCTCTTCGGG\n+GCATGTGCACACCTGACACCAACTTTTCTTACCACCTGTGCACTTTTTGTAGACTTTGGA\n+ATACCTCTCGAGGAAACTCGGTTTTGAGGACTGCTGTGCGCAAGCCGGCTTTCCTTACAT\n+TTTCCGGTCTATGTTTTTCTATATACCCTATAGTATGTCACAGAATGTCATTTTAATGGG\n+CTTAATTGCCTTTAAACCTATA\n+>UDB015350_SH176685.07FU_refs\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCT\n+GGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCC\n+TGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCC\n+GGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACAT\n+GTTTGGAAAAAATATAAATGAAATATA\n+>UDB016091_SH210668.07FU_refs\n+ATGAAATCAAAACTTTCATTGAAAGGTTGTTGCTGATATATATATATATATGTGCACACC\n+TGGATTTGAAAGTCTTCATCCTTTACCTCCCTTGTGCACGATCTGTAGCTTTGGGATGAT\n+TACAGAGTTTACTCTTTTTATTAGAGGATTCTGAATGCCCTTTGCTATGAACGTTTTTAC\n+ACACACAAATGTTTATTAGAATGTATGCTCGAGCGTGTAACAACGTGAATTGAAATA\n+>UDB016470_SH189377.07FU_refs\n+CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTT\n+TACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTT\n+CCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAA\n+CGCAATAAAATA\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_db.loc Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,54 @@ +# Copyright (C) 2014 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_affiliations_OTU to use taxonomy database for +#taxonomy affiliation. You will need to create or download Blast+ index and train your database +#for RDP classifier these data files. +#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation +#Finally you will need to create frogs_db.loc file similar to this one in your galaxy +#tool-data directory.The frogs_db.loc file has this format (longer white space characters are +#TAB characters): +# +#<unique_database_name> <file_path> +# +#First column will be the visible name in galaxy. +#So, for example, if you had 16S silva 128 indexed stored in +#/galaxy_databanks/16S/silva_128/ +#then the frogs_db.loc entry would look like this: +# +#silva 128 16S /galaxy_databanks/16S/silva_128/silva_128_16S.fasta +# +#and your /galaxy_databanks/16S/silva_128/ directory +#would contain index files: +# +#-rw-r--r-- 1 mbernard FROGS 8097966 5 déc. 16:56 bergeyTrainingTree.xml +#-rw-r--r-- 1 mbernard FROGS 1572981589 5 déc. 16:56 genus_wordConditionalProbList.txt +#-rw-r--r-- 1 mbernard FROGS 1654 5 déc. 16:56 LICENCE.txt +#-rw-r--r-- 1 mbernard FROGS 1072228 5 déc. 16:56 logWordPrior.txt +#-rw-r--r-- 1 mbernard FROGS 940834335 5 déc. 16:56 silva_128_16S.fasta +#-rw-r--r-- 1 mbernard FROGS 152606489 5 déc. 16:56 silva_128_16S.fasta.nhr +#-rw-r--r-- 1 mbernard FROGS 6918588 5 déc. 16:56 silva_128_16S.fasta.nin +#-rw-r--r-- 1 mbernard FROGS 205320030 5 déc. 16:56 silva_128_16S.fasta.nsq +#-rw-r--r-- 1 mbernard FROGS 281 5 déc. 16:56 silva_128_16S.fasta.properties +#-rw-r--r-- 1 mbernard FROGS 3420464 5 déc. 16:56 silva_128_16S.tax +#-rw-r--r-- 1 mbernard FROGS 964048 5 déc. 16:57 wordConditionalProbIndexArr.txt +# +# +#<name> <name> <file_path> +# +# EXAMPLE FOR TEST : +ITS1_test ITS1_test ${__HERE__}/frogs_db_data/ITS1.rdp.fasta + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/ITS1.rdp.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_db_data/ITS1.rdp.fasta Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,204 @@\n+>EU292260_SH086465.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Basidiomycota [id: 8] [id: 3];c__Agaricomycetes [id: 9] [id: 4];o__Russulales [id: 32] [id: 5];f__Russulaceae [id: 33] [id: 6];g__Lactarius [id: 407] [id: 7];s__Lactarius_sp [id: 1060] [id: 8]\n+TCGTACAAAATGTGAGGGGCATGTGAGGGCTGTCGCCGACTCAAAGTCGTGCACGCCCGAGCGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGGGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACCCGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCCTTGGTATTCCGAGGGGCACACCCGTTTGAGTGTCGTGAAAACCTCAACCTCTTTGGTTTCTTCTGGAGACCAAAGCAGGCTTGGACTTTGGAGGCCTTTGCTGNCACCTCTCTCTTTTGAAGGTCAGCTCCTCTTAAACGAATTAGCAGGGNCCTCTTTGCCGATCCTCGACGTGNGATAAGATGNTTCCATGTCTTGTTTCTGGCTCTGTCACTTTTGGGACCCGCTTCTAACCGTCTTGACCTTGCGTCGAGACAAGTGCTCGAGCATGTCTCCCTTCTTNGGAAGCTCCCTCGACCCCACGAACC\n+>JX436920_SH182391.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Basidiomycota [id: 8] [id: 3];c__Agaricomycetes [id: 9] [id: 4];o__Russulales [id: 32] [id: 5];f__Russulaceae [id: 33] [id: 6];g__Lactarius [id: 407] [id: 7];s__Lactarius_lanceolatus [id: 21786] [id: 9]\n+CGTGCACGCCCGAGCGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGGGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACCCGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCCTTGGTATTCCGAGGGGCACACCCGTTTGAGTGTCGTGAAAACCTCAACCTCCTTGGTTTCTTCTGGAGACCAAAGCAGGCTTGGACTTTGGAGGCCTTTGCTGGCACCTCTCTGTCAGCTCCTCTTAAATGAATTAGCAGGGTCCTCTTTGCTGATCCTTGACGTGTGATAAGATGTTTCCATGTCTTGGTTTCTGGCTCTGTCACTTTTGGGACCCGCTTCTAACCGTCTTGACCTTGCGTCGAGACAATGTTCGAGCACATCTCCCTTCTCGGGAAGCTCCCTCGACCCCACGAACC\n+>JX089579_SH215375.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Ascomycota [id: 2] [id: 10];c__Dothideomycetes [id: 52] [id: 11];o__Pleosporales [id: 212] [id: 12];f__Pleosporaceae [id: 348] [id: 13];g__Bipolaris [id: 349] [id: 14];s__Bipolaris_microstegii [id: 350] [id: 15]\n+CACAACAAAATATGAAGGCCTGGCTTCGCGGCCGGCTGAAATATTTTTTCACCCATGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCAAACCATAAACCTTTTTTTTATGCAGTTACCATCAGCGTCAGTAAAAACAATGTAATTAATTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCAAAGGGCATGCCTGTTCGAGCGTCATTTGTACCTTCAAGCTTTGCTTGGTGTTGGGTGTTTTTGTCTCCCTCTTTCTGGGAGACTCGCCTTAAAACGATTGGCAGCCGGCCTACTGGTTTCGGAGCGCAGCACATAATTTGCGCTTTGTATCAGGAGAAAAGGACGGTAATCCATCAAGACTCTACATTTTTCACT\n+>DQ898183_SH216206.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Ascomycota [id: 2] [id: 10];c__Pezizomycetes [id: 114] [id: 16];o__Pezizales [id: 115] [id: 17];f__Tuberaceae [id: 116] [id: 18];g__Tuber [id: 117] [id: 19];s__Tuber_latisporum [id: 1138] [id: 20]\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTCAGGGCATGCCTGTTCGAGCGTCACTAACAACCATCTCACAGAGAATGTGGTATTGGCCTGAGTGGGTTGCACTTGCAGTGCAAATCTCACTTGGCTGAAATGGATTGGCCAGACAAGGAGACAATGGCAACAGACTCTCAGAGTGTTTTTGAAATGCTAAACTAGTCTGTGGCAGGTTGAACTCTGAGCTAAAAGGACTGATATTTAGTGTAAACAAGAAAT\n+>JQ716403_SH219241.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Basidiomycota [id: 8] [id: 3];c__Agaricomycetes [id: 9] [id: 4];o__Hymenochaetales [id: 73] [id: 21];f__Hymenochaetaceae [id: 74] [id: 22];g__Pseudochaete [id: 1171] [id: 23];s__Pseudochaete_subrigidula [id: 1172] [id: 24]\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCA'..b'GTCCGGTCCTCAAGCGTATGGGGCTTTGTCACCCGCTTTGTAGGACTGGCCGGCGCCTGCCGATCAACCAAACTTTTTTCCAG\n+>DQ267916_SH386829.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Ascomycota [id: 2] [id: 10];c__Eurotiomycetes [id: 27] [id: 25];o__Eurotiales [id: 61] [id: 26];f__Trichocomaceae [id: 62] [id: 27];g__Penicillium [id: 63] [id: 154];s__Penicillium_ribium [id: 23950] [id: 238]\n+CCGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTATACCTTGTTGCTTCGGCGGGCCCGCCGTATGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCCCGCCGAAGACATCTCGAACTCTGTCTGAAGATTGTAGTCTGAGTCAAAATATAAATTATTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCACGGCTTGTGTGTTGGGCTCCGTCCTCCGATCCCGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTGTAGGCCCGGCCGGCGCTTGCCGATCAACCAAATTTTTATCCA\n+>AY443470_SH407688.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Ascomycota [id: 2] [id: 10];c__Eurotiomycetes [id: 27] [id: 25];o__Eurotiales [id: 61] [id: 26];f__Trichocomaceae [id: 62] [id: 27];g__Penicillium [id: 63] [id: 154];s__Penicillium_jensenii [id: 24006] [id: 239]\n+CGAGCGAGAATTCTCTGAATTCAACCTCCCACCCGTGTTTATTGTACCTTGTTGCTTCGGCGGGCCCGCCTCACGGCCGCCGGGGGGCATCTGCCCCCGGGCCCGCGCCCGCCGAAGACACCTTGAACTCTGTATGAAAATTGCAGTCTGAGTCTAAATATAAATTATTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCCCGGCTTGTGTGTTGGGTCTCGTCCCCCTTCCCGGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTGTAGGCCCGGCCGGCGCTTGCCGATCAACCAAAACTTTTTTCCAG\n+>AF033476_SH407699.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Ascomycota [id: 2] [id: 10];c__Eurotiomycetes [id: 27] [id: 25];o__Eurotiales [id: 61] [id: 26];f__Trichocomaceae [id: 62] [id: 27];g__Penicillium [id: 63] [id: 154];s__Penicillium_aurantiogriseum [id: 24009] [id: 240]\n+AAGGATCATTACCGAGTGAGGGCCCTTTGGGTCCAACCTCCCACCCGTGTTTATTTTACCTTGTTGCTTCGGCGGGCCCGCCTTTACTGGCCGCCGGGGGGCTTCACGCCCCCGGGCCCGCGCCCGCCGAAGACACCCTCGAACTCTGTCTGAAGATTGAAGTCTGAGTGAAAATATAAATTATTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCCCGGCTTGTGTGTTGGGCCCCGTCCTCCGATTCCGGGGGACGGGCCCGAAAGGCAGCGGCGGCACCGCGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCCGTAGGCCCGGCCGGCGCTTGCCGATCAACCCAAATTTTTATCCAG\n+>KM189666_SH407780.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Ascomycota [id: 2] [id: 10];c__Eurotiomycetes [id: 27] [id: 25];o__Eurotiales [id: 61] [id: 26];f__Trichocomaceae [id: 62] [id: 27];g__Penicillium [id: 63] [id: 154];s__Penicillium_brunneoconidiatum [id: 24024] [id: 241]\n+AAGGATCATTACTGAGTGAGGGCCCTCTGGGTCCAACCTCCCACCCGTGTTTATTGTACCTTGTTGCTTCGGTGAGCCCGCCTCACGGCCGCCGGGGGGCTTCTGCCCCCGGGCCCGCGCCCACCGAAGACACCATTGAACTCTGTCTGAAGATTGCAGTCTGAGCATAAACTAAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAACTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGTATTCCGGGGGGCATGCCTGTCCGAGCGTCATTGCTGCCCTCAAGCACGGCTTGTGTGTTGGGCTCCGTCCCCCCCGGGACGGGCCCGAAAGGCAGCGGCGGCACCGAGTCCGGTCCTCGAGCGTATGGGGCTTTGTCACCCGCTCTGTAGGCCCGGCCGGCGCCAGCCGACAACCCATCATCCTTTTCAG\n+>KJ638312_SH419903.07FU_refs Root;Root;k__Fungi [id: 1] [id: 2];p__Ascomycota [id: 2] [id: 10];c__Dothideomycetes [id: 52] [id: 11];o__Botryosphaeriales [id: 152] [id: 102];f__Botryosphaeriaceae [id: 153] [id: 103];g__Lasiodiplodia [id: 6585] [id: 139];s__Lasiodiplodia_mediterranea [id: 24061] [id: 242]\n+GATCATTACCGAGTTCTCGGGCTTCGGCTCGACTCTCCCACCCTTTGTGAACGTACCTCTGTTGCTTTGGCGGCTCCGGCCGCCAAAGGACCTCCAAACTCCAGTCAGTAAACGCAGACGTCTGATAAACAAGTTAATAAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTACAACCCTCAAGCTCTGCTTGGAATTGGGCACCGTCCTCGCTGCGGACGCGCCTCAAAGACCTCGGCGGTGGCTGTTCAGCCCTCAAGCGTAGTAGAATACACCTCGCTTTGGAGCGGTTGGCGTCGCCCGCCGGACGAACCTTCTGAACTTTTCTCAAGGTTGACCTCGGAT\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/ITS1.rdp.fasta.nhr |
| b |
| Binary file test-data/databases/frogs_db_data/ITS1.rdp.fasta.nhr has changed |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/ITS1.rdp.fasta.nin |
| b |
| Binary file test-data/databases/frogs_db_data/ITS1.rdp.fasta.nin has changed |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/ITS1.rdp.fasta.nsq |
| b |
| Binary file test-data/databases/frogs_db_data/ITS1.rdp.fasta.nsq has changed |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/ITS1.rdp.fasta.properties --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_db_data/ITS1.rdp.fasta.properties Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,11 @@ +# Sample ResourceBundle properties file +bergeyTree=bergeyTrainingTree.xml + +probabilityList=genus_wordConditionalProbList.txt + +probabilityIndex=wordConditionalProbIndexArr.txt + +wordPrior=logWordPrior.txt + +classifierVersion=RDP Naive Bayesian rRNA Classifier Version 2.5, May 2012 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/ITS1.rdp.tax --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_db_data/ITS1.rdp.tax Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,243 @@\n+0*Root*-1*0*rootrank\n+1*Root*0*1*root\n+2*k__Fungi [id: 1] [id: 2]*1*2*domain\n+3*p__Basidiomycota [id: 8] [id: 3]*2*3*phylum\n+4*c__Agaricomycetes [id: 9] [id: 4]*3*4*class\n+44*o__Thelephorales [id: 101] [id: 44]*4*5*order\n+45*f__Bankeraceae [id: 102] [id: 45]*44*6*family\n+46*g__Sarcodon [id: 2623] [id: 46]*45*7*genus\n+47*s__Sarcodon_quercophilus [id: 5557] [id: 47]*46*8*species\n+77*g__Hydnellum [id: 1832] [id: 77]*45*7*genus\n+91*s__Hydnellum_suaveolens [id: 6660] [id: 91]*77*8*species\n+78*s__Hydnellum_peckii [id: 5194] [id: 78]*77*8*species\n+99*f__Thelephoraceae [id: 395] [id: 99]*44*6*family\n+100*g__Thelephora [id: 1009] [id: 100]*99*7*genus\n+101*s__Thelephora_atra [id: 12419] [id: 101]*100*8*species\n+5*o__Russulales [id: 32] [id: 5]*4*5*order\n+6*f__Russulaceae [id: 33] [id: 6]*5*6*family\n+7*g__Lactarius [id: 407] [id: 7]*6*7*genus\n+9*s__Lactarius_lanceolatus [id: 21786] [id: 9]*7*8*species\n+106*s__Lactarius_semisanguifluus [id: 12599] [id: 106]*7*8*species\n+8*s__Lactarius_sp [id: 1060] [id: 8]*7*8*species\n+236*s__Lactarius_cyathuliformis [id: 23791] [id: 236]*7*8*species\n+112*o__Polyporales [id: 92] [id: 112]*4*5*order\n+113*f__Meruliaceae [id: 93] [id: 113]*112*6*family\n+114*g__Junghuhnia [id: 5553] [id: 114]*113*7*genus\n+115*s__Junghuhnia_nitida [id: 14589] [id: 115]*114*8*species\n+21*o__Hymenochaetales [id: 73] [id: 21]*4*5*order\n+22*f__Hymenochaetaceae [id: 74] [id: 22]*21*6*family\n+23*g__Pseudochaete [id: 1171] [id: 23]*22*7*genus\n+24*s__Pseudochaete_subrigidula [id: 1172] [id: 24]*23*8*species\n+62*g__Hymenochaete [id: 1143] [id: 62]*22*7*genus\n+63*s__Hymenochaete_longispora [id: 7446] [id: 63]*62*8*species\n+64*o__Boletales [id: 10] [id: 64]*4*5*order\n+82*f__Sclerodermataceae [id: 2915] [id: 82]*64*6*family\n+83*g__Pisolithus [id: 3087] [id: 83]*82*7*genus\n+84*s__Pisolithus_capsulifer [id: 10289] [id: 84]*83*8*species\n+65*f__Boletaceae [id: 418] [id: 65]*64*6*family\n+66*g__Xerocomus [id: 906] [id: 66]*65*7*genus\n+67*s__Xerocomus_porophyllus [id: 7573] [id: 67]*66*8*species\n+136*f__Suillaceae [id: 712] [id: 136]*64*6*family\n+137*g__Truncocolumella [id: 2710] [id: 137]*136*7*genus\n+138*s__Truncocolumella_rubra [id: 2711] [id: 138]*137*8*species\n+186*f__Paxillaceae [id: 3915] [id: 186]*64*6*family\n+187*g__Alpova [id: 14086] [id: 187]*186*7*genus\n+191*s__Alpova_corsicus [id: 21462] [id: 191]*187*8*species\n+188*s__Alpova_alpestris [id: 20625] [id: 188]*187*8*species\n+48*o__Agaricales [id: 14] [id: 48]*4*5*order\n+74*f__Tricholomataceae [id: 389] [id: 74]*48*6*family\n+175*g__Gamundia [id: 19071] [id: 175]*74*7*genus\n+176*s__Gamundia_leucophylla [id: 19072] [id: 176]*175*8*species\n+75*g__Tricholoma [id: 830] [id: 75]*74*7*genus\n+76*s__Tricholoma_portentosum [id: 9774] [id: 76]*75*8*species\n+196*f__Agaricaceae [id: 296] [id: 196]*48*6*family\n+197*g__Lepiota [id: 1372] [id: 197]*196*7*genus\n+198*s__Lepiota_geogenia [id: 22781] [id: 198]*197*8*species\n+107*f__Marasmiaceae [id: 15] [id: 107]*48*6*family\n+108*g__Megacollybia [id: 3474] [id: 108]*107*7*genus\n+109*s__Megacollybia_subfurfuracea [id: 13884] [id: 109]*108*8*species\n+119*f__Amanitaceae [id: 39] [id: 119]*48*6*family\n+120*g__Amanita [id: 40] [id: 120]*119*7*genus\n+190*s__Amanita_friabilis [id: 10628] [id: 190]*120*8*species\n+121*s__Amanita_franchetii [id: 14864] [id: 121]*120*8*species\n+116*f__Strophariaceae [id: 98] [id: 116]*48*6*family\n+117*g__Hypholoma [id: 1891] [id: 117]*116*7*genus\n+118*s__Hypholoma_capnoides [id: 14701] [id: 118]*117*8*species\n+184*g__Pholiota [id: 2704] [id: 184]*116*7*genus\n+185*s__Pholiota_highlandensis [id: 14001] [id: 185]*184*8*species\n+56*f__Omphalotaceae [id: 261] [id: 56]*48*6*family\n+57*g__Gymnopus [id: 262] [id: 57]*56*7*genus\n+58*s__Gymnopus_hybridus [id: 6077] [id: 58]*57*8*species\n+86*f__Entolomataceae [id: 18] [id: 86]*48*6*family\n+87*g__Entoloma [id: 19] [id: 87]*86*7*genus\n+88*s__Entoloma_sp [id: 1533] [id: 88]*87*8*species\n+122*f__Inocybaceae [id: 277] [id: 122]*48*6*family\n+123*g__Inocybe [id: 278] [id: 123]*122*'..b' 153] [id: 103]*102*6*family\n+104*g__Neofusicoccum [id: 4366] [id: 104]*103*7*genus\n+105*s__Neofusicoccum_eucalypticola [id: 12563] [id: 105]*104*8*species\n+139*g__Lasiodiplodia [id: 6585] [id: 139]*103*7*genus\n+140*s__Lasiodiplodia_crassispora [id: 8928] [id: 140]*139*8*species\n+242*s__Lasiodiplodia_mediterranea [id: 24061] [id: 242]*139*8*species\n+12*o__Pleosporales [id: 212] [id: 12]*11*5*order\n+79*f__Leptosphaeriaceae [id: 1147] [id: 79]*12*6*family\n+80*g__Leptosphaeria [id: 1164] [id: 80]*79*7*genus\n+81*s__Leptosphaeria_polylepidis [id: 9979] [id: 81]*80*8*species\n+164*f__Lindgomycetaceae [id: 1978] [id: 164]*12*6*family\n+165*g__Lindgomyces [id: 1979] [id: 165]*164*7*genus\n+166*s__Lindgomyces_breviappendiculatus [id: 17836] [id: 166]*165*8*species\n+151*f__Phaeosphaeriaceae [id: 656] [id: 151]*12*6*family\n+152*g__Neosphaerellopsis [id: 17214] [id: 152]*151*7*genus\n+153*s__Neosphaerellopsis_thailandica [id: 17215] [id: 153]*152*8*species\n+13*f__Pleosporaceae [id: 348] [id: 13]*12*6*family\n+14*g__Bipolaris [id: 349] [id: 14]*13*7*genus\n+202*s__Bipolaris_chloridis [id: 22983] [id: 202]*14*8*species\n+15*s__Bipolaris_microstegii [id: 350] [id: 15]*14*8*species\n+89*g__Curvularia [id: 4623] [id: 89]*13*7*genus\n+90*s__Curvularia_sorghina [id: 11359] [id: 90]*89*8*species\n+193*s__Curvularia_protuberata [id: 21784] [id: 193]*89*8*species\n+156*f__Didymellaceae [id: 213] [id: 156]*12*6*family\n+157*g__Allophoma [id: 6502] [id: 157]*156*7*genus\n+158*s__Allophoma_piperis [id: 17487] [id: 158]*157*8*species\n+126*c__Geoglossomycetes [id: 2059] [id: 126]*10*4*class\n+127*o__Geoglossales [id: 2060] [id: 127]*126*5*order\n+128*f__Geoglossaceae [id: 2061] [id: 128]*127*6*family\n+129*g__Geoglossum [id: 5030] [id: 129]*128*7*genus\n+130*s__Geoglossum_dunense [id: 15661] [id: 130]*129*8*species\n+25*c__Eurotiomycetes [id: 27] [id: 25]*10*4*class\n+68*o__Verrucariales [id: 175] [id: 68]*25*5*order\n+69*f__Verrucariaceae [id: 176] [id: 69]*68*6*family\n+70*g__Verrucaria [id: 1280] [id: 70]*69*7*genus\n+144*s__Verrucaria_lapidicola [id: 16391] [id: 144]*70*8*species\n+71*s__Verrucaria_hydrophila [id: 7998] [id: 71]*70*8*species\n+181*g__Dermatocarpon [id: 4840] [id: 181]*69*7*genus\n+182*s__Dermatocarpon_dolomiticum [id: 19469] [id: 182]*181*8*species\n+26*o__Eurotiales [id: 61] [id: 26]*25*5*order\n+27*f__Trichocomaceae [id: 62] [id: 27]*26*6*family\n+96*g__Talaromyces [id: 1185] [id: 96]*27*7*genus\n+97*s__Talaromyces_pittii [id: 12056] [id: 97]*96*8*species\n+28*g__Aspergillus [id: 353] [id: 28]*27*7*genus\n+201*s__Aspergillus_ivoriensis [id: 22947] [id: 201]*28*8*species\n+148*s__Aspergillus_caninus [id: 17035] [id: 148]*28*8*species\n+29*s__Aspergillus_ochraceus [id: 2572] [id: 29]*28*8*species\n+208*s__Aspergillus_microcysticus [id: 23102] [id: 208]*28*8*species\n+149*g__Rasamsonia [id: 3902] [id: 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143]*142*8*species\n+30*o__Chaetothyriales [id: 165] [id: 30]*25*5*order\n+31*f__Herpotrichiellaceae [id: 680] [id: 31]*30*6*family\n+32*g__Exophiala [id: 681] [id: 32]*31*7*genus\n+33*s__Exophiala_equina [id: 3883] [id: 33]*32*8*species\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/bergeyTrainingTree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_db_data/bergeyTrainingTree.xml Thu Feb 28 10:14:49 2019 -0500 |
| [ |
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| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/genus_wordConditionalProbList.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_db_data/genus_wordConditionalProbList.txt Thu Feb 28 10:14:49 2019 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/logWordPrior.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_db_data/logWordPrior.txt Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,65537 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|
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/frogs_db_data/wordConditionalProbIndexArr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_db_data/wordConditionalProbIndexArr.txt Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,65538 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|
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/phiX_db.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/phiX_db.loc Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,42 @@ +# Copyright (C) 2014 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_filters to identify phix contaminant. You will #need to create or download Blast+ index. +#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants +#Finally you will need to create phiX_db.loc file similar to this one in your galaxy +#tool-data directory.The phiX_db.loc file has this format (longer white space characters are +#TAB characters): +# +#<contaminant_name> <name> <file_path> +# +#First column will be the visible name in galaxy. +#So, for example, if you had phix indexed stored in +#/galaxy_databanks/phiX/ +#then the phiX_db.loc entry would look like this: +# +# +# EXAMPLE FOR TEST : +phiX_test phiX_test ${__HERE__}/phiX_db_data/phi.fa +# +#and your /galaxy_databanks/phiX/ directory +#would contain index files: +# +#-rwxrwxr-x 1 gpascal FROGS 5535 16 sept. 2015 phi.fa +#-rw-rwxr-- 1 gpascal FROGS 132 16 sept. 2015 phi.fa.nhr +#-rw-rwxr-- 1 gpascal FROGS 88 16 sept. 2015 phi.fa.nin +#-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq +# + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/phiX_db_data/phi.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/phiX_db_data/phi.fa Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,79 @@ +>gi|9626372|ref|NC_001422.1| Coliphage phiX174, no SNPs True Reference +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTAGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +GATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCTCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/phiX_db_data/phi.fa.nhr |
| b |
| Binary file test-data/databases/phiX_db_data/phi.fa.nhr has changed |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/phiX_db_data/phi.fa.nin |
| b |
| Binary file test-data/databases/phiX_db_data/phi.fa.nin has changed |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/databases/phiX_db_data/phi.fa.nsq |
| b |
| Binary file test-data/databases/phiX_db_data/phi.fa.nsq has changed |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/input/chaillou.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/chaillou.biom Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "otu_01778", "metadata": {"taxonomy": ["k__Bacteria", "p__Tenericutes", "c__Mollicutes", "o__Mycoplasmatales", "f__Mycoplasmataceae", "g__Candidatus Lumbricincola", "s__NA"]}}, {"id": "otu_01838", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Prevotellaceae", "g__Prevotella", "s__NA"]}}, {"id": "otu_01386", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Xanthomonadales", "f__Xanthomonadaceae", "g__Dyella", "s__Ginsengisoli"]}}, {"id": "otu_01835", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Planococcaceae", "g__Incertae Sedis", "s__NA"]}}, {"id": "otu_01837", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Flavobacteria", "o__Flavobacteriales", "f__Flavobacteriaceae", "g__Flavobacterium", "s__NA"]}}, {"id": "otu_01832", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Leuconostocaceae", "g__Weissella", "s__NA"]}}, {"id": "otu_01833", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Actinomycetales", "f__Actinomycetaceae", "g__Actinomyces", "s__NA"]}}, {"id": "otu_00156", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Micrococcales", "f__Brevibacteriaceae", "g__Brevibacterium", "s__Marinum"]}}, {"id": "otu_01719", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Neisseriales", "f__Neisseriaceae", "g__Neisseria", "s__Perflava"]}}, {"id": "otu_00015", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Aerococcaceae", "g__Facklamia", "s__Tabacinasalis"]}}, {"id": "otu_00769", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Sakei"]}}, {"id": "otu_00768", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Brevis"]}}, {"id": "otu_00011", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Soli"]}}, {"id": "otu_00010", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Junii"]}}, {"id": "otu_00013", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Kyonggiensis"]}}, {"id": "otu_00012", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Johnsonii"]}}, {"id": "otu_00018", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Aerococcaceae", "g__Abiotrophia", "s__Defectiva"]}}, {"id": "otu_00569", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Serratia", "s__Proteamaculans"]}}, {"id": "otu_00568", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Serratia", "s__Fonticola"]}}, {"id": "otu_00602", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Aestuarii"]}}, {"id": "otu_00386", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Comamonas", "s__Aquatica"]}}, {"id": "otu_00604", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Sibiricum"]}}, {"id"'..b'], [505, 27, 3], [505, 28, 8], [505, 29, 187], [505, 30, 3], [505, 31, 3], [505, 32, 3], [505, 33, 7], [505, 34, 2], [505, 35, 9], [505, 38, 5], [505, 40, 7], [505, 41, 36], [505, 42, 41], [505, 43, 37], [505, 44, 12], [505, 45, 7], [505, 46, 15], [505, 47, 13], [505, 48, 95], [505, 49, 6], [505, 51, 7], [505, 52, 7], [505, 53, 7], [505, 54, 36], [505, 55, 11], [505, 58, 3], [505, 59, 3], [505, 61, 2], [506, 0, 2], [506, 1, 1], [506, 2, 5], [506, 3, 11], [506, 4, 8], [506, 5, 18], [506, 6, 73], [506, 7, 11], [506, 9, 15], [506, 10, 10], [506, 12, 29], [506, 19, 5], [506, 32, 5], [506, 41, 11], [506, 42, 3], [506, 43, 12], [506, 44, 3], [506, 47, 3], [506, 48, 125], [506, 49, 11], [506, 50, 2], [506, 51, 4], [506, 52, 4], [506, 54, 42], [506, 55, 7], [506, 56, 3], [506, 59, 8], [506, 61, 3], [506, 62, 4], [506, 63, 4], [507, 3, 3], [507, 5, 3], [507, 7, 4], [507, 32, 3], [507, 34, 2], [507, 35, 9], [507, 36, 6], [507, 37, 1], [507, 39, 2], [507, 40, 7], [507, 41, 33], [507, 43, 20], [507, 45, 4], [507, 46, 3], [507, 47, 3], [507, 48, 2], [507, 49, 4], [507, 51, 2], [507, 52, 8], [507, 53, 8], [507, 55, 3], [507, 57, 29], [507, 58, 101], [507, 59, 41], [507, 60, 3], [507, 61, 2], [507, 62, 7], [507, 63, 20]], "generated_by": null, "matrix_type": "sparse", "shape": [508, 64], "format_url": "http://biom-format.org", "date": "2016-02-19T14:01:52", "type": "OTU table", "id": null, "columns": [{"id": "DLT0.LOT08", "metadata": null}, {"id": "DLT0.LOT05", "metadata": null}, {"id": "DLT0.LOT03", "metadata": null}, {"id": "DLT0.LOT07", "metadata": null}, {"id": "DLT0.LOT06", "metadata": null}, {"id": "DLT0.LOT01", "metadata": null}, {"id": "DLT0.LOT04", "metadata": null}, {"id": "DLT0.LOT10", "metadata": null}, {"id": "MVT0.LOT05", "metadata": null}, {"id": "MVT0.LOT01", "metadata": null}, {"id": "MVT0.LOT06", "metadata": null}, {"id": "MVT0.LOT07", "metadata": null}, {"id": "MVT0.LOT03", "metadata": null}, {"id": "MVT0.LOT09", "metadata": null}, {"id": "MVT0.LOT08", "metadata": null}, {"id": "MVT0.LOT10", "metadata": null}, {"id": "BHT0.LOT01", "metadata": null}, {"id": "BHT0.LOT07", "metadata": null}, {"id": "BHT0.LOT06", "metadata": null}, {"id": "BHT0.LOT03", "metadata": null}, {"id": "BHT0.LOT10", "metadata": null}, {"id": "BHT0.LOT05", "metadata": null}, {"id": "BHT0.LOT04", "metadata": null}, {"id": "BHT0.LOT08", "metadata": null}, {"id": "VHT0.LOT02", "metadata": null}, {"id": "VHT0.LOT10", "metadata": null}, {"id": "VHT0.LOT03", "metadata": null}, {"id": "VHT0.LOT01", "metadata": null}, {"id": "VHT0.LOT08", "metadata": null}, {"id": "VHT0.LOT06", "metadata": null}, {"id": "VHT0.LOT07", "metadata": null}, {"id": "VHT0.LOT04", "metadata": null}, {"id": "SFT0.LOT08", "metadata": null}, {"id": "SFT0.LOT07", "metadata": null}, {"id": "SFT0.LOT06", "metadata": null}, {"id": "SFT0.LOT03", "metadata": null}, {"id": "SFT0.LOT02", "metadata": null}, {"id": "SFT0.LOT05", "metadata": null}, {"id": "SFT0.LOT04", "metadata": null}, {"id": "SFT0.LOT01", "metadata": null}, {"id": "FST0.LOT07", "metadata": null}, {"id": "FST0.LOT08", "metadata": null}, {"id": "FST0.LOT05", "metadata": null}, {"id": "FST0.LOT06", "metadata": null}, {"id": "FST0.LOT01", "metadata": null}, {"id": "FST0.LOT03", "metadata": null}, {"id": "FST0.LOT10", "metadata": null}, {"id": "FST0.LOT02", "metadata": null}, {"id": "FCT0.LOT06", "metadata": null}, {"id": "FCT0.LOT10", "metadata": null}, {"id": "FCT0.LOT05", "metadata": null}, {"id": "FCT0.LOT03", "metadata": null}, {"id": "FCT0.LOT08", "metadata": null}, {"id": "FCT0.LOT02", "metadata": null}, {"id": "FCT0.LOT07", "metadata": null}, {"id": "FCT0.LOT01", "metadata": null}, {"id": "CDT0.LOT10", "metadata": null}, {"id": "CDT0.LOT08", "metadata": null}, {"id": "CDT0.LOT05", "metadata": null}, {"id": "CDT0.LOT04", "metadata": null}, {"id": "CDT0.LOT06", "metadata": null}, {"id": "CDT0.LOT09", "metadata": null}, {"id": "CDT0.LOT07", "metadata": null}, {"id": "CDT0.LOT02", "metadata": null}]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/input/demultiplex_barcode.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/demultiplex_barcode.txt Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +MgArd0001_A ACAGCGT ACGTACA +MgArd0002 ACAGCGT ACGTCAG +MgArd0003 ACAGCGT ACTAGCA +MgArd0004 ACAGCGT ACTCGTC +MgArd0009 ACAGTAG ACGTACA +MgArd0010 ACAGTAG ACGTCAG +MgArd0011 ACAGTAG ACTAGCA +MgArd0012 ACAGTAG ACTCGTC +MgArd0001_B ACAGCGC ACGTACT |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/input/demultiplex_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/demultiplex_summary.txt Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +#sample count +ambiguous 1 +MgArd0009 1 +MgArd0011 1 +MgArd0004 1 +MgArd0002 1 +MgArd0010 1 +MgArd0001_B 0 +MgArd0001_A 1 +unmatched 1 +MgArd0003 1 +MgArd0012 1 |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/input/demultiplex_test2_R1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/demultiplex_test2_R1.fq Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,40 @@ +@MgArd0001_A +ACAGCGTCAGGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGGTATTAGCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACGTACA ++ +CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIJJIJHHHHFF@DEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD +@MgArd0002 +ACAGCGTGCAGGAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCTGAAAAAAAATAAAAATAACTGCAACGAATTGACGTCAG ++ +#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHE:9@CC?ACBCCCC:@A8>CC?######################### +@MgArd0003 +ACAGCGTGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGGTATTAGCATCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACTAGCA ++ +CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIJJIJHHHHFEDEEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD +@MgArd0004 +ACAGCGTGGAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTTGAAAAAAAATAAAAATAACTGCAACGAATTGACTCGTC ++ +#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHE:9@CC?ABBCCCC:@A8>CC?######################### +@MgArd0009 +ACAGTAGGCAGGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGTAGCATCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACGTACA ++ +CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIHFF@DFFFEEDEEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD +@MgArd0010 +ACAGTAGGTGCAGGAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATTGCCGTCTGAAAAAAAATAAAAATAACTGCAACGAATTGACGTCAG ++ +#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHECDCDBB=BBCCCC:@A8>CC?######################### +@MgArd0011 +ACAGTAGAGGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGGTTAGCATCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACTAGCA ++ +CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIHFF@DFFFEEDEEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD +@MgArd0012 +ACAGTAGTGCAGGAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTGCCGTCTGAAAAAAAATAAAAATAACTGCAACGAATTGACTCGTC ++ +#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHECDCDBB=BBCCCC:@A8>CC?######################### +@unmatched +AAAAAAAAAAAAAAAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTGCCGTCTGAAAAAAAATAAAAATAACTGCAACGAATTGACTCGTC ++ +#1=DDFFDHHFFFCGGIEGGGIIJEHHIIJIJIIGAGHIGIEBGHHECDCDBB=BBCCCC:@A8>CC?######################### +@ambiguous +ACAGCGACAGGATAAATTCTGCCTGTTGGTTGCAATCGAGCCATAGGTATTAGCTAAGAAAAAGGTACAACTGCAGGCTAGACGCGACGTACC ++ +CCCFFFFFHHHHHJJIJJJJIJJJIJJJIIJJJJJJJJJIJJJJIJIJJIJHHHHFF@DEDDDDDDDD@CDDDACDDDDDDDDDDDCDDDDDD |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/input/demultiplex_test2_R2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/demultiplex_test2_R2.fq Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,40 @@ +@MgArd0001 +AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATAGGTGGAGAAAGAAATAAACGTACA ++ +JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB +@MgArd0002 +AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATATCAGGCTAACGTCAG ++ +JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?########################### +@MgArd0003 +AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATGGTGGAAAGAAATAATGAACTAGCA ++ +JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB +@MgArd0004 +AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATATGCAGGCTACTCGTC ++ +JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?########################### +@MgArd0009 +AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATGGTGGAGAAGAAATAATGACGTACA ++ +JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB +@MgArd0010 +AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATTGCAGGCTAACGTCAG ++ +JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?########################### +@MgArd0011 +AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATGGATGGAGAAAGAAATAAACTAGCA ++ +JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB +@MgArd0012 +AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATATCAGGCTAACTCGTC ++ +JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?########################### +@unmatched +AAAAAAAAACGAATAGTGCTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAAAATAAAATTATAATAGATATAAAAAAAAAAAAAA ++ +JJJJJJJJJJJJ@@@DDBDDFHDHHG:CFAHGIGI@CGCFD9DHIFHGGDH/?/?@E<FCBD;;DHAH=<BB9=5,;;>>-;AC?########################### +@ambiguous +AAAAAAAAACGATGAACAGAGGGAGGAAATCTAAAGCTATAACACAAAAAAAAACGTCCTTTGCTATGAGGAAGGAAGACAGAGAATAGGTGGAGAAAGAAATAAACGTACA ++ +JJJJJJJJJJJJCC@FFFFFHHHDFIGJJJJJJJJJJJIJIJIJJJJJJJIJJIGGAHHHFFFFFEFECEECEDDBDDDDDDDDCCDDD:@BAA?BDCCDCCCDDDDCDCDB |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/input/sample_metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/sample_metadata.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,65 @@ + EnvType Description FoodType +BHT0.LOT01 BoeufHache LOT1 Meat +BHT0.LOT03 BoeufHache LOT3 Meat +BHT0.LOT04 BoeufHache LOT4 Meat +BHT0.LOT05 BoeufHache LOT5 Meat +BHT0.LOT06 BoeufHache LOT6 Meat +BHT0.LOT07 BoeufHache LOT7 Meat +BHT0.LOT08 BoeufHache LOT8 Meat +BHT0.LOT10 BoeufHache LOT10 Meat +VHT0.LOT01 VeauHache LOT1 Meat +VHT0.LOT02 VeauHache LOT2 Meat +VHT0.LOT03 VeauHache LOT3 Meat +VHT0.LOT04 VeauHache LOT4 Meat +VHT0.LOT06 VeauHache LOT6 Meat +VHT0.LOT07 VeauHache LOT7 Meat +VHT0.LOT08 VeauHache LOT8 Meat +VHT0.LOT10 VeauHache LOT10 Meat +DLT0.LOT01 DesLardons LOT1 Meat +DLT0.LOT03 DesLardons LOT3 Meat +DLT0.LOT04 DesLardons LOT4 Meat +DLT0.LOT05 DesLardons LOT5 Meat +DLT0.LOT06 DesLardons LOT6 Meat +DLT0.LOT07 DesLardons LOT7 Meat +DLT0.LOT08 DesLardons LOT8 Meat +DLT0.LOT10 DesLardons LOT10 Meat +MVT0.LOT01 MerguezVolaille LOT1 Meat +MVT0.LOT03 MerguezVolaille LOT3 Meat +MVT0.LOT05 MerguezVolaille LOT5 Meat +MVT0.LOT06 MerguezVolaille LOT6 Meat +MVT0.LOT07 MerguezVolaille LOT7 Meat +MVT0.LOT08 MerguezVolaille LOT8 Meat +MVT0.LOT09 MerguezVolaille LOT9 Meat +MVT0.LOT10 MerguezVolaille LOT10 Meat +SFT0.LOT01 SaumonFume LOT1 Seafood +SFT0.LOT02 SaumonFume LOT2 Seafood +SFT0.LOT03 SaumonFume LOT3 Seafood +SFT0.LOT04 SaumonFume LOT4 Seafood +SFT0.LOT05 SaumonFume LOT5 Seafood +SFT0.LOT06 SaumonFume LOT6 Seafood +SFT0.LOT07 SaumonFume LOT7 Seafood +SFT0.LOT08 SaumonFume LOT8 Seafood +FST0.LOT01 FiletSaumon LOT1 Seafood +FST0.LOT02 FiletSaumon LOT2 Seafood +FST0.LOT03 FiletSaumon LOT3 Seafood +FST0.LOT05 FiletSaumon LOT5 Seafood +FST0.LOT06 FiletSaumon LOT6 Seafood +FST0.LOT07 FiletSaumon LOT7 Seafood +FST0.LOT08 FiletSaumon LOT8 Seafood +FST0.LOT10 FiletSaumon LOT10 Seafood +FCT0.LOT01 FiletCabillaud LOT1 Seafood +FCT0.LOT02 FiletCabillaud LOT2 Seafood +FCT0.LOT03 FiletCabillaud LOT3 Seafood +FCT0.LOT05 FiletCabillaud LOT5 Seafood +FCT0.LOT06 FiletCabillaud LOT6 Seafood +FCT0.LOT07 FiletCabillaud LOT7 Seafood +FCT0.LOT08 FiletCabillaud LOT8 Seafood +FCT0.LOT10 FiletCabillaud LOT10 Seafood +CDT0.LOT02 Crevette LOT2 Seafood +CDT0.LOT04 Crevette LOT4 Seafood +CDT0.LOT05 Crevette LOT5 Seafood +CDT0.LOT06 Crevette LOT6 Seafood +CDT0.LOT07 Crevette LOT7 Seafood +CDT0.LOT08 Crevette LOT8 Seafood +CDT0.LOT09 Crevette LOT9 Seafood +CDT0.LOT10 Crevette LOT10 Seafood |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/input/test_dataset.tar.gz |
| b |
| Binary file test-data/input/test_dataset.tar.gz has changed |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/input/tree.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/tree.nwk Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,1 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|
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/01-prepro-flash.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-flash.fasta Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,85566 @@\n+>01_97184;size=5 reference=AB747657_SH134902.07FU_refs position=1..151 errors=130%A \n+CTGAGTATTTGTCTTTTAAAGACATCTCTCTATCCATACACTCTTTTTTTTAAAAAGACATGATTTATACAGTTAGTCTGAATGATTTTTTAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_61824;size=7 reference=KJ922376_SH187578.07FU_refs position=1..170 \n+TACCCTTGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCTCCAGGACCACACCATAAACCTTTTTTATGCAGTTGCAATCAGCGTCAGTACAACAAATGTAAATCATTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_36260;size=6 reference=JN192372_SH093189.07FU_refs position=1..193 \n+GCGGCCGGCTGAATATTTTTTTTCACCCATGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCAAACCATAAACCTTTTTCTTATGCAGTTTCCATCAGCGTCAGTAAAAACAATGTAATTATTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_68944;size=5 reference=JX272968_SH208843.07FU_refs position=1..194 \n+CCGAGTGAGGGTCCCCTCCGGGGGGCCCAACCTCCCACCCGTGTCTACTGTACCATGTTGCTTCGGCGGGCGCGCCCGTGCCCGCCGGAGACCCCTTGAACGCTGTTGTGAATGAGGTTGTCTGAGTGAGATTGCAAACTGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_53837;size=8 reference=KJ638312_SH419903.07FU_refs position=1..194 \n+GATCATTACCGAGTTCTCGGGCTTCGGCTCGACTCTCCCACCCTTTGTGAACGTACCTCTGTTGCTTTGGCGGCTCCGGCCGCCAAAGGACCTCCAAACTCCAGTCAGTAAACGCAGACGTCTGATAAACAAGTTAATAAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_97017;size=9 reference=GU237816_SH186616.07FU_refs position=1..198 errors=164%A \n+ATCATTACCTAGAGTTGTGGGCTCTGCCTACCATCTCTTACCCATGTCTTTTGAGTACCTTCGTTTCCTCGGCGGGTCCGCCCGCCGATCGGACAACACTTAAACCCTTTGTAATTGAAATCAGCGTCTGAAAAAACTTTAATAGTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_2879;size=6 reference=KP744516_SH528288.07FU_refs position=1..198 errors=121%A \n+CCGAGTGAGGGTCTTCAAAGGCTCAACCTCCCAAACCCCTTGTATATCACCGAGAGTTTTATTGTTGCTTCGGTGGGTCCACAGTGCCCACCGAAGACCCACCAAAAATCCTAGTAAGAGTGTCGTCTGAGTAATTAAAAAATAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGC\n+>01_62211;size=4 reference=DQ103550_SH211946.07FU_refs position=1..202 errors=124%C \n+GGAAGGATCATTACCGAGTTCTCGAGCTTCGGCTCGACTCTCCCACCCTTTGTGAACACACCTCTGTTGCCTCGGCGGCCGCTCCGGCCGCCGAAGGACCTTCAAACTCCAGTCAGTAAACGCAGACGTCTGATAAACAAGTCAATGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_44950;size=6 reference=HE861827_SH187575.07FU_refs position=1..202 errors=146%A \n+TACAATATGAAGGCTTCGGCTGGATTATTTATTTCACCCTTGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCACACCATAAACCTTTTTTGTTAATGCAGTCAGCGTCAGTACAACAAATGTAAATCATTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_2696;size=9 reference=JQ746601_SH188617.07FU_refs position=1..210 errors=162%G \n+TTGAAATAAACCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTGTAGACTTTCCAAGTCTATGTTGCTTCATTTACCCCAATGTATGTTAATAGAATGTTGTCTTTTATAATATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_19311;size=7 reference=HQ880789_SH123218.07FU_refs position=1..211 errors=22%G \n+CCGAGTTTTCAACTCCCTAACCCTTTTGTGAACCTACCTATTGTTGCTTCGGCGGACTCGCCCCAGCCGGACGCGGACTGGACCAGCGGCCGCCGGGGACCCTCAAACTCTTGTATTATCAGCATCTTCTGAATACGCCGCAAGGCAAAACAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGC\n+>01_58799;size=9 reference=KP165574_SH188638.07FU_refs position=1..213 \n+TTGAAATAAACCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTTGTAGACCTTTCAGGTCTATGTTTTCTCATTTTACCCCAATGTATGTCGATAGAATGTTGTGCCTTTATAATGTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_36019;size=8 reference=KP013190_SH094425.07FU_refs position=1..213 errors=144%A \n+TTGAAATAAATCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTTGTAGACCCTTCAAGGTCTATGTCGCTTAATTTACCCCAAACAAATAATAGAATGTTGTGCCTTTGAAAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_235;size=6 reference=EF652441_SH091530.07FU_refs_singleton position=1..215 \n+AAGGATCATTACCGAGTGTAGGGTGCCTCCGGGCGCCCAACCTCCCACCCGTGACTACCTAACCCTGTTGCTTCGGCGGGGCGCCCCCCCGGGGGGCCGCCGCCGGGGACTACTGAACCTCCTGTCTGAGCCTGATGCAGTCTGAGCTTTGATATTAAATAGTCAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_52735;size=9 reference=JX436920_SH182391.07FU_refs '..b'ACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>02_82087_FROGS_combined;size=1 R1_desc:reference=UDB001581_SH219736.07FU_refs position=1..250 errors=80%G;R2_desc=R2_desc=reference=UDB001581_SH219736.07FU_refs position=1..250 errors=115+G \n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGGACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTCTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>03_40377_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=109+A;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=132%G \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACAACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGCGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_89678_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=124+C;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTCTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_32422_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=183+A;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=22%T \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATAGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCACGCATCGATGAAGAACGCAGC\n+>03_1160_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=126%G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=75+C \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTGCTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/01-prepro-flash.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-flash.html Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,799 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <https://www.gnu.org/licenses/>.\n+-->\n+<html>\n+ <head>\n+ <title>FROGS Pre-process</title>\n+ <meta charset="UTF-8">\n+ <meta name="version" content="r3.0-v1.0">\n+ <!-- CSS -->\n+ \n+ \n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"></link>\n+ <style type="text/css">\n+ #js-alert {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ #content {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ .clear {\n+ clear: both;\n+ height: 0px;\n+ width: 100%;\n+ float: none !important;\n+ }\n+ ul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 0px;\n+\t\t\t\tmargin-bottom: 15px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 20px;\n+\t\t\t\twidth: 20px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t\t\t.container input:checked ~ .checkmark {\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\topacity:1;\n+\t\t\t}\n+\n+\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n+\t\t\t.checkmark:after {\n+\t\t\t\tcontent: "";\n+\t\t\t\tposition: absolute;\n+\t\t\t\tdisplay: none;\n+\t\t\t}\n+\n+\t\t\t/* Show the checkmark when checked */\n+\t\t\t.container input:checked ~ .checkmark:after {\n+\t\t\t\tdisplay: block;\n+\t\t\t}\n+\n+\t\t\t/* Style the checkmark/indicator */\n+\t\t\t.container .checkmark:after {\n+\t\t\t\tleft: 7px;\n+\t\t\t\ttop: 3px;\n+\t\t\t\twidth: 6px;\n+\t\t\t\theight: 10px;\n+\t\t\t\tborder: solid white;\n+\t\t\t\tborder-wi'..b'oad("artificial combined", false, "filterBySample-table-artificialCombined", false); \n+ }else{\n+ $("#filterBySample-table-artificialCombined").prev("h2").remove();\n+ $("#filterBySample-table-artificialCombined").remove();\n+ }\n+ /*$("select").addClass("selectpicker");\n+ $(".dataTables_length select").selectpicker({\n+\t\t\t\t\tstyle: \'btn-info\',\n+\t\t\t\t\tsize: 2,\n+\t\t\t\t\twidth : \'60px\'\n+\t\t\t\t});\n+\t\t\t\t$(\'.selectpicker\').selectpicker(\'refresh\');\n+\t\t\t\t//$(\'select\').selectpicker(\'refresh\');\n+\t\t\t\t*/\n+ });\n+ </script>\n+ </head>\n+ <body>\n+ <!-- Alert -->\n+ <p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+ </p>\n+ \n+ <!-- Content -->\n+ <div id="content" class="hidden">\n+\t\t\t<h2 class="pb-2-first mt-4 mb-2 border-bottom" style="margin-top: 1rem">Preprocess summary</h2>\n+ <div id="filter-summary"></div>\n+ \n+ <div id="filter-log">\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Details on merged sequences</h2>\n+ <table id="filterBySample-table-combined" class="table table-striped">\n+ <thead>\n+\t\t\t\t\t\t<!--\n+ <tr>\n+ <th class="title">Filtering by sample : details on full length amplicon reads</th>\n+ </tr>\n+ -->\n+ </thead>\n+ <tbody></tbody>\n+ <tfoot>\n+ <tr>\n+ <th>\n+ <span class="table-action">With selection:</span> \n+ <button id="display-spl-lengths" class="btn table-action fusion-right" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="before-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display amplicon lengths</span> </button>\n+ <button id="display-after-spl-lengths" class="btn table-action" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="after-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display preprocessed amplicon lengths</span></button>\n+ </th>\n+ </tr>\n+ </tfoot>\n+ </table>\n+ <h2 class="pb-2 mt-4 mb-2 border-bottom">Details on artificial combined sequences</h2>\n+ <table id="filterBySample-table-artificialCombined" class="table table-striped">\n+ <thead>\n+ </thead>\n+ <tbody></tbody>\n+ </table>\n+ </div>\n+ </div>\n+ \n+ \n+ \n+ <!-- Modals -->\n+ <div class="modal" id="lengths-modal" tabindex="-1" role="dialog" aria-hidden="true">\n+ <div class="modal-dialog modal-lg">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <h4 class="modal-title">Amplicons lengths</h4>\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ \n+ \n+ </div>\n+ <div class="modal-body">\n+ <div id="lengths-chart"></div>\n+ </div>\n+ <div class="modal-footer">\n+ <button class="btn table-action fusion-right" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n+ </div>\n+ </div>\n+ </div>\n+ </div>\n+ </body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/01-prepro-flash.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-flash.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b"@@ -0,0 +1,363 @@\n+## Application\n+Software: preprocess.py (version: 3.1)\n+Command: /home/maria/workspace/git/FROGS/FROGS_master/test/../app/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --expected-amplicon-size 420 --merge-software flash --nb-cpus 4 --mismatch-rate 0.15 --keep-unmerged --input-archive /home/maria/workspace/git/FROGS/FROGS-wrapper_dev/test-data/input/temp/test_dataset.tar.gz --output-dereplicated res/01-prepro-flash.fasta --output-count res/01-prepro-flash.tsv --summary res/01-prepro-flash.html --log-file res/01-prepro-flash.log\n+\n+\n+##Sample\n+R1 : res/1550052675.22_3437_01_R1.fastq\n+R2 : res/1550052675.22_3437_01_R2.fastq\n+Sample name : 01\n+nb seq before process : 30000\n+##Commands\n+########################################################################################################\n+# Join overlapping paired reads. (flash version : v1.2.11)\n+Command:\n+\tflash --threads 1 --allow-outies --min-overlap 43 --max-overlap 133 --max-mismatch-density 0.15 --compress res/1550052675.22_3437_01_R1.fastq res/1550052675.22_3437_01_R2.fastq --output-directory res --output-prefix 1550052676.19_3438_01_flash 2> res/1550052676.19_3438_01_flash.stderr\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:16\n+\tend: 13 Feb 2019 11:11:22\n+\n+Results:\n+\tnb seq paired-end assembled: 17622\n+########################################################################################################\n+# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 1.18)\n+Command:\n+\tcutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res/1550052676.19_3438_01_cutadapt_5prim_trim.fastq.gz res/1550052676.19_3438_01_flash.extendedFrags.fastq.gz > res/1550052676.19_3438_01_cutadapt_5prim_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:22\n+\tend: 13 Feb 2019 11:11:25\n+\n+Results:\n+\tnb seq with 5' primer : 17622\n+########################################################################################################\n+# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 1.18)\n+Command:\n+\tcutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res/1550052676.19_3438_01_cutadapt.fastq.gz res/1550052676.19_3438_01_cutadapt_5prim_trim.fastq.gz > res/1550052676.19_3438_01_cutadapt_3prim_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:26\n+\tend: 13 Feb 2019 11:11:30\n+\n+Results:\n+\tnb seq with 3' primer : 17622\n+########################################################################################################\n+# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.5.0)\n+Command:\n+\tfilterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res/1550052676.19_3438_01_cutadapt.fastq.gz --output-file res/1550052676.19_3438_01_N_and_length_filter.fasta --log-file res/1550052676.19_3438_01_N_and_length_filter_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:30\n+\tend: 13 Feb 2019 11:11:31\n+\n+Results:\n+\tnb seq with expected length : 17622\n+\tnb seq without N : 17622\n+########################################################################################################\n+# Concatenate paired reads. (combine_and_split.py version : )\n+Command:\n+\tcombine_and_split.py --reads1 res/1550052676.19_3438_01_flash.notCombined_1.fastq.gz --reads2 res/1550052676.19_3438_01_flash.notCombined_2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res/1550052676.19_3438_01_artificial_combined.fastq.gz\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:31\n+\tend: 13 Feb 2019 11:11:38\n+\n+Results:\n+\tnb seq paired-end assembled: 12378\n+########################################################################################################\n+# Removes reads without the 5' primer "..b"#############################################\n+# Concatenate paired reads. (combine_and_split.py version : )\n+Command:\n+\tcombine_and_split.py --reads1 res/1550052676.18_3440_03_flash.notCombined_1.fastq.gz --reads2 res/1550052676.18_3440_03_flash.notCombined_2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res/1550052676.18_3440_03_artificial_combined.fastq.gz\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:30\n+\tend: 13 Feb 2019 11:11:37\n+\n+Results:\n+\tnb seq paired-end assembled: 12536\n+########################################################################################################\n+# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 1.18)\n+Command:\n+\tcutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res/1550052676.18_3440_03_art_comb_cutadapt_5prim_trim.fastq.gz res/1550052676.18_3440_03_artificial_combined.fastq.gz > res/1550052676.18_3440_03_art_comb_cutadapt_5prim_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:38\n+\tend: 13 Feb 2019 11:11:40\n+\n+Results:\n+\tnb seq with 5' primer : 12536\n+########################################################################################################\n+# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 1.18)\n+Command:\n+\tcutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res/1550052676.18_3440_03_art_comb_cutadapt.fastq.gz res/1550052676.18_3440_03_art_comb_cutadapt_5prim_trim.fastq.gz > res/1550052676.18_3440_03_art_comb_cutadapt_3prim_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:41\n+\tend: 13 Feb 2019 11:11:43\n+\n+Results:\n+\tnb seq with 3' primer : 12536\n+########################################################################################################\n+# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.5.0)\n+Command:\n+\tfilterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res/1550052676.18_3440_03_art_comb_cutadapt.fastq.gz --output-file res/1550052676.18_3440_03_art_N_filter.fasta --log-file res/1550052676.18_3440_03_art_N_filter_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:44\n+\tend: 13 Feb 2019 11:11:45\n+\n+Results:\n+\tnb seq with expected length : 12536\n+\tnb seq without N : 12536\n+########################################################################################################\n+# Replace join tag. (combine_and_split.py version : )\n+Command:\n+\tcombine_and_split.py --reads1 res/1550052676.18_3440_03_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res/1550052676.18_3440_03_art_XtoN.fasta\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:45\n+\tend: 13 Feb 2019 11:11:49\n+\n+########################################################################################################\n+# Dereplicates sample sequences. (derepSamples.py version : 1.6.1)\n+Command:\n+\tderepSamples.py --sequences-files res/1550052676.18_3440_03_N_and_length_filter.fasta res/1550052676.18_3440_03_art_XtoN.fasta --dereplicated-file res/1550052675.22_3437_03_filtered.fasta --count-file res/1550052676.18_3440_03_derep_count.tsv\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:49\n+\tend: 13 Feb 2019 11:11:51\n+\n+\n+\n+##Sample\n+All\n+##Commands\n+########################################################################################################\n+# Dereplicates together sequences from several samples. (derepSamples.py version : 1.6.1)\n+Command:\n+\tderepSamples.py --nb-cpus 4 --size-separator ';size=' --samples-ref res/1550052675.22_3437_derep_inputs.tsv --dereplicated-file res/01-prepro-flash.fasta --count-file res/01-prepro-flash.tsv\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:52\n+\tend: 13 Feb 2019 11:11:53\n+\n" |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/01-prepro-flash.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-flash.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/01-prepro-vsearch.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-vsearch.fasta Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,106306 @@\n+>03_41215;size=1 reference=EF420145_SH015623.07FU_refs_singleton position=1..238 errors=181%T \n+ACCTGCGGAAGGATCATTATTGAAGTAAACCTGATGGGCTGTCGCTGGCTCTCTAGGGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGGCCTTCCCAGGTCTATGTTGCTTCATTTGCCCCCCGATGTATGTCGATAGAATGTAATGTGCCTATAAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_45209;size=4 reference=AY615141_SH195460.07FU_refs position=1..239 \n+GGAAGGATCATTACCGAGTTGACTCGAGCTCCGGCTCGACTCTCCCACCCTATGTGTACCTACCTCTGTTGCTTTGGCGGGCCGCGGTCCTCCGCACCGGCCCCCTTTGGGGGCTGGCCAGCGCCCGCCAGAGGACCACAAAACTCCAGTCAGTAAACGTTGCAGTCTGAAAACCAAGTTAATAAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>02_37093;size=2 reference=AY953383_SH113362.07FU_refs position=1..239 \n+TACTGAGTTTTTGTACTCTATAAACCATGTGTGAACGTACCTATCTTGTAGTGAGATGAATGCTGTTTTGGTGGTAGGGCCCTTCTGAAGAGAGGGCACCGCTGCCAGCAGTATAGTCTCACCACTATAAAACTCTTTTATTATTTTCTAGATTTTTCATTGCTGAGTGGCATAACTATAAAAAAGTTAAAACTTTCAACAACGGATCTCTTGGCTCTAGCATCGATGAAGAACGCAGC\n+>01_85648;size=10 reference=UDB011541_SH194446.07FU_refs position=1..241 errors=144%A \n+GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\n+>01_1077;size=27 reference=FJ860822_SH177722.07FU_refs position=1..242 errors=219%G \n+CATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_10600;size=30 reference=UDB016470_SH189377.07FU_refs position=1..242 errors=81%G \n+CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_4137;size=45 reference=AJ786644_SH470265.07FU_refs_singleton position=1..243 errors=149%T \n+CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>01_55980;size=44 reference=EF669607_SH109271.07FU_refs_singleton position=1..243 errors=144%C \n+CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_49457;size=124 reference=GQ159830_SH222371.07FU_refs position=1..244 errors=122%C \n+TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>01_97871;size=336 reference=GQ169315_SH195598.07FU_refs position=1..245 \n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_93240;size=1 reference=GQ169315_SH195598.07FU_refs position=1..245 errors=174%A \n+TGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTTAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>01_59;size=923 reference=JN711441_SH022548.07FU_refs_singleton position=1..248 errors=206%T \n+AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n+>02_'..b'AACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>03_40377_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=109+A;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=132%G \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACAACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGCGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>02_30957_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=115%A;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=246+T \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCACAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_89678_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=124+C;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTCTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>01_32422_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=183+A;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=22%T \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATAGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCACGCATCGATGAAGAACGCAGC\n+>03_1160_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=126%G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=75+C \n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTGCTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/01-prepro-vsearch.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-vsearch.html Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,799 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <https://www.gnu.org/licenses/>.\n+-->\n+<html>\n+ <head>\n+ <title>FROGS Pre-process</title>\n+ <meta charset="UTF-8">\n+ <meta name="version" content="r3.0-v1.0">\n+ <!-- CSS -->\n+ \n+ \n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"></link>\n+ <style type="text/css">\n+ #js-alert {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ #content {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ .clear {\n+ clear: both;\n+ height: 0px;\n+ width: 100%;\n+ float: none !important;\n+ }\n+ ul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 0px;\n+\t\t\t\tmargin-bottom: 15px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 20px;\n+\t\t\t\twidth: 20px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t\t\t.container input:checked ~ .checkmark {\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\topacity:1;\n+\t\t\t}\n+\n+\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n+\t\t\t.checkmark:after {\n+\t\t\t\tcontent: "";\n+\t\t\t\tposition: absolute;\n+\t\t\t\tdisplay: none;\n+\t\t\t}\n+\n+\t\t\t/* Show the checkmark when checked */\n+\t\t\t.container input:checked ~ .checkmark:after {\n+\t\t\t\tdisplay: block;\n+\t\t\t}\n+\n+\t\t\t/* Style the checkmark/indicator */\n+\t\t\t.container .checkmark:after {\n+\t\t\t\tleft: 7px;\n+\t\t\t\ttop: 3px;\n+\t\t\t\twidth: 6px;\n+\t\t\t\theight: 10px;\n+\t\t\t\tborder: solid white;\n+\t\t\t\tborder-wi'..b'oad("artificial combined", false, "filterBySample-table-artificialCombined", false); \n+ }else{\n+ $("#filterBySample-table-artificialCombined").prev("h2").remove();\n+ $("#filterBySample-table-artificialCombined").remove();\n+ }\n+ /*$("select").addClass("selectpicker");\n+ $(".dataTables_length select").selectpicker({\n+\t\t\t\t\tstyle: \'btn-info\',\n+\t\t\t\t\tsize: 2,\n+\t\t\t\t\twidth : \'60px\'\n+\t\t\t\t});\n+\t\t\t\t$(\'.selectpicker\').selectpicker(\'refresh\');\n+\t\t\t\t//$(\'select\').selectpicker(\'refresh\');\n+\t\t\t\t*/\n+ });\n+ </script>\n+ </head>\n+ <body>\n+ <!-- Alert -->\n+ <p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+ </p>\n+ \n+ <!-- Content -->\n+ <div id="content" class="hidden">\n+\t\t\t<h2 class="pb-2-first mt-4 mb-2 border-bottom" style="margin-top: 1rem">Preprocess summary</h2>\n+ <div id="filter-summary"></div>\n+ \n+ <div id="filter-log">\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Details on merged sequences</h2>\n+ <table id="filterBySample-table-combined" class="table table-striped">\n+ <thead>\n+\t\t\t\t\t\t<!--\n+ <tr>\n+ <th class="title">Filtering by sample : details on full length amplicon reads</th>\n+ </tr>\n+ -->\n+ </thead>\n+ <tbody></tbody>\n+ <tfoot>\n+ <tr>\n+ <th>\n+ <span class="table-action">With selection:</span> \n+ <button id="display-spl-lengths" class="btn table-action fusion-right" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="before-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display amplicon lengths</span> </button>\n+ <button id="display-after-spl-lengths" class="btn table-action" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="after-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display preprocessed amplicon lengths</span></button>\n+ </th>\n+ </tr>\n+ </tfoot>\n+ </table>\n+ <h2 class="pb-2 mt-4 mb-2 border-bottom">Details on artificial combined sequences</h2>\n+ <table id="filterBySample-table-artificialCombined" class="table table-striped">\n+ <thead>\n+ </thead>\n+ <tbody></tbody>\n+ </table>\n+ </div>\n+ </div>\n+ \n+ \n+ \n+ <!-- Modals -->\n+ <div class="modal" id="lengths-modal" tabindex="-1" role="dialog" aria-hidden="true">\n+ <div class="modal-dialog modal-lg">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <h4 class="modal-title">Amplicons lengths</h4>\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ \n+ \n+ </div>\n+ <div class="modal-body">\n+ <div id="lengths-chart"></div>\n+ </div>\n+ <div class="modal-footer">\n+ <button class="btn table-action fusion-right" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n+ </div>\n+ </div>\n+ </div>\n+ </div>\n+ </body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/01-prepro-vsearch.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-vsearch.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b"@@ -0,0 +1,363 @@\n+## Application\n+Software: preprocess.py (version: 3.1)\n+Command: /home/maria/workspace/git/FROGS/FROGS_master/test/../app/preprocess.py illumina --min-amplicon-size 44 --max-amplicon-size 490 --five-prim-primer GGCGVACGGGTGAGTAA --three-prim-primer GTGCCAGCNGCNGCGG --R1-size 267 --R2-size 266 --merge-software vsearch --nb-cpus 4 --mismatch-rate 0.15 --keep-unmerged --input-archive /home/maria/workspace/git/FROGS/FROGS-wrapper_dev/test-data/input/temp/test_dataset.tar.gz --output-dereplicated res/01-prepro-vsearch.fasta --output-count res/01-prepro-vsearch.tsv --summary res/01-prepro-vsearch.html --log-file res/01-prepro-vsearch.log\n+\n+\n+##Sample\n+R1 : res/1550052713.63_3625_01_R1.fastq\n+R2 : res/1550052713.63_3625_01_R2.fastq\n+Sample name : 01\n+nb seq before process : 30000\n+##Commands\n+########################################################################################################\n+# join overlapping paired reads (vsearch version : v2.6.2_linux_x86_64)\n+Command:\n+\tvsearch --threads 1 --fastq_mergepairs res/1550052713.63_3625_01_R1.fastq --reverse res/1550052713.63_3625_01_R2.fastq --fastqout res/1550052714.69_3626_01_vsearch.assembled.fastq --fastqout_notmerged_fwd res/1550052714.69_3626_01_vsearch.unassembled_R1.fastq --fastqout_notmerged_rev res/1550052714.69_3626_01_vsearch.unassembled_R2.fastq --fastq_allowmergestagger --fastq_ascii 33 --fastq_maxdiffs 39 --fastq_minovlen 43 2> res/1550052714.69_3626_01_vsearch.log\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:54\n+\tend: 13 Feb 2019 11:11:56\n+\n+Results:\n+\tnb seq paired-end assembled: 13893\n+########################################################################################################\n+# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 1.18)\n+Command:\n+\tcutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res/1550052714.69_3626_01_cutadapt_5prim_trim.fastq.gz res/1550052714.69_3626_01_vsearch.assembled.fastq > res/1550052714.69_3626_01_cutadapt_5prim_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:56\n+\tend: 13 Feb 2019 11:11:58\n+\n+Results:\n+\tnb seq with 5' primer : 13893\n+########################################################################################################\n+# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 1.18)\n+Command:\n+\tcutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res/1550052714.69_3626_01_cutadapt.fastq.gz res/1550052714.69_3626_01_cutadapt_5prim_trim.fastq.gz > res/1550052714.69_3626_01_cutadapt_3prim_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:11:58\n+\tend: 13 Feb 2019 11:12:01\n+\n+Results:\n+\tnb seq with 3' primer : 13893\n+########################################################################################################\n+# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.5.0)\n+Command:\n+\tfilterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res/1550052714.69_3626_01_cutadapt.fastq.gz --output-file res/1550052714.69_3626_01_N_and_length_filter.fasta --log-file res/1550052714.69_3626_01_N_and_length_filter_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:02\n+\tend: 13 Feb 2019 11:12:02\n+\n+Results:\n+\tnb seq with expected length : 13893\n+\tnb seq without N : 13893\n+########################################################################################################\n+# Concatenate paired reads. (combine_and_split.py version : )\n+Command:\n+\tcombine_and_split.py --reads1 res/1550052714.69_3626_01_vsearch.unassembled_R1.fastq --reads2 res/1550052714.69_3626_01_vsearch.unassembled_R2.fastq -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res/1550052714.69_3626_01_artificial_combined.fastq.gz\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:03\n+\tend: 13 Feb 2019 11:12:11\n+\n+Results:\n+\tnb seq pai"..b"#########################################\n+# Concatenate paired reads. (combine_and_split.py version : )\n+Command:\n+\tcombine_and_split.py --reads1 res/1550052714.68_3628_03_vsearch.unassembled_R1.fastq --reads2 res/1550052714.68_3628_03_vsearch.unassembled_R2.fastq -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res/1550052714.68_3628_03_artificial_combined.fastq.gz\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:03\n+\tend: 13 Feb 2019 11:12:11\n+\n+Results:\n+\tnb seq paired-end assembled: 16123\n+########################################################################################################\n+# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 1.18)\n+Command:\n+\tcutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res/1550052714.68_3628_03_art_comb_cutadapt_5prim_trim.fastq.gz res/1550052714.68_3628_03_artificial_combined.fastq.gz > res/1550052714.68_3628_03_art_comb_cutadapt_5prim_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:12\n+\tend: 13 Feb 2019 11:12:15\n+\n+Results:\n+\tnb seq with 5' primer : 16123\n+########################################################################################################\n+# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 1.18)\n+Command:\n+\tcutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res/1550052714.68_3628_03_art_comb_cutadapt.fastq.gz res/1550052714.68_3628_03_art_comb_cutadapt_5prim_trim.fastq.gz > res/1550052714.68_3628_03_art_comb_cutadapt_3prim_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:16\n+\tend: 13 Feb 2019 11:12:20\n+\n+Results:\n+\tnb seq with 3' primer : 16123\n+########################################################################################################\n+# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.5.0)\n+Command:\n+\tfilterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res/1550052714.68_3628_03_art_comb_cutadapt.fastq.gz --output-file res/1550052714.68_3628_03_art_N_filter.fasta --log-file res/1550052714.68_3628_03_art_N_filter_log.txt\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:20\n+\tend: 13 Feb 2019 11:12:21\n+\n+Results:\n+\tnb seq with expected length : 16123\n+\tnb seq without N : 16123\n+########################################################################################################\n+# Replace join tag. (combine_and_split.py version : )\n+Command:\n+\tcombine_and_split.py --reads1 res/1550052714.68_3628_03_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res/1550052714.68_3628_03_art_XtoN.fasta\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:21\n+\tend: 13 Feb 2019 11:12:29\n+\n+########################################################################################################\n+# Dereplicates sample sequences. (derepSamples.py version : 1.6.1)\n+Command:\n+\tderepSamples.py --sequences-files res/1550052714.68_3628_03_N_and_length_filter.fasta res/1550052714.68_3628_03_art_XtoN.fasta --dereplicated-file res/1550052713.63_3625_03_filtered.fasta --count-file res/1550052714.68_3628_03_derep_count.tsv\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:29\n+\tend: 13 Feb 2019 11:12:30\n+\n+\n+\n+##Sample\n+All\n+##Commands\n+########################################################################################################\n+# Dereplicates together sequences from several samples. (derepSamples.py version : 1.6.1)\n+Command:\n+\tderepSamples.py --nb-cpus 4 --size-separator ';size=' --samples-ref res/1550052713.63_3625_derep_inputs.tsv --dereplicated-file res/01-prepro-vsearch.fasta --count-file res/01-prepro-vsearch.tsv\n+\n+Execution:\n+\tstart: 13 Feb 2019 11:12:30\n+\tend: 13 Feb 2019 11:12:31\n+\n" |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/01-prepro-vsearch.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/01-prepro-vsearch.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/02-clustering.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/02-clustering.biom Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"comment": "na", "seed_id": "01_58367"}}, {"id": "Cluster_2", "metadata": {"comment": "na", "seed_id": "01_57964"}}, {"id": "Cluster_3", "metadata": {"comment": "na", "seed_id": "01_67063"}}, {"id": "Cluster_4", "metadata": {"comment": "na", "seed_id": "01_80623"}}, {"id": "Cluster_5", "metadata": {"comment": "na", "seed_id": "01_256"}}, {"id": "Cluster_6", "metadata": {"comment": "na", "seed_id": "01_54434"}}, {"id": "Cluster_7", "metadata": {"comment": "na", "seed_id": "01_44905"}}, {"id": "Cluster_8", "metadata": {"comment": "na", "seed_id": "01_81"}}, {"id": "Cluster_9", "metadata": {"comment": "na", "seed_id": "01_92283"}}, {"id": "Cluster_10", "metadata": {"comment": "na", "seed_id": "01_84442"}}, {"id": "Cluster_11", "metadata": {"comment": "na", "seed_id": "01_50"}}, {"id": "Cluster_12", "metadata": {"comment": "na", "seed_id": "01_39187"}}, {"id": "Cluster_13", "metadata": {"comment": "na", "seed_id": "01_97"}}, {"id": "Cluster_14", "metadata": {"comment": "na", "seed_id": "01_81865"}}, {"id": "Cluster_15", "metadata": {"comment": "na", "seed_id": "01_151"}}, {"id": "Cluster_16", "metadata": {"comment": "na", "seed_id": "01_97361"}}, {"id": "Cluster_17", "metadata": {"comment": "na", "seed_id": "01_71178"}}, {"id": "Cluster_18", "metadata": {"comment": "na", "seed_id": "01_75"}}, {"id": "Cluster_19", "metadata": {"comment": "na", "seed_id": "01_47826"}}, {"id": "Cluster_20", "metadata": {"comment": "na", "seed_id": "01_78640"}}, {"id": "Cluster_21", "metadata": {"comment": "na", "seed_id": "01_99"}}, {"id": "Cluster_22", "metadata": {"comment": "na", "seed_id": "01_38"}}, {"id": "Cluster_23", "metadata": {"comment": "na", "seed_id": "01_87091"}}, {"id": "Cluster_24", "metadata": {"comment": "na", "seed_id": "01_59"}}, {"id": "Cluster_25", "metadata": {"comment": "na", "seed_id": "01_165"}}, {"id": "Cluster_26", "metadata": {"comment": "na", "seed_id": "01_75264"}}, {"id": "Cluster_27", "metadata": {"comment": "na", "seed_id": "01_40"}}, {"id": "Cluster_28", "metadata": {"comment": "na", "seed_id": "01_90154"}}, {"id": "Cluster_29", "metadata": {"comment": "na", "seed_id": "01_102"}}, {"id": "Cluster_30", "metadata": {"comment": "na", "seed_id": "01_30455"}}, {"id": "Cluster_31", "metadata": {"comment": "na", "seed_id": "01_87"}}, {"id": "Cluster_32", "metadata": {"comment": "na", "seed_id": "01_11"}}, {"id": "Cluster_33", "metadata": {"comment": "na", "seed_id": "01_443"}}, {"id": "Cluster_34", "metadata": {"comment": "na", "seed_id": "01_75598"}}, {"id": "Cluster_35", "metadata": {"comment": "na", "seed_id": "01_94826"}}, {"id": "Cluster_36", "metadata": {"comment": "na", "seed_id": "01_53126"}}, {"id": "Cluster_37", "metadata": {"comment": "na", "seed_id": "01_73924"}}, {"id": "Cluster_38", "metadata": {"comment": "na", "seed_id": "01_324"}}, {"id": "Cluster_39", "metadata": {"comment": "na", "seed_id": "01_35137"}}, {"id": "Cluster_40", "metadata": {"comment": "na", "seed_id": "01_53083"}}, {"id": "Cluster_41", "metadata": {"comment": "na", "seed_id": "01_32761"}}, {"id": "Cluster_42", "metadata": {"comment": "na", "seed_id": "01_30"}}, {"id": "Cluster_43", "metadata": {"comment": "na", "seed_id": "01_81788"}}, {"id": "Cluster_44", "metadata": {"comment": "na", "seed_id": "01_80125"}}, {"id": "Cluster_45_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_59702_FROGS_combined"}}, {"id": "Cluster_46_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_81428_FROGS_combined"}}, {"id": "Cluster_47_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_725_FROGS_combined"}}, {"id": "Cluster_48_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_54177_FROGS_combined"}}, {"id": "Cluster_49", "metadata": {"comment": "na", "seed_id": "01_97871"}}, {"id": "Cluster_50", "metadata": {"comment": "na", "seed_id": "01_49457"}}, {"id": "Cluster_51", "metadata": {"comment": "na", "seed_id": "01_53983"}}, {"id": "Clus'..b'95, 0, 1], [44196, 0, 1], [44197, 0, 1], [44198, 0, 1], [44199, 0, 1], [44200, 0, 1], [44201, 0, 1], [44202, 0, 1], [44203, 0, 1], [44204, 0, 1], [44205, 0, 1], [44206, 0, 1], [44207, 0, 1], [44208, 0, 1], [44209, 0, 1], [44210, 0, 1], [44211, 0, 1], [44212, 0, 1], [44213, 0, 1], [44214, 0, 1], [44215, 0, 1], [44216, 0, 1], [44217, 0, 1], [44218, 0, 1], [44219, 0, 1], [44220, 0, 1], [44221, 0, 1], [44222, 0, 1], [44223, 0, 1], [44224, 0, 1], [44225, 0, 1], [44226, 0, 1], [44227, 0, 1], [44228, 0, 1], [44229, 0, 1], [44230, 0, 1], [44231, 0, 1], [44232, 0, 1], [44233, 0, 1], [44234, 0, 1], [44235, 0, 1], [44236, 0, 1], [44237, 0, 1], [44238, 0, 1], [44239, 0, 1], [44240, 0, 1], [44241, 0, 1], [44242, 0, 1], [44243, 0, 1], [44244, 0, 1], [44245, 0, 1], [44246, 0, 1], [44247, 0, 1], [44248, 0, 1], [44249, 0, 1], [44250, 0, 1], [44251, 0, 1], [44252, 0, 1], [44253, 0, 1], [44254, 0, 1], [44255, 0, 1], [44256, 0, 1], [44257, 0, 1], [44258, 0, 1], [44259, 0, 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[44326, 0, 1], [44327, 0, 1], [44328, 0, 1], [44329, 0, 1], [44330, 0, 1], [44331, 0, 1], [44332, 0, 1], [44333, 0, 1], [44334, 0, 1], [44335, 0, 1], [44336, 0, 1], [44337, 0, 1], [44338, 0, 1], [44339, 0, 1], [44340, 0, 1], [44341, 0, 1], [44342, 0, 1], [44343, 0, 1], [44344, 0, 1], [44345, 0, 1], [44346, 0, 1], [44347, 0, 1], [44348, 0, 1], [44349, 0, 1], [44350, 0, 1], [44351, 0, 1], [44352, 0, 1], [44353, 0, 1], [44354, 0, 1], [44355, 0, 1], [44356, 0, 1], [44357, 0, 1], [44358, 0, 1], [44359, 0, 1], [44360, 0, 1], [44361, 0, 1], [44362, 0, 1], [44363, 0, 1], [44364, 0, 1], [44365, 0, 1], [44366, 0, 1], [44367, 0, 1], [44368, 0, 1], [44369, 0, 1], [44370, 0, 1], [44371, 0, 1], [44372, 0, 1], [44373, 0, 1], [44374, 0, 1], [44375, 0, 1], [44376, 0, 1], [44377, 0, 1], [44378, 0, 1], [44379, 0, 1], [44380, 0, 1], [44381, 0, 1], [44382, 0, 1], [44383, 0, 1], [44384, 0, 1], [44385, 0, 1], [44386, 0, 1], [44387, 0, 1], [44388, 0, 1], [44389, 0, 1], [44390, 0, 1], [44391, 0, 1], [44392, 0, 1], [44393, 0, 1], [44394, 0, 1], [44395, 0, 1], [44396, 0, 1], [44397, 0, 1], [44398, 0, 1], [44399, 0, 1], [44400, 0, 1], [44401, 0, 1], [44402, 0, 1], [44403, 0, 1], [44404, 0, 1], [44405, 0, 1], [44406, 0, 1], [44407, 0, 1], [44408, 0, 1], [44409, 0, 1], [44410, 0, 1], [44411, 0, 1], [44412, 0, 1], [44413, 0, 1], [44414, 0, 1], [44415, 0, 1], [44416, 0, 1], [44417, 0, 1], [44418, 0, 1], [44419, 0, 1], [44420, 0, 1], [44421, 0, 1], [44422, 0, 1], [44423, 0, 1], [44424, 0, 1], [44425, 0, 1], [44426, 0, 1], [44427, 0, 1], [44428, 0, 1], [44429, 0, 1], [44430, 0, 1], [44431, 0, 1], [44432, 0, 1], [44433, 0, 1], [44434, 0, 1], [44435, 0, 1], [44436, 0, 1], [44437, 0, 1], [44438, 0, 1], [44439, 0, 1], [44440, 0, 1]], "generated_by": "swarm", "matrix_type": "sparse", "shape": [44441, 3], "format_url": "http://biom-format.org", "date": "2019-02-13T11:13:13", "type": "OTU table", "id": null, "columns": [{"id": "01", "metadata": null}, {"id": "02", "metadata": null}, {"id": "03", "metadata": null}]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/02-clustering.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/02-clustering.fasta Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,88882 @@\n+>Cluster_1 reference=JQ279537_SH175098.07FU_refs position=1..250 errors=228%A\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=206%G\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3 reference=GU474801_SH104786.07FU_refs_singleton position=1..250 errors=198%T\n+GAAGGATCATTACTGAAGAACTATATCGAGTTTTTTTATACCCTTTTGTTTACCTACCCTATTGCTTCCACTGGACAGGTTTCACCTTGTGTGGGTCCTCTCTGGCTTGTGTGAAAAGCACCTGCCAGACAGACGTTGCTGGTGGGAAGAACTATTTACTAAAACTTGATTTTTAAAAAAAAATACAATGTCTGAATAATTTCCTTTAATGAAATAAAACTTTCAACAACGGATCTCTAGGCTCTTGCATCGATGAAGAACGCAGT\n+>Cluster_4 reference=UDB015350_SH176685.07FU_refs position=1..250 errors=245%A\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_5 reference=JQ716403_SH219241.07FU_refs position=1..250 errors=163%G\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_6 reference=UDB002317_SH221025.07FU_refs position=1..250 errors=215%C\n+CTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGCTGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGAGGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATTTTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTAAATGATAAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_7 reference=DQ898183_SH216206.07FU_refs position=1..249\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_8 reference=AF456924_SH097201.07FU_refs position=1..250\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_9 reference=JF747094_SH197643.07FU_refs position=1..249 errors=246%T\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10 reference=HQ714696_SH221416.07FU_refs position=1..250 errors=249%T\n+ATCCGGAGGGGAGATGAAGAGGGAATTTAGTAGGAACCGTAGGCATTGTCGCTGGCCTTTGGAAACAAACGCATGTGCACATCTCGAAAGTCTTACTTAGTACCTCGATCTCTTTCCTTTTGTGAACCCCTTTTCTTACACCTGTGCACCCATTGTAGGTCCCGCGAGGGATCCTATGTCTCTATCTACTCTTAAATGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTTGGTTGGCGGCAGTAAAGAACCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11 reference=UDB000320_SH220111.07FU_refs position=1..250\n+TCGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGGAGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGA'..b'TAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_15675_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=127%G;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=230+A\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGAGTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATTCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_9282_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=218%A;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=226+C\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCATTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTGTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_17530_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=34%C,144+G\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATCGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGGTCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2099_FROGS_combined R1_desc:reference=UDB001581_SH219736.07FU_refs position=1..250 errors=134%T;R2_desc=R2_desc=reference=UDB001581_SH219736.07FU_refs position=1..250 errors=89+G\n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTTCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGCAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_4257_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=124+C;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTCTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/02-clustering.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/02-clustering.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,69 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/clustering.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/clustering.py --distance 3 --denoising --input-fasta res/01-prepro-vsearch.fasta --input-count res/01-prepro-vsearch.tsv --output-biom res/02-clustering.biom --output-fasta res/02-clustering.fasta --output-compo res/02-clustering_compo.tsv --log-file res/02-clustering.log --nb-cpus 4 + +######################################################################################################## +# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0) +Command: + sortAbundancies.py --size-separator ';size=' --input-file res/01-prepro-vsearch.fasta --output-file res/1550052751.99_3808_01-prepro-vsearch_sorted.fasta + +Execution: + start: 13 Feb 2019 11:12:32 + end: 13 Feb 2019 11:12:32 + +repalce N tags by A. in: res/1550052751.99_3808_01-prepro-vsearch_sorted.fasta out : res/1550052751.99_3808_01-prepro-vsearch_sorted_NtoA.fasta +######################################################################################################## +# Clustering sequences. (swarm version : 2.2.2) +Command: + swarm --differences 1 --threads 4 --log res/1550052751.99_3808_01-prepro-vsearch_denoising_log.txt --output-file res/1550052751.99_3808_01-prepro-vsearch_denoising_composition.txt res/1550052751.99_3808_01-prepro-vsearch_sorted_NtoA.fasta + +Execution: + start: 13 Feb 2019 11:12:32 + end: 13 Feb 2019 11:12:50 + +######################################################################################################## +# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1) +Command: + extractSwarmsFasta.py --input-fasta res/1550052751.99_3808_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res/1550052751.99_3808_01-prepro-vsearch_denoising_composition.txt --output-fasta res/1550052751.99_3808_01-prepro-vsearch_denoising_seeds.fasta + +Execution: + start: 13 Feb 2019 11:12:50 + end: 13 Feb 2019 11:12:50 + +######################################################################################################## +# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0) +Command: + sortAbundancies.py --size-separator '_' --input-file res/1550052751.99_3808_01-prepro-vsearch_denoising_resizedSeeds.fasta --output-file res/1550052751.99_3808_01-prepro-vsearch_denoising_sortedSeeds.fasta + +Execution: + start: 13 Feb 2019 11:12:51 + end: 13 Feb 2019 11:12:51 + +######################################################################################################## +# Clustering sequences. (swarm version : 2.2.2) +Command: + swarm --differences 3 --threads 4 --log res/1550052751.99_3808_01-prepro-vsearch_swarm_log.txt --output-file res/1550052751.99_3808_01-prepro-vsearch_swarmD3_composition.txt res/1550052751.99_3808_01-prepro-vsearch_denoising_sortedSeeds.fasta + +Execution: + start: 13 Feb 2019 11:12:51 + end: 13 Feb 2019 11:13:13 + +######################################################################################################## +# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0) +Command: + swarm2biom.py --clusters-file res/02-clustering_compo.tsv --count-file res/01-prepro-vsearch.tsv --output-file res/02-clustering.biom + +Execution: + start: 13 Feb 2019 11:13:13 + end: 13 Feb 2019 11:13:14 + +######################################################################################################## +# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1) +Command: + extractSwarmsFasta.py --input-fasta res/1550052751.99_3808_01-prepro-vsearch_denoising_sortedSeeds.fasta --input-swarms res/1550052751.99_3808_01-prepro-vsearch_swarmD3_composition.txt --output-fasta res/1550052751.99_3808_01-prepro-vsearch_final_seeds.fasta + +Execution: + start: 13 Feb 2019 11:13:14 + end: 13 Feb 2019 11:13:14 + +repalce A tags by N. in: res/1550052751.99_3808_01-prepro-vsearch_final_seeds.fasta out : res/02-clustering.fasta |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/02-clustering_compo.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/02-clustering_compo.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/03-chimera.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/03-chimera.biom Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"comment": "na", "seed_id": "01_58367"}}, {"id": "Cluster_2", "metadata": {"comment": "na", "seed_id": "01_57964"}}, {"id": "Cluster_3", "metadata": {"comment": "na", "seed_id": "01_67063"}}, {"id": "Cluster_4", "metadata": {"comment": "na", "seed_id": "01_80623"}}, {"id": "Cluster_5", "metadata": {"comment": "na", "seed_id": "01_256"}}, {"id": "Cluster_6", "metadata": {"comment": "na", "seed_id": "01_54434"}}, {"id": "Cluster_7", "metadata": {"comment": "na", "seed_id": "01_44905"}}, {"id": "Cluster_8", "metadata": {"comment": "na", "seed_id": "01_81"}}, {"id": "Cluster_9", "metadata": {"comment": "na", "seed_id": "01_92283"}}, {"id": "Cluster_10", "metadata": {"comment": "na", "seed_id": "01_84442"}}, {"id": "Cluster_11", "metadata": {"comment": "na", "seed_id": "01_50"}}, {"id": "Cluster_12", "metadata": {"comment": "na", "seed_id": "01_39187"}}, {"id": "Cluster_13", "metadata": {"comment": "na", "seed_id": "01_97"}}, {"id": "Cluster_14", "metadata": {"comment": "na", "seed_id": "01_81865"}}, {"id": "Cluster_15", "metadata": {"comment": "na", "seed_id": "01_151"}}, {"id": "Cluster_16", "metadata": {"comment": "na", "seed_id": "01_97361"}}, {"id": "Cluster_17", "metadata": {"comment": "na", "seed_id": "01_71178"}}, {"id": "Cluster_18", "metadata": {"comment": "na", "seed_id": "01_75"}}, {"id": "Cluster_19", "metadata": {"comment": "na", "seed_id": "01_47826"}}, {"id": "Cluster_20", "metadata": {"comment": "na", "seed_id": "01_78640"}}, {"id": "Cluster_21", "metadata": {"comment": "na", "seed_id": "01_99"}}, {"id": "Cluster_22", "metadata": {"comment": "na", "seed_id": "01_38"}}, {"id": "Cluster_23", "metadata": {"comment": "na", "seed_id": "01_87091"}}, {"id": "Cluster_24", "metadata": {"comment": "na", "seed_id": "01_59"}}, {"id": "Cluster_25", "metadata": {"comment": "na", "seed_id": "01_165"}}, {"id": "Cluster_26", "metadata": {"comment": "na", "seed_id": "01_75264"}}, {"id": "Cluster_27", "metadata": {"comment": "na", "seed_id": "01_40"}}, {"id": "Cluster_28", "metadata": {"comment": "na", "seed_id": "01_90154"}}, {"id": "Cluster_29", "metadata": {"comment": "na", "seed_id": "01_102"}}, {"id": "Cluster_30", "metadata": {"comment": "na", "seed_id": "01_30455"}}, {"id": "Cluster_31", "metadata": {"comment": "na", "seed_id": "01_87"}}, {"id": "Cluster_32", "metadata": {"comment": "na", "seed_id": "01_11"}}, {"id": "Cluster_33", "metadata": {"comment": "na", "seed_id": "01_443"}}, {"id": "Cluster_34", "metadata": {"comment": "na", "seed_id": "01_75598"}}, {"id": "Cluster_35", "metadata": {"comment": "na", "seed_id": "01_94826"}}, {"id": "Cluster_36", "metadata": {"comment": "na", "seed_id": "01_53126"}}, {"id": "Cluster_37", "metadata": {"comment": "na", "seed_id": "01_73924"}}, {"id": "Cluster_38", "metadata": {"comment": "na", "seed_id": "01_324"}}, {"id": "Cluster_39", "metadata": {"comment": "na", "seed_id": "01_35137"}}, {"id": "Cluster_40", "metadata": {"comment": "na", "seed_id": "01_53083"}}, {"id": "Cluster_41", "metadata": {"comment": "na", "seed_id": "01_32761"}}, {"id": "Cluster_42", "metadata": {"comment": "na", "seed_id": "01_30"}}, {"id": "Cluster_43", "metadata": {"comment": "na", "seed_id": "01_81788"}}, {"id": "Cluster_44", "metadata": {"comment": "na", "seed_id": "01_80125"}}, {"id": "Cluster_45_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_59702_FROGS_combined"}}, {"id": "Cluster_46_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_81428_FROGS_combined"}}, {"id": "Cluster_47_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_725_FROGS_combined"}}, {"id": "Cluster_48_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_54177_FROGS_combined"}}, {"id": "Cluster_49", "metadata": {"comment": "na", "seed_id": "01_97871"}}, {"id": "Cluster_50", "metadata": {"comment": "na", "seed_id": "01_49457"}}, {"id": "Cluster_51", "metadata": {"comment": "na", "seed_id": "01_53983"}}, {"id": "Clus'..b'71, 0, 1], [44172, 0, 1], [44173, 0, 1], [44174, 0, 1], [44175, 0, 1], [44176, 0, 1], [44177, 0, 1], [44178, 0, 1], [44179, 0, 1], [44180, 0, 1], [44181, 0, 1], [44182, 0, 1], [44183, 0, 1], [44184, 0, 1], [44185, 0, 1], [44186, 0, 1], [44187, 0, 1], [44188, 0, 1], [44189, 0, 1], [44190, 0, 1], [44191, 0, 1], [44192, 0, 1], [44193, 0, 1], [44194, 0, 1], [44195, 0, 1], [44196, 0, 1], [44197, 0, 1], [44198, 0, 1], [44199, 0, 1], [44200, 0, 1], [44201, 0, 1], [44202, 0, 1], [44203, 0, 1], [44204, 0, 1], [44205, 0, 1], [44206, 0, 1], [44207, 0, 1], [44208, 0, 1], [44209, 0, 1], [44210, 0, 1], [44211, 0, 1], [44212, 0, 1], [44213, 0, 1], [44214, 0, 1], [44215, 0, 1], [44216, 0, 1], [44217, 0, 1], [44218, 0, 1], [44219, 0, 1], [44220, 0, 1], [44221, 0, 1], [44222, 0, 1], [44223, 0, 1], [44224, 0, 1], [44225, 0, 1], [44226, 0, 1], [44227, 0, 1], [44228, 0, 1], [44229, 0, 1], [44230, 0, 1], [44231, 0, 1], [44232, 0, 1], [44233, 0, 1], [44234, 0, 1], [44235, 0, 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[44302, 0, 1], [44303, 0, 1], [44304, 0, 1], [44305, 0, 1], [44306, 0, 1], [44307, 0, 1], [44308, 0, 1], [44309, 0, 1], [44310, 0, 1], [44311, 0, 1], [44312, 0, 1], [44313, 0, 1], [44314, 0, 1], [44315, 0, 1], [44316, 0, 1], [44317, 0, 1], [44318, 0, 1], [44319, 0, 1], [44320, 0, 1], [44321, 0, 1], [44322, 0, 1], [44323, 0, 1], [44324, 0, 1], [44325, 0, 1], [44326, 0, 1], [44327, 0, 1], [44328, 0, 1], [44329, 0, 1], [44330, 0, 1], [44331, 0, 1], [44332, 0, 1], [44333, 0, 1], [44334, 0, 1], [44335, 0, 1], [44336, 0, 1], [44337, 0, 1], [44338, 0, 1], [44339, 0, 1], [44340, 0, 1], [44341, 0, 1], [44342, 0, 1], [44343, 0, 1], [44344, 0, 1], [44345, 0, 1], [44346, 0, 1], [44347, 0, 1], [44348, 0, 1], [44349, 0, 1], [44350, 0, 1], [44351, 0, 1], [44352, 0, 1], [44353, 0, 1], [44354, 0, 1], [44355, 0, 1], [44356, 0, 1], [44357, 0, 1], [44358, 0, 1], [44359, 0, 1], [44360, 0, 1], [44361, 0, 1], [44362, 0, 1], [44363, 0, 1], [44364, 0, 1], [44365, 0, 1], [44366, 0, 1], [44367, 0, 1], [44368, 0, 1], [44369, 0, 1], [44370, 0, 1], [44371, 0, 1], [44372, 0, 1], [44373, 0, 1], [44374, 0, 1], [44375, 0, 1], [44376, 0, 1], [44377, 0, 1], [44378, 0, 1], [44379, 0, 1], [44380, 0, 1], [44381, 0, 1], [44382, 0, 1], [44383, 0, 1], [44384, 0, 1], [44385, 0, 1], [44386, 0, 1], [44387, 0, 1], [44388, 0, 1], [44389, 0, 1], [44390, 0, 1], [44391, 0, 1], [44392, 0, 1], [44393, 0, 1], [44394, 0, 1], [44395, 0, 1], [44396, 0, 1], [44397, 0, 1], [44398, 0, 1], [44399, 0, 1], [44400, 0, 1], [44401, 0, 1], [44402, 0, 1], [44403, 0, 1], [44404, 0, 1], [44405, 0, 1], [44406, 0, 1], [44407, 0, 1], [44408, 0, 1], [44409, 0, 1], [44410, 0, 1], [44411, 0, 1], [44412, 0, 1], [44413, 0, 1], [44414, 0, 1], [44415, 0, 1], [44416, 0, 1]], "generated_by": "swarm", "matrix_type": "sparse", "shape": [44417, 3], "format_url": "http://biom-format.org", "date": "2019-02-13T11:13:13", "type": "OTU table", "id": null, "columns": [{"id": "01", "metadata": null}, {"id": "02", "metadata": null}, {"id": "03", "metadata": null}]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/03-chimera.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/03-chimera.fasta Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,88834 @@\n+>Cluster_1 reference=JQ279537_SH175098.07FU_refs position=1..250 errors=228%A\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=206%G\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3 reference=GU474801_SH104786.07FU_refs_singleton position=1..250 errors=198%T\n+GAAGGATCATTACTGAAGAACTATATCGAGTTTTTTTATACCCTTTTGTTTACCTACCCTATTGCTTCCACTGGACAGGTTTCACCTTGTGTGGGTCCTCTCTGGCTTGTGTGAAAAGCACCTGCCAGACAGACGTTGCTGGTGGGAAGAACTATTTACTAAAACTTGATTTTTAAAAAAAAATACAATGTCTGAATAATTTCCTTTAATGAAATAAAACTTTCAACAACGGATCTCTAGGCTCTTGCATCGATGAAGAACGCAGT\n+>Cluster_4 reference=UDB015350_SH176685.07FU_refs position=1..250 errors=245%A\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_5 reference=JQ716403_SH219241.07FU_refs position=1..250 errors=163%G\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_6 reference=UDB002317_SH221025.07FU_refs position=1..250 errors=215%C\n+CTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGCTGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGAGGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATTTTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTAAATGATAAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_7 reference=DQ898183_SH216206.07FU_refs position=1..249\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_8 reference=AF456924_SH097201.07FU_refs position=1..250\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_9 reference=JF747094_SH197643.07FU_refs position=1..249 errors=246%T\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10 reference=HQ714696_SH221416.07FU_refs position=1..250 errors=249%T\n+ATCCGGAGGGGAGATGAAGAGGGAATTTAGTAGGAACCGTAGGCATTGTCGCTGGCCTTTGGAAACAAACGCATGTGCACATCTCGAAAGTCTTACTTAGTACCTCGATCTCTTTCCTTTTGTGAACCCCTTTTCTTACACCTGTGCACCCATTGTAGGTCCCGCGAGGGATCCTATGTCTCTATCTACTCTTAAATGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTTGGTTGGCGGCAGTAAAGAACCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11 reference=UDB000320_SH220111.07FU_refs position=1..250\n+TCGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGGAGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGA'..b'TAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_15675_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=127%G;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=230+A\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGAGTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATTCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_9282_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=218%A;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=226+C\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCATTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTGTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_17530_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=34%C,144+G\n+TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATCGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGGTCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2099_FROGS_combined R1_desc:reference=UDB001581_SH219736.07FU_refs position=1..250 errors=134%T;R2_desc=R2_desc=reference=UDB001581_SH219736.07FU_refs position=1..250 errors=89+G\n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTTCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGCAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_4257_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=124+C;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTCTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/03-chimera.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/03-chimera.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,49 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/remove_chimera.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/remove_chimera.py --input-fasta res/02-clustering.fasta --input-biom res/02-clustering.biom --non-chimera res/03-chimera.fasta --out-abundance res/03-chimera.biom --summary res/03-chimera.html --log-file res/03-chimera.log --nb-cpus 4 + +######################################################################################################## +# Removes PCR chimera by samples. (parallelChimera.py version : 0.7.1 [vsearch v2.6.2_linux_x86_64]) +Command: + parallelChimera.py --lenient-filter --nb-cpus 4 --sequences res/02-clustering.fasta --biom res/02-clustering.biom --non-chimera res/03-chimera.fasta --out-abundance res/03-chimera.biom --summary res/1550052794.75_3868_03-chimera.fasta_summary.tsv --log-file res/1550052794.75_3868_03-chimera.fasta_tmp.log + +Execution: + start: 13 Feb 2019 11:13:14 + end: 13 Feb 2019 11:13:53 + + + +##Sample : 01 +## Vsearch command: vsearch --uchime_denovo res/1550052794.82_3873_01.fasta.tmp --nonchimeras res/1550052794.82_3873_01.fasta --uchimeout res/1550052794.82_3873_01.fasta.log +##Results +sample_name: 01 +nb_chimera: 14 +chimera_abun: 14 +max_chimera_abun: 1 +nb_non_chimera: 14795 +non_chimera_abun: 29986 + +##Sample : 02 +## Vsearch command: vsearch --uchime_denovo res/1550052794.82_3873_02.fasta.tmp --nonchimeras res/1550052794.82_3873_02.fasta --uchimeout res/1550052794.82_3873_02.fasta.log +##Results +sample_name: 02 +nb_chimera: 7 +chimera_abun: 7 +max_chimera_abun: 1 +nb_non_chimera: 14930 +non_chimera_abun: 29993 + +##Sample : 03 +## Vsearch command: vsearch --uchime_denovo res/1550052794.82_3873_03.fasta.tmp --nonchimeras res/1550052794.82_3873_03.fasta --uchimeout res/1550052794.82_3873_03.fasta.log +##Results +sample_name: 03 +nb_chimera: 3 +chimera_abun: 3 +max_chimera_abun: 1 +nb_non_chimera: 14899 +non_chimera_abun: 29997 + + +## Removes the chimera observation from BIOM. + + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/04-filters.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/04-filters.biom Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"comment": "na", "seed_id": "01_58367"}}, {"id": "Cluster_2", "metadata": {"comment": "na", "seed_id": "01_57964"}}, {"id": "Cluster_3", "metadata": {"comment": "na", "seed_id": "01_67063"}}, {"id": "Cluster_4", "metadata": {"comment": "na", "seed_id": "01_80623"}}, {"id": "Cluster_5", "metadata": {"comment": "na", "seed_id": "01_256"}}, {"id": "Cluster_6", "metadata": {"comment": "na", "seed_id": "01_54434"}}, {"id": "Cluster_7", "metadata": {"comment": "na", "seed_id": "01_44905"}}, {"id": "Cluster_8", "metadata": {"comment": "na", "seed_id": "01_81"}}, {"id": "Cluster_9", "metadata": {"comment": "na", "seed_id": "01_92283"}}, {"id": "Cluster_10", "metadata": {"comment": "na", "seed_id": "01_84442"}}, {"id": "Cluster_11", "metadata": {"comment": "na", "seed_id": "01_50"}}, {"id": "Cluster_12", "metadata": {"comment": "na", "seed_id": "01_39187"}}, {"id": "Cluster_13", "metadata": {"comment": "na", "seed_id": "01_97"}}, {"id": "Cluster_14", "metadata": {"comment": "na", "seed_id": "01_81865"}}, {"id": "Cluster_15", "metadata": {"comment": "na", "seed_id": "01_151"}}, {"id": "Cluster_16", "metadata": {"comment": "na", "seed_id": "01_97361"}}, {"id": "Cluster_17", "metadata": {"comment": "na", "seed_id": "01_71178"}}, {"id": "Cluster_18", "metadata": {"comment": "na", "seed_id": "01_75"}}, {"id": "Cluster_19", "metadata": {"comment": "na", "seed_id": "01_47826"}}, {"id": "Cluster_20", "metadata": {"comment": "na", "seed_id": "01_78640"}}, {"id": "Cluster_21", "metadata": {"comment": "na", "seed_id": "01_99"}}, {"id": "Cluster_22", "metadata": {"comment": "na", "seed_id": "01_38"}}, {"id": "Cluster_23", "metadata": {"comment": "na", "seed_id": "01_87091"}}, {"id": "Cluster_24", "metadata": {"comment": "na", "seed_id": "01_59"}}, {"id": "Cluster_25", "metadata": {"comment": "na", "seed_id": "01_165"}}, {"id": "Cluster_26", "metadata": {"comment": "na", "seed_id": "01_75264"}}, {"id": "Cluster_27", "metadata": {"comment": "na", "seed_id": "01_40"}}, {"id": "Cluster_28", "metadata": {"comment": "na", "seed_id": "01_90154"}}, {"id": "Cluster_29", "metadata": {"comment": "na", "seed_id": "01_102"}}, {"id": "Cluster_30", "metadata": {"comment": "na", "seed_id": "01_30455"}}, {"id": "Cluster_31", "metadata": {"comment": "na", "seed_id": "01_87"}}, {"id": "Cluster_32", "metadata": {"comment": "na", "seed_id": "01_11"}}, {"id": "Cluster_33", "metadata": {"comment": "na", "seed_id": "01_443"}}, {"id": "Cluster_34", "metadata": {"comment": "na", "seed_id": "01_75598"}}, {"id": "Cluster_35", "metadata": {"comment": "na", "seed_id": "01_94826"}}, {"id": "Cluster_36", "metadata": {"comment": "na", "seed_id": "01_53126"}}, {"id": "Cluster_37", "metadata": {"comment": "na", "seed_id": "01_73924"}}, {"id": "Cluster_38", "metadata": {"comment": "na", "seed_id": "01_324"}}, {"id": "Cluster_39", "metadata": {"comment": "na", "seed_id": "01_35137"}}, {"id": "Cluster_40", "metadata": {"comment": "na", "seed_id": "01_53083"}}, {"id": "Cluster_41", "metadata": {"comment": "na", "seed_id": "01_32761"}}, {"id": "Cluster_42", "metadata": {"comment": "na", "seed_id": "01_30"}}, {"id": "Cluster_43", "metadata": {"comment": "na", "seed_id": "01_81788"}}, {"id": "Cluster_44", "metadata": {"comment": "na", "seed_id": "01_80125"}}, {"id": "Cluster_45_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_59702_FROGS_combined"}}, {"id": "Cluster_46_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_81428_FROGS_combined"}}, {"id": "Cluster_47_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_725_FROGS_combined"}}, {"id": "Cluster_48_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "01_54177_FROGS_combined"}}, {"id": "Cluster_49", "metadata": {"comment": "na", "seed_id": "01_97871"}}, {"id": "Cluster_50", "metadata": {"comment": "na", "seed_id": "01_49457"}}, {"id": "Cluster_51", "metadata": {"comment": "na", "seed_id": "01_53983"}}, {"id": "Clus'..b'": "Cluster_10102_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "02_32476_FROGS_combined"}}, {"id": "Cluster_12367_FROGS_combined", "metadata": {"comment": "WARNING", "seed_id": "02_44718_FROGS_combined"}}], "matrix_element_type": "int", "format": "Biological Observation Matrix 1.0.0", "data": [[0, 0, 339], [0, 1, 318], [0, 2, 345], [1, 0, 320], [1, 1, 337], [1, 2, 317], [2, 0, 332], [2, 1, 315], [2, 2, 313], [3, 0, 322], [3, 1, 330], [3, 2, 307], [4, 0, 308], [4, 1, 327], [4, 2, 324], [5, 0, 321], [5, 1, 318], [5, 2, 319], [6, 0, 320], [6, 1, 318], [6, 2, 310], [7, 0, 284], [7, 1, 322], [7, 2, 341], [8, 0, 320], [8, 1, 302], [8, 2, 323], [9, 0, 329], [9, 1, 305], [9, 2, 320], [10, 0, 300], [10, 1, 312], [10, 2, 331], [11, 0, 334], [11, 1, 308], [11, 2, 299], [12, 0, 319], [12, 1, 321], [12, 2, 300], [13, 0, 326], [13, 1, 287], [13, 2, 326], [14, 0, 312], [14, 1, 302], [14, 2, 323], [15, 0, 346], [15, 1, 308], [15, 2, 285], [16, 0, 304], [16, 1, 324], [16, 2, 307], [17, 0, 333], [17, 1, 291], [17, 2, 308], [18, 0, 302], [18, 1, 299], [18, 2, 334], [19, 0, 338], [19, 1, 319], [19, 2, 277], [20, 0, 289], [20, 1, 315], [20, 2, 335], [21, 0, 305], [21, 1, 297], [21, 2, 326], [22, 0, 336], [22, 1, 265], [22, 2, 324], [23, 0, 323], [23, 1, 299], [23, 2, 303], [24, 0, 302], [24, 1, 288], [24, 2, 338], [25, 0, 293], [25, 1, 342], [25, 2, 290], [26, 0, 304], [26, 1, 299], [26, 2, 317], [27, 0, 294], [27, 1, 315], [27, 2, 313], [28, 0, 320], [28, 1, 292], [28, 2, 307], [29, 0, 286], [29, 1, 332], [29, 2, 300], [30, 0, 316], [30, 1, 286], [30, 2, 317], [31, 0, 298], [31, 1, 323], [31, 2, 294], [32, 0, 323], [32, 1, 297], [32, 2, 298], [33, 0, 290], [33, 1, 318], [33, 2, 307], [34, 0, 301], [34, 1, 310], [34, 2, 303], [35, 0, 292], [35, 1, 295], [35, 2, 325], [36, 0, 298], [36, 1, 328], [36, 2, 280], [37, 0, 313], [37, 1, 290], [37, 2, 304], [38, 0, 280], [38, 1, 305], [38, 2, 319], [39, 0, 314], [39, 1, 298], [39, 2, 282], [40, 0, 310], [40, 1, 299], [40, 2, 284], [41, 0, 290], [41, 1, 300], [41, 2, 283], [42, 0, 282], [42, 1, 290], [42, 2, 283], [43, 0, 295], [43, 1, 297], [43, 2, 294], [44, 0, 339], [44, 1, 299], [44, 2, 333], [45, 0, 321], [45, 1, 354], [45, 2, 266], [46, 0, 285], [46, 1, 268], [46, 2, 283], [47, 0, 320], [47, 1, 288], [47, 2, 302], [48, 0, 113], [48, 1, 123], [48, 2, 101], [49, 0, 31], [49, 1, 44], [49, 2, 49], [50, 0, 31], [50, 1, 36], [50, 2, 34], [51, 0, 9], [51, 1, 14], [51, 2, 22], [52, 0, 19], [52, 1, 13], [52, 2, 12], [53, 0, 9], [53, 1, 11], [53, 2, 10], [54, 0, 13], [54, 1, 7], [54, 2, 7], [55, 0, 3], [55, 1, 3], [55, 2, 4], [56, 0, 1], [56, 1, 3], [56, 2, 5], [57, 0, 4], [57, 1, 4], [57, 2, 2], [58, 0, 7], [58, 1, 5], [58, 2, 1], [59, 0, 6], [59, 1, 4], [59, 2, 2], [60, 0, 6], [60, 1, 9], [60, 2, 2], [61, 0, 3], [61, 1, 10], [61, 2, 4], [62, 0, 8], [62, 1, 4], [62, 2, 7], [63, 0, 3], [63, 1, 6], [63, 2, 3], [64, 0, 3], [64, 1, 5], [64, 2, 7], [65, 0, 3], [65, 1, 10], [65, 2, 7], [66, 0, 6], [66, 1, 7], [66, 2, 5], [67, 0, 2], [67, 1, 5], [67, 2, 1], [68, 0, 1], [68, 1, 3], [68, 2, 4], [69, 0, 5], [69, 1, 3], [69, 2, 4], [70, 0, 3], [70, 1, 4], [70, 2, 4], [71, 0, 3], [71, 1, 4], [71, 2, 3], [72, 0, 4], [72, 1, 3], [72, 2, 2], [73, 0, 5], [73, 1, 3], [73, 2, 2], [74, 0, 4], [74, 1, 4], [74, 2, 4], [75, 0, 7], [75, 1, 4], [75, 2, 7], [76, 0, 1], [76, 1, 6], [76, 2, 6], [77, 0, 3], [77, 1, 2], [77, 2, 2], [78, 0, 4], [78, 1, 3], [78, 2, 1], [79, 0, 3], [79, 1, 1], [79, 2, 4], [80, 0, 2], [80, 1, 4], [80, 2, 6], [81, 0, 2], [81, 1, 2], [81, 2, 3], [82, 0, 3], [82, 1, 5], [82, 2, 2], [83, 0, 3], [83, 1, 9], [83, 2, 3], [84, 0, 1], [84, 1, 4], [84, 2, 5], [85, 0, 5], [85, 1, 1], [85, 2, 1]], "generated_by": "swarm", "matrix_type": "sparse", "shape": [86, 3], "format_url": "http://biom-format.org", "date": "2019-02-13T11:13:13", "type": "OTU table", "id": null, "columns": [{"id": "01", "metadata": null}, {"id": "02", "metadata": null}, {"id": "03", "metadata": null}]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/04-filters.excluded --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/04-filters.excluded Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,44329 @@\n+#Present in minus of 3 samples\tAbundance < 5e-05\tPresent in databank of contaminants\n+Cluster_57\tCluster_57\t\n+Cluster_60\tCluster_60\t\n+Cluster_61_FROGS_combined\tCluster_61_FROGS_combined\t\n+Cluster_62_FROGS_combined\tCluster_62_FROGS_combined\t\n+Cluster_63_FROGS_combined\tCluster_63_FROGS_combined\t\n+Cluster_64_FROGS_combined\tCluster_64_FROGS_combined\t\n+Cluster_65_FROGS_combined\tCluster_65_FROGS_combined\t\n+Cluster_66_FROGS_combined\tCluster_66_FROGS_combined\t\n+Cluster_67_FROGS_combined\tCluster_67_FROGS_combined\t\n+Cluster_68_FROGS_combined\tCluster_68_FROGS_combined\t\n+Cluster_69_FROGS_combined\tCluster_69_FROGS_combined\t\n+Cluster_70_FROGS_combined\tCluster_70_FROGS_combined\t\n+Cluster_71_FROGS_combined\tCluster_71_FROGS_combined\t\n+Cluster_72_FROGS_combined\tCluster_72_FROGS_combined\t\n+Cluster_73_FROGS_combined\tCluster_73_FROGS_combined\t\n+Cluster_74_FROGS_combined\tCluster_74_FROGS_combined\t\n+Cluster_75_FROGS_combined\tCluster_75_FROGS_combined\t\n+Cluster_76_FROGS_combined\tCluster_76_FROGS_combined\t\n+Cluster_77_FROGS_combined\tCluster_77_FROGS_combined\t\n+Cluster_78_FROGS_combined\tCluster_78_FROGS_combined\t\n+Cluster_79_FROGS_combined\tCluster_79_FROGS_combined\t\n+Cluster_80_FROGS_combined\tCluster_80_FROGS_combined\t\n+Cluster_81_FROGS_combined\tCluster_81_FROGS_combined\t\n+Cluster_82_FROGS_combined\tCluster_82_FROGS_combined\t\n+Cluster_83_FROGS_combined\tCluster_83_FROGS_combined\t\n+Cluster_84_FROGS_combined\tCluster_84_FROGS_combined\t\n+Cluster_85_FROGS_combined\tCluster_85_FROGS_combined\t\n+Cluster_86_FROGS_combined\tCluster_86_FROGS_combined\t\n+Cluster_87_FROGS_combined\tCluster_87_FROGS_combined\t\n+Cluster_88_FROGS_combined\tCluster_88_FROGS_combined\t\n+Cluster_89_FROGS_combined\tCluster_89_FROGS_combined\t\n+Cluster_90_FROGS_combined\tCluster_90_FROGS_combined\t\n+Cluster_91_FROGS_combined\tCluster_91_FROGS_combined\t\n+Cluster_92_FROGS_combined\tCluster_92_FROGS_combined\t\n+Cluster_93_FROGS_combined\tCluster_93_FROGS_combined\t\n+Cluster_94_FROGS_combined\tCluster_94_FROGS_combined\t\n+Cluster_95_FROGS_combined\tCluster_95_FROGS_combined\t\n+Cluster_96_FROGS_combined\tCluster_96_FROGS_combined\t\n+Cluster_97_FROGS_combined\tCluster_97_FROGS_combined\t\n+Cluster_98_FROGS_combined\tCluster_98_FROGS_combined\t\n+Cluster_99_FROGS_combined\tCluster_99_FROGS_combined\t\n+Cluster_100_FROGS_combined\tCluster_100_FROGS_combined\t\n+Cluster_101_FROGS_combined\tCluster_101_FROGS_combined\t\n+Cluster_102_FROGS_combined\tCluster_102_FROGS_combined\t\n+Cluster_103_FROGS_combined\tCluster_103_FROGS_combined\t\n+Cluster_104_FROGS_combined\tCluster_104_FROGS_combined\t\n+Cluster_105_FROGS_combined\tCluster_105_FROGS_combined\t\n+Cluster_106_FROGS_combined\tCluster_106_FROGS_combined\t\n+Cluster_107_FROGS_combined\tCluster_107_FROGS_combined\t\n+Cluster_108_FROGS_combined\tCluster_108_FROGS_combined\t\n+Cluster_109_FROGS_combined\tCluster_109_FROGS_combined\t\n+Cluster_110_FROGS_combined\tCluster_110_FROGS_combined\t\n+Cluster_111_FROGS_combined\tCluster_111_FROGS_combined\t\n+Cluster_112_FROGS_combined\tCluster_112_FROGS_combined\t\n+Cluster_113_FROGS_combined\tCluster_113_FROGS_combined\t\n+Cluster_114_FROGS_combined\tCluster_114_FROGS_combined\t\n+Cluster_115_FROGS_combined\tCluster_115_FROGS_combined\t\n+Cluster_117_FROGS_combined\tCluster_117_FROGS_combined\t\n+Cluster_118_FROGS_combined\tCluster_118_FROGS_combined\t\n+Cluster_120_FROGS_combined\tCluster_120_FROGS_combined\t\n+Cluster_121_FROGS_combined\tCluster_121_FROGS_combined\t\n+Cluster_122_FROGS_combined\tCluster_122_FROGS_combined\t\n+Cluster_123_FROGS_combined\tCluster_123_FROGS_combined\t\n+Cluster_124_FROGS_combined\tCluster_124_FROGS_combined\t\n+Cluster_125_FROGS_combined\tCluster_125_FROGS_combined\t\n+Cluster_126_FROGS_combined\tCluster_126_FROGS_combined\t\n+Cluster_127_FROGS_combined\tCluster_127_FROGS_combined\t\n+Cluster_128_FROGS_combined\tCluster_128_FROGS_combined\t\n+Cluster_129_FROGS_combined\tCluster_129_FROGS_combined\t\n+Cluster_130_FROGS_combined\tCluster_130_FROGS_combined\t\n+Cluster_131_FROGS_combined\tCluster_131_FROGS_combined\t\n+Cluster_132_FROGS_combined\tCluster_132_FROGS_combined\t\n+Cl'..b'ined\tCluster_44374_FROGS_combined\t\n+Cluster_44377_FROGS_combined\tCluster_44375_FROGS_combined\t\n+Cluster_44378_FROGS_combined\tCluster_44376_FROGS_combined\t\n+Cluster_44379_FROGS_combined\tCluster_44377_FROGS_combined\t\n+Cluster_44380_FROGS_combined\tCluster_44378_FROGS_combined\t\n+Cluster_44381_FROGS_combined\tCluster_44379_FROGS_combined\t\n+Cluster_44382_FROGS_combined\tCluster_44380_FROGS_combined\t\n+Cluster_44383_FROGS_combined\tCluster_44381_FROGS_combined\t\n+Cluster_44384_FROGS_combined\tCluster_44382_FROGS_combined\t\n+Cluster_44385_FROGS_combined\tCluster_44383_FROGS_combined\t\n+Cluster_44386_FROGS_combined\tCluster_44384_FROGS_combined\t\n+Cluster_44387_FROGS_combined\tCluster_44385_FROGS_combined\t\n+Cluster_44388_FROGS_combined\tCluster_44386_FROGS_combined\t\n+Cluster_44389_FROGS_combined\tCluster_44387_FROGS_combined\t\n+Cluster_44390_FROGS_combined\tCluster_44388_FROGS_combined\t\n+Cluster_44391_FROGS_combined\tCluster_44389_FROGS_combined\t\n+Cluster_44392_FROGS_combined\tCluster_44390_FROGS_combined\t\n+Cluster_44393_FROGS_combined\tCluster_44391_FROGS_combined\t\n+Cluster_44394_FROGS_combined\tCluster_44392_FROGS_combined\t\n+Cluster_44395_FROGS_combined\tCluster_44393_FROGS_combined\t\n+Cluster_44396_FROGS_combined\tCluster_44394_FROGS_combined\t\n+Cluster_44397_FROGS_combined\tCluster_44395_FROGS_combined\t\n+Cluster_44398_FROGS_combined\tCluster_44396_FROGS_combined\t\n+Cluster_44399_FROGS_combined\tCluster_44397_FROGS_combined\t\n+Cluster_44400_FROGS_combined\tCluster_44398_FROGS_combined\t\n+Cluster_44401_FROGS_combined\tCluster_44399_FROGS_combined\t\n+Cluster_44402_FROGS_combined\tCluster_44400_FROGS_combined\t\n+Cluster_44403_FROGS_combined\tCluster_44401_FROGS_combined\t\n+Cluster_44404_FROGS_combined\tCluster_44402_FROGS_combined\t\n+Cluster_44405_FROGS_combined\tCluster_44403_FROGS_combined\t\n+Cluster_44406_FROGS_combined\tCluster_44404_FROGS_combined\t\n+Cluster_44407_FROGS_combined\tCluster_44405_FROGS_combined\t\n+Cluster_44408_FROGS_combined\tCluster_44406_FROGS_combined\t\n+Cluster_44409_FROGS_combined\tCluster_44407_FROGS_combined\t\n+Cluster_44410_FROGS_combined\tCluster_44408_FROGS_combined\t\n+Cluster_44411_FROGS_combined\tCluster_44409_FROGS_combined\t\n+Cluster_44412_FROGS_combined\tCluster_44410_FROGS_combined\t\n+Cluster_44413_FROGS_combined\tCluster_44411_FROGS_combined\t\n+Cluster_44414_FROGS_combined\tCluster_44412_FROGS_combined\t\n+Cluster_44415_FROGS_combined\tCluster_44413_FROGS_combined\t\n+Cluster_44416_FROGS_combined\tCluster_44414_FROGS_combined\t\n+Cluster_44417_FROGS_combined\tCluster_44415_FROGS_combined\t\n+Cluster_44418_FROGS_combined\tCluster_44416_FROGS_combined\t\n+Cluster_44419_FROGS_combined\tCluster_44417_FROGS_combined\t\n+Cluster_44420_FROGS_combined\tCluster_44418_FROGS_combined\t\n+Cluster_44421_FROGS_combined\tCluster_44419_FROGS_combined\t\n+Cluster_44422_FROGS_combined\tCluster_44420_FROGS_combined\t\n+Cluster_44423_FROGS_combined\tCluster_44421_FROGS_combined\t\n+Cluster_44424_FROGS_combined\tCluster_44422_FROGS_combined\t\n+Cluster_44425_FROGS_combined\tCluster_44423_FROGS_combined\t\n+Cluster_44426_FROGS_combined\tCluster_44424_FROGS_combined\t\n+Cluster_44427_FROGS_combined\tCluster_44425_FROGS_combined\t\n+Cluster_44428_FROGS_combined\tCluster_44426_FROGS_combined\t\n+Cluster_44429_FROGS_combined\tCluster_44427_FROGS_combined\t\n+Cluster_44430_FROGS_combined\tCluster_44428_FROGS_combined\t\n+Cluster_44431_FROGS_combined\tCluster_44429_FROGS_combined\t\n+Cluster_44432_FROGS_combined\tCluster_44430_FROGS_combined\t\n+Cluster_44433_FROGS_combined\tCluster_44431_FROGS_combined\t\n+Cluster_44434_FROGS_combined\tCluster_44432_FROGS_combined\t\n+Cluster_44435_FROGS_combined\tCluster_44433_FROGS_combined\t\n+Cluster_44436_FROGS_combined\tCluster_44434_FROGS_combined\t\n+Cluster_44437_FROGS_combined\tCluster_44435_FROGS_combined\t\n+Cluster_44438_FROGS_combined\tCluster_44436_FROGS_combined\t\n+Cluster_44439_FROGS_combined\tCluster_44437_FROGS_combined\t\n+Cluster_44440_FROGS_combined\tCluster_44438_FROGS_combined\t\n+Cluster_44441_FROGS_combined\tCluster_44439_FROGS_combined\t\n+\tCluster_44440_FROGS_combined\t\n+\tCluster_44441_FROGS_combined\t\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/04-filters.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/04-filters.fasta Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,172 @@\n+>Cluster_1 reference=JQ279537_SH175098.07FU_refs position=1..250 errors=228%A\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=206%G\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3 reference=GU474801_SH104786.07FU_refs_singleton position=1..250 errors=198%T\n+GAAGGATCATTACTGAAGAACTATATCGAGTTTTTTTATACCCTTTTGTTTACCTACCCTATTGCTTCCACTGGACAGGTTTCACCTTGTGTGGGTCCTCTCTGGCTTGTGTGAAAAGCACCTGCCAGACAGACGTTGCTGGTGGGAAGAACTATTTACTAAAACTTGATTTTTAAAAAAAAATACAATGTCTGAATAATTTCCTTTAATGAAATAAAACTTTCAACAACGGATCTCTAGGCTCTTGCATCGATGAAGAACGCAGT\n+>Cluster_4 reference=UDB015350_SH176685.07FU_refs position=1..250 errors=245%A\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_5 reference=JQ716403_SH219241.07FU_refs position=1..250 errors=163%G\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_6 reference=UDB002317_SH221025.07FU_refs position=1..250 errors=215%C\n+CTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGCTGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGAGGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATTTTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTAAATGATAAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_7 reference=DQ898183_SH216206.07FU_refs position=1..249\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_8 reference=AF456924_SH097201.07FU_refs position=1..250\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_9 reference=JF747094_SH197643.07FU_refs position=1..249 errors=246%T\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10 reference=HQ714696_SH221416.07FU_refs position=1..250 errors=249%T\n+ATCCGGAGGGGAGATGAAGAGGGAATTTAGTAGGAACCGTAGGCATTGTCGCTGGCCTTTGGAAACAAACGCATGTGCACATCTCGAAAGTCTTACTTAGTACCTCGATCTCTTTCCTTTTGTGAACCCCTTTTCTTACACCTGTGCACCCATTGTAGGTCCCGCGAGGGATCCTATGTCTCTATCTACTCTTAAATGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTTGGTTGGCGGCAGTAAAGAACCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11 reference=UDB000320_SH220111.07FU_refs position=1..250\n+TCGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGGAGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGATC'..b'AACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_1253_FROGS_combined R1_desc:reference=UDB000320_SH220111.07FU_refs position=1..250 errors=71%A;R2_desc=R2_desc=reference=UDB000320_SH220111.07FU_refs position=1..250 errors=223+C\n+TCGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGGAGCGCGTCCTATCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGCGAGGGCTGTCGCTGACTTCAAAGTGCGTGCACGCCGGAGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2726_FROGS_combined R1_desc:reference=KF732310_SH222414.07FU_refs position=1..250 errors=95%A;R2_desc=R2_desc=reference=KF732310_SH222414.07FU_refs position=1..250 errors=97+G\n+TTGAAATAAACCTGATGAGTTGCTGCTGGCTCTCTTGGGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTAGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTTGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGCTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2042_FROGS_combined R1_desc:reference=KF732249_SH136099.07FU_refs_singleton position=1..250;R2_desc=R2_desc=reference=KF732249_SH136099.07FU_refs_singleton position=1..250 errors=214+C\n+TTGAAATAAACCTGATGAGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACACTCGTCATCTTTGTATATTCACCTGTGCATCTTTTGTAGACCCTTGGGTATCTCTCTGATTGCTTTTAGCACTCAGGATTGAGGATTGACTTCCTGTCTCTTCTTACATTTCCAGGTCTATGTTTCTTAATATACCCTAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAATCTATACAACTTTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATGTGCACACTCGTCATCTTTGTATATTCACCTGTGGCATCTTTTGTAGACCCTTGGGTATCTCTCTGATTGCTTTTAGCACTCAGGATTGAGGATTGACTTCCTGTCTCTTCTTACATTTCCAGGTCTATGTTTCTTAATATACCCTAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2099_FROGS_combined R1_desc:reference=UDB001581_SH219736.07FU_refs position=1..250 errors=134%T;R2_desc=R2_desc=reference=UDB001581_SH219736.07FU_refs position=1..250 errors=89+G\n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTTCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGCAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_4257_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=124+C;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTCTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/04-filters.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/04-filters.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,26 @@ +## Application +Software: filters.py (version: 3.1) +Command: /home/maria/workspace/git/FROGS/FROGS_master/test/../app/filters.py --min-abundance 0.00005 --min-sample-presence 3 --nb-cpus 1 --contaminant /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/phi.fa --input-biom res/03-chimera.biom --input-fasta res/03-chimera.fasta --output-fasta res/04-filters.fasta --output-biom res/04-filters.biom --excluded res/04-filters.excluded --summary res/04-filters.html --log-file res/04-filters.log + +######################################################################################################## +# Removes contaminant sequences. (removeConta.py version : 0.2.0) +Command: + removeConta.py --nb-cpus 1 --word-size 40 --min-identity 0.8 --min-coverage 0.8 --input-fasta res/03-chimera.fasta --contaminant-db /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/phi.fa --input-biom res/03-chimera.biom --clean-fasta res/1550052834.11_3905_cleaned_sequences.fasta --clean-biom res/1550052834.11_3905_cleaned_abundance.biom --conta-fasta res/1550052834.11_3905_contaminated_sequences.fasta --log-file res/1550052834.11_3905_clean.log + +Execution: + start: 13 Feb 2019 11:13:54 + end: 13 Feb 2019 11:14:02 + +Results: + number of processed sequences: 44417 + number of removed contaminated sequences: 0 + +######################################################################################################## +# Updates fasta file based on sequence in biom file. (biomFastaUpdate.py version : 1.0.1) +Command: + biomFastaUpdate.py --input-biom res/04-filters.biom --input-fasta res/03-chimera.fasta --output-file res/04-filters.fasta --log res/1550052834.11_3905_update_fasta_log.txt + +Execution: + start: 13 Feb 2019 11:14:02 + end: 13 Feb 2019 11:14:02 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/05-itsx.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/05-itsx.html Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,400 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <https://www.gnu.org/licenses/>.\n+-->\n+<html>\n+\t<head>\n+\t\t<title>FROGS ITSx</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="2.0.1">\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t\n+ \n+ \n+\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\t\t\t\n+\t\t\t\n+\t\t\t\n+\t\t</style>\n+\t\t<script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script>\n+\t\t<script type="text/javascript" src="https://code.highcharts.com/4.1.4/highcharts.js"></script>\n+\t\t<script type="text/javascript" src="https://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>\n+\t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script>\n+\t\t<script type="text/javascript">\n+\t\t\t/***************************************************************\n+\t\t\t* Copyright notice\n+\t\t\t*\n+\t\t\t* (c) 2014 PF bioinformatique de Toulouse\n+\t\t\t* All rights reserved\n+\t\t\t* \n+\t\t\t*\n+\t\t\t* This script is an adaptation of the venny script developed by\n+\t\t\t* Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:\n+\t\t\t* Oliveros, J.C. (2007) VENNY. An interactive tool for comparing \n+\t\t\t* lists with Venn Diagrams.\n+\t\t\t* https://bioinfogp.cnb.csic.es/tools/venny/index.html.\n+\t\t\t* It is distributed under the terms of the GNU General Public \n+\t\t\t* License as published by the Free Software Foundation; either \n+\t\t\t* version 2 of the License, or (at your option) any later version.\n+\t\t\t*\n+\t\t\t* The GNU General Public License can be found at\n+\t\t\t* https://www.gnu.org/copyleft/gpl.html.\n+\t\t\t*\n+\t\t\t* This script is distributed in the hope that it will be useful,\n+\t\t\t* but WITHOUT ANY WARRANTY; without even the implied warranty of\n+\t\t\t* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+\t\t\t* GNU General Public License for more details.\n+\t\t\t*\n+\t\t\t* This copyright notice MUST APPEAR in all copies of the script!\n+\t\t\t***************************************************************/\n+\t\t\t!function(){"use strict";function s(s,t){var e,l=Object.keys(t);for(e=0;e<l.length;e++)s=s.replace(new RegExp("\\\\{"+l[e]+"\\\\}","gi"),t[l[e]]);return s}function t(s){var t,e,l;if(!s)throw new Error("cannot create a random attribute name for a'..b'undance-filtered\').highcharts( pie_param(\'Abundance\', abundance_filtered_data, \'Sequences\') );\n+\t\t\t}\n+\t\t\t\n+\t\t\tvar samples_filters_load = function( container_id ){\n+\t\t\t\tvar sample_table_titles = ["Sample name", "Initial", "Kept", "Initial abundance", "Kept abundance"];\n+\t\t\t\tvar sample_table_data = new Array();\n+\t\t\t\tfor( var sample in by_samples_results ){\n+\t\t\t\t\tsample_data = [sample, by_samples_results[sample][\'initial\'], by_samples_results[sample][\'kept\'], by_samples_results[sample][\'initial_ab\'], by_samples_results[sample][\'kept_ab\']] ;\n+\t\t\t\t\t\n+\t\t\t\t\t\n+\t\t\t\t\tsample_table_data.push( sample_data );\n+\t\t\t\t}\n+\t\t\t\t$(\'#\' + container_id).append( table("OTUs removed by sample", sample_table_titles, sample_table_data) );\n+\t\t\t\t$(\'#\' + container_id + \' table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#\' + container_id + \' table\').DataTable({\n+\t\t\t\t\t"sDom": \'<"top"<"#details-csv-export"><"clear">lf>rt<"bottom"ip><"clear">\'\n+\t\t\t\t});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n+\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n+\t\t\t\t$(\'#details-csv-export\').datatableExport({\n+\t\t\t\t\t\'table_id\': "details-table"\n+\t\t\t\t});\n+\t\t\t}\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Data\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t\n+\t\t\tvar global_results = {"nb_seq_kept": 45574, "nb_clstr_kept": 86, "nb_clstr_ini": 86, "nb_seq_ini": 45574} ; \n+\t\t\t/* Example: \n+\t\t\t\t{\n+\t\t\t\t\t\'nb_clstr_kept\': 100,\n+\t\t\t\t\t\'nb_clstr_ini\': 300,\n+\t\t\t\t\t\'nb_seq_kept\': 100,\n+\t\t\t\t\t\'nb_seq_ini\': 100000\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\tvar by_samples_results = {"02": {"initial_ab": 15140, "filtered": {}, "initial": 86, "kept": 86, "kept_ab": 15140}, "03": {"initial_ab": 15167, "filtered": {}, "initial": 86, "kept": 86, "kept_ab": 15167}, "01": {"initial_ab": 15267, "filtered": {}, "initial": 86, "kept": 86, "kept_ab": 15267}} ;\n+\t\t\t/* Example:\n+\t\t\t\t{\n+\t\t\t\t\t\'sampleA\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterA\': 10,\n+\t\t\t\t\t\t\t\'filterB\': 20\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 75,\n+\t\t\t\t\t\t\'kept\': 50\n+\t\t\t\t\t},\n+\t\t\t\t\t\'sampleB\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterB\': 20,\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 110,\n+\t\t\t\t\t\t\'kept\': 90\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\t\n+\t\t\t\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Main\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t$(function() {\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Load active tab\n+\t\t\t\tglobal_filters_load();\n+\t\t\t\tsamples_filters_load( "filter-log" );\n+\t\t\t\t\n+\t\t\t});\n+\t\t</script>\n+\n+\t</head>\n+\t<body>\n+\t\t<!-- Alert -->\n+\t\t<p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+ <!-- Content -->\n+ <div id="content" class="hidden">\n+\t\t\t\n+\t\t\t<div id="tab-content" class="tab-content">\n+\t\t\t\t<div id="view-by-filters" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<div id="filter-summary">\n+\t\t \t\t<h1 class="pb-2 mt-4 mb-2 border-bottom">Filters (ITSx) summary</h1>\n+\t\t \t\t<div class="row">\n+\t\t\t \t\t<div id="nb-filtered" class="col-md-6"></div> \n+\t\t\t \t\t<div id="abundance-filtered" class="col-md-6"></div>\n+\t\t \t\t</div>\n+\t\t \t\t<h1 class="pb-2 mt-4 mb-2 border-bottom">Filters (ITSx) by samples</h1>\n+\t\t \t\t<div id="view-by-samples" role="tabpanel" class="tab-pane">\n+\t\t\t\t\t\t\t<div id="filter-log"></div>\n+\t\t\t\t\t\t</div>\n+\t\t\t\t\t</div>\n+\t\t </div>\n+ </div>\n+ </div>\n+\t</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/05-itsx.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/05-itsx.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,61 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/itsx.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/itsx.py --input-fasta res/04-filters.fasta --input-biom res/04-filters.biom --region ITS1 --nb-cpus 4 --out-abundance res/05-itsx.biom --summary res/05-itsx.html --log-file res/05-itsx.log --out-fasta res/05-itsx.fasta --out-removed res/05-itsx-excluded.tsv + +######################################################################################################## +# identifies ITS sequences and extracts the ITS region (parallelITSx.py version : 1.0.0 [ITSx 1.0.11]) +Command: + parallelITSx.py -f res/04-filters.fasta -b res/04-filters.biom --nb-cpus 4 --its ITS1 -o res/05-itsx.fasta -m res/05-itsx-excluded.tsv -a res/05-itsx.biom --log-file res/1550052843.84_3916_ITSx.log + +Execution: + start: 13 Feb 2019 11:14:03 + end: 13 Feb 2019 11:14:15 + +Results: + +# split res/04-filters.fasta in 3 fasta files +Results + Wrote 29 records to res/1550052844.03_3921_04-filters.fasta_0 + Wrote 29 records to res/1550052844.03_3921_04-filters.fasta_1 + Wrote 28 records to res/1550052844.03_3921_04-filters.fasta_2 + +## Input file : 1550052844.03_3921_04-filters.fasta_0 +## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_0 +## ITSx command: ITSx -i /home/maria/workspace/git/FROGS/FROGS_master/test/res/1550052844.03_3921_04-filters.fasta_0 -o 1550052844.03_3921_04-filters --preserve T -t F --save_regions all +##Results + nb full (removed): 0 + nb no_detections (removed): 0 + nb SSU (removed): 0 + nb ITS2 (removed): 0 + nb ITS1 (kept): 29 + nb LSU (removed): 0 + nb 5_8S (removed): 0 + +## Input file : 1550052844.03_3921_04-filters.fasta_1 +## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_1 +## ITSx command: ITSx -i /home/maria/workspace/git/FROGS/FROGS_master/test/res/1550052844.03_3921_04-filters.fasta_1 -o 1550052844.03_3921_04-filters --preserve T -t F --save_regions all +##Results + nb full (removed): 0 + nb no_detections (removed): 0 + nb SSU (removed): 0 + nb ITS2 (removed): 0 + nb ITS1 (kept): 29 + nb LSU (removed): 0 + nb 5_8S (removed): 0 + +## Input file : 1550052844.03_3921_04-filters.fasta_2 +## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_2 +## ITSx command: ITSx -i /home/maria/workspace/git/FROGS/FROGS_master/test/res/1550052844.03_3921_04-filters.fasta_2 -o 1550052844.03_3921_04-filters --preserve T -t F --save_regions all +##Results + nb full (removed): 0 + nb no_detections (removed): 0 + nb SSU (removed): 0 + nb ITS2 (removed): 0 + nb ITS1 (kept): 28 + nb LSU (removed): 0 + nb 5_8S (removed): 0 + + +## Removes the observations after ITSx. + + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/06-affiliation.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/06-affiliation.biom Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "evalue": "0.0", "aln_length": 337, "perc_query_coverage": 100.0, "subject": "JQ279537_SH175098.07FU_refs"}], "seed_id": "01_58367"}}, {"id": "Cluster_2", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_cyathuliformis"], "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_cyathuliformis"], "evalue": "4.90e-134", "aln_length": 252, "perc_query_coverage": 100.0, "subject": "HQ714785_SH330547.07FU_refs"}], "seed_id": "01_57964"}}, {"id": "Cluster_3", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Pezizaceae", "g__Terfezia", "s__Terfezia_claveryi"], "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Pezizaceae", "g__Terfezia", "s__Terfezia_claveryi"], "evalue": "8.56e-142", "aln_length": 266, "perc_query_coverage": 100.0, "subject": "GU474801_SH104786.07FU_refs_singleton"}], "seed_id": "01_67063"}}, {"id": "Cluster_4", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Inocybaceae", "g__Inocybe", "s__Inocybe_sindonia"], "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Inocybaceae", "g__Inocybe", "s__Inocybe_sindonia"], "evalue": "4.60e-170", "aln_length": 317, "perc_query_coverage": 100.0, "subject": "UDB015350_SH176685.07FU_refs"}], "seed_id": "01_80623"}}, {"id": "Cluster_5", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "evalue": "7.94e-178", "aln_length": 331, "perc_query_coverage": 100.0, "subject": "JQ716403_SH219241.07FU_refs"}], "seed_id": "01_256"}}, {"id": "Cluster_6", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "evalue": "9.52e-162", "aln_length": 302, "perc_query_coverage": 100.0, "subject": "UDB002317_SH221025.07FU_refs"}], "seed_id": "01_54434"}}, {"id": "Cluster_7", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "evalue": "2.25e-132", "aln_length": 249, "perc_query_coverage": 100.0, "subject": "DQ898183_SH216206.07FU_refs"}], "seed_id": "01_44905"}}, {"id": "Cluster_8", "metadata": {"comment": "na", "blast_taxonomy": ["Root", 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2, 7], [66, 0, 6], [66, 1, 7], [66, 2, 5], [67, 0, 2], [67, 1, 5], [67, 2, 1], [68, 0, 1], [68, 1, 3], [68, 2, 4], [69, 0, 5], [69, 1, 3], [69, 2, 4], [70, 0, 3], [70, 1, 4], [70, 2, 4], [71, 0, 3], [71, 1, 4], [71, 2, 3], [72, 0, 4], [72, 1, 3], [72, 2, 2], [73, 0, 5], [73, 1, 3], [73, 2, 2], [74, 0, 4], [74, 1, 4], [74, 2, 4], [75, 0, 7], [75, 1, 4], [75, 2, 7], [76, 0, 1], [76, 1, 6], [76, 2, 6], [77, 0, 3], [77, 1, 2], [77, 2, 2], [78, 0, 4], [78, 1, 3], [78, 2, 1], [79, 0, 3], [79, 1, 1], [79, 2, 4], [80, 0, 2], [80, 1, 4], [80, 2, 6], [81, 0, 2], [81, 1, 2], [81, 2, 3], [82, 0, 3], [82, 1, 5], [82, 2, 2], [83, 0, 3], [83, 1, 9], [83, 2, 3], [84, 0, 1], [84, 1, 4], [84, 2, 5], [85, 0, 5], [85, 1, 1], [85, 2, 1]], "generated_by": "swarm", "matrix_type": "sparse", "shape": [86, 3], "format_url": "http://biom-format.org", "date": "2019-02-13T11:13:13", "type": "OTU table", "id": null, "columns": [{"id": "01", "metadata": null}, {"id": "02", "metadata": null}, {"id": "03", "metadata": null}]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/06-affiliation.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/06-affiliation.html Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,545 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<html>\n+\t<head>\n+\t\t<title>FROGS Affiliation</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="1.0.2">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"></link>\n+\t\t<style type="text/css">\n+ #js-alert {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ #content {\n+ width: 90%;\n+ margin-right: auto;\n+ margin-left: auto;\n+ }\n+ .clear {\n+ clear: both;\n+ height: 0px;\n+ width: 100%;\n+ float: none !important;\n+ }\n+ ul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 0px;\n+\t\t\t\tmargin-bottom: 15px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 20px;\n+\t\t\t\twidth: 20px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t\t\t.container input:checked ~ .checkmark {\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\topacity:1;\n+\t\t\t}\n+\n+\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n+\t\t\t.checkmark:after {\n+\t\t\t\tcontent: "";\n+\t\t\t\tposition: absolute;\n+\t\t\t\tdisplay: none;\n+\t\t\t}\n+\n+\t\t\t/* Show the checkmark when checked */\n+\t\t\t.container input:checked ~ .checkmark:after {\n+\t\t\t\tdisplay: block;\n+\t\t\t}\n+\n+\t\t\t/* Style the checkmark/indicator */\n+\t\t\t.container .checkmark:after {\n+\t\t\t\tleft: 7px;\n+\t\t\t\ttop: 3px;\n+\t\t\t\twidth: 6px;\n+\t\t\t\theight: 10px;\n+\t\t\t\tborder: solid white;\n+\t\t\t\tborder-width: 0 3px 3px 0;\n+\t\t\t\t-webkit-transform: rotate(45deg);\n+'..b': [\n+\t\t\t [0, color],\n+\t\t\t [1, Highcharts.Color(color).brighten(-0.3).get(\'rgb\')] // darken\n+\t\t\t ]\n+\t\t\t };\n+\t\t\t });\n+\t\t\t \n+\t\t\t\tvar pie_series = [\n+\t\t\t\t\t["With affiliation", global_results["nb_clstr_with_affi"]],\n+\t\t\t\t\t["Without affiliation", (global_results["nb_clstr"] - global_results["nb_clstr_with_affi"])]\n+\t\t\t\t]\n+\t\t\t\t$(\'#clstr-ratio-affi\').highcharts( pie_param("OTUs affiliation", pie_series, \'OTUs\') );\n+\t\t\t\t\n+\t\t\t\tvar pie_series = [\n+\t\t\t\t\t["With affiliation", global_results["nb_seq_with_affi"]],\n+\t\t\t\t\t["Without affiliation", (global_results["nb_seq"] - global_results["nb_seq_with_affi"])]\n+\t\t\t\t]\n+\t\t\t\t$(\'#seq-ratio-affi\').highcharts( pie_param("Sequences affiliation", pie_series, \'sequences\') );\n+\t\t\t\t\n+\t\t\t\tHighcharts.getOptions().colors = std_color ;\n+\t\t\t\t\n+\t\t\t\tvar histogram_series = [\n+\t\t\t\t\t{\n+\t\t\t\t\t\t\'name\': \'OTUs\',\n+\t\t\t\t\t\t\'data\': global_results["nb_clstr_ambiguous"].map(function(num) {\n+\t\t\t\t\t\t\tvar prct = (num/global_results["nb_clstr"])*10000/100 ;\n+\t\t\t\t\t\t\treturn( parseFloat(numberDisplay(prct)) );\n+\t\t\t\t\t\t})\n+\t\t\t\t\t}, {\n+\t\t\t\t\t\t\'name\': \'Sequences\',\n+\t\t\t\t\t\t\'data\': global_results["nb_seq_ambiguous"].map(function(num) {\n+\t\t\t\t\t\t\tvar prct = (num/global_results["nb_seq"])*10000/100 ;\n+\t\t\t\t\t\t\treturn( parseFloat(numberDisplay(prct)) );\n+\t\t\t\t\t\t})\n+\t\t\t\t\t}\n+\t\t\t\t];\n+\t\t\t\t$(\'#clstr-multi-affi\').highcharts( histogram_param(\'Multi-affiliation by taxonomic rank\', \'% of multi-affiliated\', taxonomy_ranks, histogram_series, \'%\') );\n+\t\t\t\t\n+\t\t\t\t// Display data by sample\n+\t\t\t\tvar table_categories = [ \'Sample\', \'Nb OTUs\', \'% OTUs affiliated by blast\', \'Nb seq\', \'% seq affiliated by blast\' ];\n+\t\t\t\tvar table_series = new Array();\n+\t\t\t\tfor( var sample_name in sample_results ){\n+\t\t\t\t\ttable_series.push([\n+\t\t\t\t\t\tsample_name,\n+\t\t\t\t\t\tsample_results[sample_name][\'nb_clstr\'],\n+\t\t\t\t\t\tMath.round(((sample_results[sample_name][\'nb_clstr_with_affi\']/sample_results[sample_name][\'nb_clstr\'])*10000)/100),\n+\t\t\t\t\t\tsample_results[sample_name][\'nb_seq\'],\n+\t\t\t\t\t\tMath.round(((sample_results[sample_name][\'nb_seq_with_affi\']/sample_results[sample_name][\'nb_seq\'])*10000)/100)\n+\t\t\t\t\t]);\n+\t\t\t\t};\n+\t\t\t\t$(\'#samples-details\').append( table("Blast affiliation by sample", table_categories, table_series) );\n+\t\t\t\t$(\'#samples-details table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#samples-details table\').DataTable({\n+\t\t\t\t\t//"sDom": \'<"top"<"#details-csv-export"><"clear">lf>rt<"bottom"ip><"clear">\'\n+\t\t\t\t\tdom: \t"<\'#details-csv-export\'><\'row\'<\'col-sm-5\'l><\'col-sm-7\'f>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-12\'tr>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-5\'i><\'col-sm-7\'p>>",\n+\t\t\t\t\t\t\t"pagingType": "simple"\n+\t\t\t\t});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn btn-primary" ><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n+\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n+\t\t\t\t$(\'#details-csv-export\').datatableExport({\n+\t\t\t\t\t\'table_id\': "details-table"\n+\t\t\t\t});\n+\t\t\t});\n+\t\t</script>\n+\t</head>\n+\t<body>\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t<div id="content" class="hidden">\n+\t\t\t<div id="global-summary">\n+\t\t\t\t<h2 class="pb-2-first mt-4 mb-2 border-bottom" style="margin-top: 1rem">Blast affiliation summary</h2>\n+\t\t\t\t<div class="row">\n+\t\t\t\t\t<div class="col-md-1"></div>\n+\t\t\t\t\t<div id="clstr-ratio-affi" class="col-md-5"></div>\n+\t\t\t\t\t<div id="seq-ratio-affi" class="col-md-5"></div>\n+\t\t\t\t\t<div class="col-md-1"></div>\n+\t\t\t\t</div>\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Blast multi-affiliation summary</h2>\n+\t\t\t\t<div class="row">\n+\t\t\t\t\t<div class="col-md-1"></div>\n+\t\t\t\t\t<div id="clstr-multi-affi" class="col-md-10"></div>\n+\t\t\t\t\t<div class="col-md-1"></div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t\t<div id="samples-details">\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Blast affiliation by sample</h2>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n' |
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| diff -r 000000000000 -r 59bc96331073 test-data/references/06-affiliation.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/06-affiliation.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,76 @@ +## Application +Software: affiliation_OTU.py (version: 3.1) +Command: /home/maria/workspace/git/FROGS/FROGS_master/test/../app/affiliation_OTU.py --reference /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta --input-fasta res/04-filters.fasta --input-biom res/04-filters.biom --output-biom res/06-affiliation.biom --summary res/06-affiliation.html --log-file res/06-affiliation.log --nb-cpus 4 --java-mem 2 + +Nb seq : 86 + with nb seq artificially combined :34 + +######################################################################################################## +# Split on tag. (combine_and_split.py version : ) +Command: + combine_and_split.py --reads1 res/1550052855.96_4147_04-filters.fasta_FROGS_combined -s NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --split-output1 res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R1.fasta --split-output2 res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R2.fasta + +Execution: + start: 13 Feb 2019 11:14:15 + end: 13 Feb 2019 11:14:16 + +######################################################################################################## +# blast taxonomic affiliation (blastn version : 2.7.1+) +Command: + blastn -num_threads 1 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R1.fasta -out res/1550052855.96_4147_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R1.fasta.blast -db /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta + +Execution: + start: 13 Feb 2019 11:14:16 + end: 13 Feb 2019 11:14:16 + +######################################################################################################## +# blast taxonomic affiliation (blastn version : 2.7.1+) +Command: + blastn -num_threads 1 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R2.fasta -out res/1550052855.96_4147_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R2.fasta.blast -db /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta + +Execution: + start: 13 Feb 2019 11:14:16 + end: 13 Feb 2019 11:14:16 + +######################################################################################################## +# needleall taxonomic affiliation (needleall_on_bestBlast.py version : r3.0-v1.0 [needleall EMBOSS:6.6.0.0]) +Command: + needleall_on_bestBlast.py -r /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta -f res/1550052855.96_4147_04-filters.fasta_FROGS_combined --query-blast-R1 res/1550052855.96_4147_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R1.fasta.blast --query-blast-R2 res/1550052855.96_4147_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R2.fasta.blast -s res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.sam -l res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.log + +Execution: + start: 13 Feb 2019 11:14:16 + end: 13 Feb 2019 11:14:33 + + # Parsing blast alignment results to reduce reference databse + Reducing reference databases to 90 sequences + + # Needlall version: EMBOSS:6.6.0.0 + # Needlall command: needleall -asequence res/1550052856.58_4164_ITS1.rdp.fasta -bsequence res/1550052855.96_4147_04-filters.fasta_FROGS_combined -outfile res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.sam -aformat3 sam -gapopen 10.0 -gapextend 0.5 -errfile res/1550052856.58_4164_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.sam_needle_errorfile.txt + +######################################################################################################## +# convert NeedleAll Sam output in blast like tsv output sorted by bitscore (needleallSam_to_tsv.py version : r3.0-v1.0) +Command: + needleallSam_to_tsv.py -n res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.sam -r /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta -b res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.blast_like + +Execution: + start: 13 Feb 2019 11:14:33 + end: 13 Feb 2019 11:14:34 + +######################################################################################################## +# blast taxonomic affiliation (blastn version : 2.7.1+) +Command: + blastn -num_threads 1 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res/1550052855.96_4147_04-filters.fasta_FROGS_full_length -out res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_full_length.blast -db /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta + +Execution: + start: 13 Feb 2019 11:14:34 + end: 13 Feb 2019 11:14:34 + +######################################################################################################## +# Add Blast and/or RDP affiliation to biom (addAffiliation2biom.py version : 2.3.0) +Command: + addAffiliation2biom.py -f /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta -i res/04-filters.biom -o res/06-affiliation.biom -b res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_full_length.blast res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.blast_like + +Execution: + start: 13 Feb 2019 11:14:34 + end: 13 Feb 2019 11:14:34 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/07-affiliation_postprocessed.compo.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/07-affiliation_postprocessed.compo.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,86 @@ +Cluster_1 +Cluster_2 +Cluster_45_FROGS_combined +Cluster_3 +Cluster_4 +Cluster_5 +Cluster_6 +Cluster_10 +Cluster_7 +Cluster_8 +Cluster_9 +Cluster_11 +Cluster_12 +Cluster_46_FROGS_combined +Cluster_13 +Cluster_21 +Cluster_14 +Cluster_16 +Cluster_15 +Cluster_19 +Cluster_17 +Cluster_20 +Cluster_18 +Cluster_25 +Cluster_22 +Cluster_24 +Cluster_26 +Cluster_23 +Cluster_28 +Cluster_27 +Cluster_29 +Cluster_31 +Cluster_33 +Cluster_30 +Cluster_34 +Cluster_32 +Cluster_35 +Cluster_36 +Cluster_48_FROGS_combined +Cluster_38 +Cluster_37 +Cluster_39 +Cluster_40 +Cluster_41 +Cluster_44 +Cluster_42 +Cluster_43 +Cluster_47_FROGS_combined +Cluster_49 +Cluster_50 +Cluster_51 +Cluster_52 +Cluster_53 +Cluster_54 +Cluster_55 +Cluster_875_FROGS_combined +Cluster_463_FROGS_combined +Cluster_2418_FROGS_combined +Cluster_1179_FROGS_combined +Cluster_346_FROGS_combined +Cluster_280_FROGS_combined +Cluster_8094_FROGS_combined +Cluster_626_FROGS_combined +Cluster_116_FROGS_combined +Cluster_2726_FROGS_combined +Cluster_119_FROGS_combined +Cluster_1736_FROGS_combined +Cluster_2358_FROGS_combined +Cluster_582_FROGS_combined +Cluster_5119_FROGS_combined +Cluster_2010_FROGS_combined +Cluster_2326_FROGS_combined +Cluster_10102_FROGS_combined +Cluster_7577_FROGS_combined +Cluster_59_FROGS_combined +Cluster_56 +Cluster_2042_FROGS_combined +Cluster_58_FROGS_combined +Cluster_2099_FROGS_combined +Cluster_3240_FROGS_combined +Cluster_1482_FROGS_combined +Cluster_1253_FROGS_combined +Cluster_4257_FROGS_combined +Cluster_7410_FROGS_combined +Cluster_12367_FROGS_combined +Cluster_2886_FROGS_combined |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/07-affiliation_postprocessed.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/07-affiliation_postprocessed.log Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,31 @@ +## Application +Software: affiliation_postprocess.py (version: 3.1) +Command: /home/maria/workspace/git/FROGS/FROGS_master/test/../app/affiliation_postprocess.py --input-biom res/06-affiliation.biom --input-fasta res/04-filters.fasta --reference /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/Unite_extract_ITS1.fasta --output-biom res/07-affiliation_postprocessed.biom --output-compo res/07-affiliation_postprocessed.compo.tsv --output-fasta res/07-affiliation_postprocessed.fasta --log-file res/07-affiliation_postprocessed.log + +######################################################################################################## +# Select smallest reference as affiliation. (select_inclusive_amplicon.py version : ) +Command: + select_inclusive_amplicon.py --ITS-reference /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/Unite_extract_ITS1.fasta -b res/06-affiliation.biom -o res/1550052874.36_4187_06-affiliation.biom_resolve_inclusiv_its.biom --log-file res/1550052874.36_4187_06-affiliation.biom_resolve_inclusiv_its.log + +Execution: + start: 13 Feb 2019 11:14:34 + end: 13 Feb 2019 11:14:34 + + # nb OTU : 86 + # nb OTU with multiaffiliations : 0 + # nb OTU with multiaffiliations resolved : 0 + # nb multiaffiliations removed : 0 + +######################################################################################################## +# Aggregate OTU that share taxonomic affiliation with at least I% identity and C% coverage (aggregate_affiliated_otus.py version : ) +Command: + aggregate_affiliated_otus.py -b res/1550052874.36_4187_06-affiliation.biom_resolve_inclusiv_its.biom -f res/04-filters.fasta --identity 99.0 --coverage 99.0 --output-biom res/07-affiliation_postprocessed.biom --output-compo res/07-affiliation_postprocessed.compo.tsv --output-fasta res/07-affiliation_postprocessed.fasta --log-file res/1550052874.36_4187_06-affiliation.biom_aggregation.log + +Execution: + start: 13 Feb 2019 11:14:34 + end: 13 Feb 2019 11:14:34 + + # nb OTU in : 86 + # nb OTU out : 86 + # nb OTU aggregated : 0 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/08-clustersStat.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/08-clustersStat.html Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,915 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<html>\n+\t<head>\n+\t\t<title>FROGS Cluster stat</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="1.4.1">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t#hc-graph {\n+\t\t\t\theight: 500px;\n+\t\t\t\toverflow: auto;\n+\t\t\t}\n+\t\t\t#hc-warning {\n+\t\t\t\tmargin-top: 8px;\n+\t\t\t}\n+\t\t\t#hc-newick {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tposition: absolute;\n+\t\t\t\tbackground-color: white;\n+\t\t\t\tborder: 1px solid lightgrey;\n+\t\t\t\tborder-radius:5px;\n+\t\t\t\tpadding: 5px 5px 5px 5px;\n+\t\t\t\tmargin-top: 10px;\n+\t\t\t}\n+\t\t\t#dispersion {\n+\t\t\t\theight: 1000px;\n+\t\t\t}\n+\t\t\t#twofigs{\n+\t\t\t\theight: 600px;\n+\t\t\t}\n+\t\t\t.label-badge {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: -10px;\n+\t\t\t\tleft: -10px;\n+\t\t\t}\n+\t\t\t.badge-primary{\n+\t\t\t\tbackground-color:#8EADAC;\n+\t\t\t}\n+\t\t\t.graph-nb {\n+\t\t\t\tcolor: #95959C;\n+\t\t\t\tfont-style: italic;\n+\t\t\t\ttext-align: center;\n+\t\t\t}\n+\t\t\t.circle {\n+\t\t\t\tborder-style: solid;\n+\t\t\t\tborder-width: 3px;\n+\t\t\t\tborder-radius: 50px;\n+\t\t\t\tbox-shadow: 2px 2px 2px #555;\n+\t\t\t\tborder-color: 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#8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t.page-link{\n+\t\t\t\tco'..b'\'#\' + container_id).highcharts( seq_by_depth );\n+\t\t\t\t\t$(\'#\' + container_id).append(\'<p class="graph-nb">N.B.: Select area to zoom in.</p>\');\n+\t\t\t}\n+\n+\t\t\t\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Data\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\tvar clusters_sizes = [7, 8, 9, 10, 11, 12, 13, 15, 17, 18, 19, 20, 27, 30, 44, 45, 101, 124, 337, 836, 855, 873, 886, 893, 894, 904, 906, 907, 910, 912, 914, 915, 918, 919, 920, 922, 925, 928, 932, 934, 935, 937, 939, 940, 941, 943, 945, 947, 948, 954, 958, 959, 960, 971, 974, 1002] ;\n+\t\t\tvar series = [{\n+\t\t\t\t\'name\': "All",\n+\t\t\t\t\'data\': [3, 4, 2, 6, 1, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 2, 1, 1, 2, 1, 3, 1, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1]\n+\t\t\t}];\n+\t\t\tvar sum_series = new Array() ;\n+\t\t\tvar samples_distrib = {"02": {"shared_observations": 86, "own_seq": 0, "shared_seq": 15140, "own_observations": 0}, "03": {"shared_observations": 86, "own_seq": 0, "shared_seq": 15167, "own_observations": 0}, "01": {"shared_observations": 86, "own_seq": 0, "shared_seq": 15267, "own_observations": 0}} ;\n+\t\t\tvar newick = "((02,(01,03):0.034):0.038);" ;\n+\n+\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Main\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t$(function() {\t\t\t\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\n+\t\t\t\t// Load active tab\n+\t\t\t\tcluster_distrib_load( "cluster-distrib" );\n+\t\t\t\t\n+\t\t\t\t// Add tab listener\n+\t\t\t\t$(\'.nav-tabs a\').click(function (e) {\n+\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t$(this).tab(\'show\');\n+\t\t\t\t\tif( $(this).attr(\'href\') == "#sequence-distrib" && $(\'#sequence-distrib\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#sequence-distrib\').removeClass("disabled");\n+\t\t\t\t\t\tsequence_distrib_load( "sequence-distrib" );\n+\t\t\t\t\t} else if( $(this).attr(\'href\') == "#samples-distrib" && $(\'#samples-distrib\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#samples-distrib\').removeClass("disabled");\n+\t\t\t\t\t\tsample_table_load( "samples-distrib-table" );\n+\t\t\t\t\t\thierarchical_clustering_load( "samples-distrib-hc" );\n+\t\t\t\t\t}\n+\t\t\t\t})\n+\t\t\t});\n+\t\t</script>\n+\t</head>\n+\t<body>\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+\t\t<div id="content" class="hidden">\n+\t\t\t<ul class="nav nav-tabs">\n+\t\t\t\t<li class="nav-item active"><a class="nav-link active" href="#cluster-distrib">Clusters distribution</a></li>\n+\t\t\t\t<li class="nav-item active"><a class="nav-link" href="#sequence-distrib">Sequences distribution</a></li>\n+\t\t\t\t<li class="nav-item active"><a class="nav-link" href="#samples-distrib">Samples distribution</a></li>\n+\t\t\t</ul>\n+\t\t\t<div class="tab-content">\n+\t\t\t\t<div id="cluster-distrib" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<div class="row">\n+\t\t\t\t\t\t<div class="col-md-2"></div>\n+\t\t\t\t\t\t<div id="nb-clusters" class="col-sm-6 col-md-4"></div>\n+\t\t\t\t\t\t<div id="nb-sequences" class="col-sm-6 col-md-4"></div>\n+\t\t\t\t\t\t<div class="col-md-2"></div>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t\t<div id="sequence-distrib" role="tabpanel" class="tab-pane disabled"></div>\n+\t\t\t\t<div id="samples-distrib" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<div>\n+\t\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Sequences count</h2>\n+\t\t\t\t\t\t<div id="samples-distrib-table"></div>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div>\n+\t\t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Hierarchical clustering</h2>\n+\t\t\t\t\t\t<div id="samples-distrib-hc"></div>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n' |
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| diff -r 000000000000 -r 59bc96331073 test-data/references/08-clustersStat.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/08-clustersStat.log Thu Feb 28 10:14:49 2019 -0500 |
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| @@ -0,0 +1,22 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/clusters_stat.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/clusters_stat.py --input-biom res/06-affiliation.biom --output-file res/08-clustersStat.html --log-file res/08-clustersStat.log + +######################################################################################################## +# Hierarchical classification on observation proportions. (biomTools.py version : 0.10.1) +Command: + biomTools.py hclassification --distance-method braycurtis --linkage-method average --input-file res/06-affiliation.biom --output-file res/1550052874.54_4197_HClassif.newick > res/1550052874.54_4197_HClassif_log.txt + +Execution: + start: 13 Feb 2019 11:14:34 + end: 13 Feb 2019 11:14:36 + +######################################################################################################## +# Writes by abundance the number of clusters. (biomTools.py version : 0.10.1) +Command: + biomTools.py obsdepth --input-file res/06-affiliation.biom --output-file res/1550052874.54_4197_depths.tsv + +Execution: + start: 13 Feb 2019 11:14:36 + end: 13 Feb 2019 11:14:36 + |
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| diff -r 000000000000 -r 59bc96331073 test-data/references/09-affiliationsStat.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/09-affiliationsStat.html Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,1196 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<html>\n+\t<head>\n+\t\t<title>FROGS Affiliations stat</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="1.3.0">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t/*\n+\t\t\t * jDistrib 0.1.0 - CSS jDistrib Library\t\n+\t\t\t *\t\t \n+\t\t\t * Copyright (c) 2015 Escudie Frederic\n+\t\t\t * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.\n+\t\t\t */\n+\t\t\t#sunburst-graph{margin-left:auto;margin-right:auto}.jDistrib-walk-rank{height:100%;margin-right:2px;padding:8px;float:left;border-top-right-radius:7px;border-bottom-right-radius:7px;cursor:pointer;box-shadow:1px 1px 1px #555}.jDistrib-walk-rank-size{margin-left:5px;padding:4px;background-color:#FFF;color:#648a89;border-radius:9px;text-align:center;font-size:10px;font-family:sans-serif}.jDistrib-root-label{font-weight:700;cursor:pointer}.jDistrib-arc-label{cursor:pointer}.jDistrib-arc{cursor:pointer;stroke:#fff;fill-rule:evenodd}.jDistrib-tooltip{position:absolute;padding:10px;font:12px sans-serif;background:#8EADAC;border:0;border-radius:8px;pointer-events:none}.jDistrib-empty-details{color:#fff;background-color:#8EADAC;padding:15px;margin-bottom:20px;border:1px solid transparent;border-radius:4px}.jDistrib-table-details>tbody>tr:nth-of-type(2n+1){background-color:#F5F5F5}.jDistrib-table-details{border:1px solid #DDD;border-radius:8px;border-spacing:1px;border-collapse:separate}.jDistrib-table-details td,th{padding:2px 8px}.jDistrib-table-details .number{text-align:right}.jDistrib-export-toggle{height:30px;width:30px;padding:1px}.jDistrib-export-toggle div{background-color:#636363;border-radius:2px;height:3px;margin-top:2px;margin-bottom:2px}\n+\t\t</style>\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\t.set-datatype {\n+\t\t\t\twidth: 200px;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t}\n+\t\t\t.table-action {\n+\t\t\t\tvertical-align: middle;\n+\t\t\t\tmargin-right: 20px;\n+\t\t\t}\n+\t\t\t.fusion-left {\n+\t\t\t\tposition:relative;\n+\t\t\t\tz-index:2;\t\t\n+\t\t\t\tmargin-right: 0px;\n+\t\t\t\tmargin-bottom: 0px;\n+\t\t\t\tborder-top-left-radius: 4px;\n+\t\t\t\tborder-bottom-left-radius: 4px;\n+\t\t\t}\n+\t\t\t.fusion-right {\n+\t\t\t\tborder-top-left-radius: 0px;\n+\t\t\t\tborder-bottom-left-radius: 0px;\n+\t\t\t\tmargin-left:-6px;\n+\t\t\t}\n+\t\t\tselect.table-action {\n+\t\t\t\tpadding: 6px 12px;\n+\t\t\t\tfont-size: 14px;\n+\t\t\t\tfont-weight: 400;\n+\t\t\t\tline-height: 1.42857;\n+\t\t\t\tbox-shadow: 0px 1px 1px rgba(0, 0, 0, 0.075);\n+\t\t\t\tcolor: #555;\n+\t\t\t\tbackground-color: #FFF;\n+\t\t\t\tbackground-image: none;\n+\t\t\t\tborder: 1px solid #CCC;\n+\t\t\t}\n+\t\t\t#sunburst-detail table {\n+\t\t\t\tmargin-left: auto;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t}\t\n+\t\t\t#sunburst-detail p {\n+\t\t\t\ttext-align: center;\n+\t\t\t}\n+\t\t\t#sunburst-menu i'..b'class="nav-item active"><a class="nav-link active" href="#tax-distrib">Taxonomy distribution</a></li>\n+\t\t\t\t<li class="nav-item" id="bootstrap-nav-tab"><a class="nav-link" href="#bootstrap-distrib">Bootstrap distribution</a></li>\n+\t\t\t\t<li class="nav-item" id="alignment-nav-tab"><a class="nav-link" href="#alignment-distrib">Alignment distribution</a></li>\n+\t\t\t</ul>\n+\t\t\t<div id="tab-content" class="tab-content">\n+\t\t\t\t<div id="tax-distrib" role="tabpanel" class="tab-pane active">\n+\t\t\t\t\t<button id="display-global-sunburst" class="btn d-block mx-auto" data-toggle="modal" data-target="#sunburst-modal">\n+\t\t\t\t\t\t<span class="fa fa-pie-chart" aria-hidden="true"> Display global distribution</span>\n+\t\t\t\t\t</button>\n+\t\t\t\t\t<table id="taxBySample-table" class="table table-striped">\n+\t\t\t\t\t\t<thead>\n+\t\t\t\t\t\t</thead>\n+\t\t\t\t\t\t<tbody></tbody>\n+\t\t\t\t\t\t<tfoot>\n+\t\t\t\t\t\t\t<tr>\n+\t\t\t\t\t\t\t\t<th>\n+\t\t\t\t\t\t\t\t\t<span class="table-action">With selection:</span>\n+\t\t\t\t\t\t\t\t\t<select id="rarefaction-level" name="select" class="table-action fusion-left"></select>\n+\t\t\t\t\t\t\t\t\t<button id="display-rarefaction" class="btn table-action fusion-right" disabled data-toggle="modal" data-target="#rarefaction-modal"><span class="fa fa-line-chart" aria-hidden="true"> Display rarefaction</span></button>\n+\t\t\t\t\t\t\t\t\t<button id="display-spl-sunburst" class="btn table-action" disabled data-toggle="modal" data-target="#sunburst-modal"><span class="fa fa-pie-chart" aria-hidden="true"> Display distribution</span></button>\n+\t\t\t\t\t\t\t\t</th>\n+\t\t\t\t\t\t\t</tr>\n+\t\t\t\t\t\t</tfoot>\n+\t\t\t\t\t</table>\n+\t\t\t\t</div>\n+\t\t\t\t<div id="bootstrap-distrib" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<div id="bootstrap-barplot"></div>\n+\t\t\t\t\t<div id="set-bootstrap-barplot" class="set-datatype">\n+\t\t\t\t\t\t<button id="bootstrap-clstr-btn" type="button" class="btn btn-md btn-block">by OTUs</button>\n+\t\t\t\t\t\t<button id="bootstrap-seq-btn" type="button" class="btn btn-md btn-block">by sequences</button>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t\t<div id="alignment-distrib" role="tabpanel" class="tab-pane disabled">\n+\t\t\t\t\t<div id="alignment-heatmap"></div>\n+\t\t\t\t\t<div id="set-alignment-heatmap" class="set-datatype">\n+\t\t\t\t\t\t<button id="heatmap-clstr-btn" type="button" class="btn btn-md btn-block" disabled>by OTUs</button>\n+\t\t\t\t\t\t<button id="heatmap-seq-btn" type="button" class="btn btn-md btn-block">by sequences</button>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t\t\n+\t\t<div class="modal" id="sunburst-modal" tabindex="-1" role="dialog" aria-hidden="true">\n+\t\t\t<div class="modal-dialog modal-lg">\n+\t\t\t\t<div class="modal-content">\n+\t\t\t\t\t<div class="modal-header">\n+\t\t\t\t\t\t<h6 class="modal-title">Taxa distribution</h6>\n+\t\t\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div class="modal-body">\n+\t\t\t\t\t\t<div id="sunburst-walktrace"></div>\n+\t\t\t\t\t\t<div id="sunburst-graph"></div>\n+\t\t\t\t\t\t<div>\n+\t\t\t\t\t\t\t</br><h6>Detail on selected:</h6>\n+\t\t\t\t\t\t\t<div id="sunburst-detail"></div>\n+\t\t\t\t\t\t</div>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div class="modal-footer">\n+\t\t\t\t\t\t<span id="sunburst-menu"></span>\n+\t\t\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t\t<div class="modal" id="rarefaction-modal" tabindex="-1" role="dialog" aria-hidden="true">\n+\t\t\t<div class="modal-dialog modal-lg">\n+\t\t\t\t<div class="modal-content">\n+\t\t\t\t\t<div class="modal-header">\n+\t\t\t\t\t\t<h6 class="modal-title">Rarefaction</h6>\n+\t\t\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div class="modal-body">\n+\t\t\t\t\t\t<div id="rarefaction-chart"></div>\n+\t\t\t\t\t</div>\n+\t\t\t\t\t<div class="modal-footer">\n+\t\t\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/09-affiliationsStat.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/09-affiliationsStat.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,22 @@ +## Application +Software: affiliations_stat.py (version: 3.1) +Command: /home/maria/workspace/git/FROGS/FROGS_master/test/../app/affiliations_stat.py --input-biom res/06-affiliation.biom --output-file res/09-affiliationsStat.html --log-file res/09-affiliationsStat.log --tax-consensus-tag blast_taxonomy --identity-tag perc_identity --coverage-tag perc_query_coverage --multiple-tag blast_affiliations --rarefaction-ranks Family Genus Species + +######################################################################################################## +# Writes by sample the rarefaction data for rank(s) 4, 5, 6. (biomTools.py version : 0.10.1) +Command: + biomTools.py rarefaction --input-file res/06-affiliation.biom --output-file-pattern res/1550052876.48_4207_rarefaction_rank_##RANK##.tsv --taxonomy-key "blast_taxonomy" --step-size 432 --ranks 4 5 6 + +Execution: + start: 13 Feb 2019 11:14:36 + end: 13 Feb 2019 11:14:37 + +######################################################################################################## +# Produces a taxonomy tree with counts by sample. (biomTools.py version : 0.10.1) +Command: + biomTools.py treeCount --input-file res/06-affiliation.biom --taxonomy-key "blast_taxonomy" --output-enewick res/1550052876.48_4207_taxCount.enewick --output-samples res/1550052876.48_4207_taxCount_ids.tsv + +Execution: + start: 13 Feb 2019 11:14:37 + end: 13 Feb 2019 11:14:37 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/10-biom2tsv-affiliation_multihit.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/10-biom2tsv-affiliation_multihit.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +#observation_name blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/10-biom2tsv.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/10-biom2tsv.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,22 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/biom_to_tsv.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/biom_to_tsv.py --input-biom res/06-affiliation.biom --input-fasta res/04-filters.fasta --output-tsv res/10-biom2tsv.tsv --output-multi-affi res/10-biom2tsv-affiliation_multihit.tsv --log-file res/10-biom2tsv.log + +######################################################################################################## +# Converts a BIOM file in TSV file. (biom2tsv.py version : 1.4.1) +Command: + biom2tsv.py --input-file res/06-affiliation.biom --input-fasta res/04-filters.fasta --output-file res/10-biom2tsv.tsv --fields 'comment' 'blast_taxonomy' '@blast_subject' '@blast_perc_identity' '@blast_perc_query_coverage' '@blast_evalue' '@blast_aln_length' 'seed_id' '@seed_sequence' '@observation_name' '@observation_sum' '@sample_count' + +Execution: + start: 13 Feb 2019 11:14:37 + end: 13 Feb 2019 11:14:37 + +######################################################################################################## +# Extracts multi-affiliations data from a FROGS BIOM file. (multiAffiFromBiom.py version : 1.3.0) +Command: + multiAffiFromBiom.py --input-file res/06-affiliation.biom --output-file res/10-biom2tsv-affiliation_multihit.tsv + +Execution: + start: 13 Feb 2019 11:14:37 + end: 13 Feb 2019 11:14:37 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/10-biom2tsv.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/10-biom2tsv.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,87 @@\n+#comment\tblast_taxonomy\tblast_subject\tblast_perc_identity\tblast_perc_query_coverage\tblast_evalue\tblast_aln_length\tseed_id\tseed_sequence\tobservation_name\tobservation_sum\t01\t02\t03\n+na\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Hymenochaete;s__Hymenochaete_longispora\tJQ279537_SH175098.07FU_refs\t100.0\t100.0\t0.0\t337\t01_58367\tCTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_1\t1002\t339\t318\t345\n+na\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_cyathuliformis\tHQ714785_SH330547.07FU_refs\t100.0\t100.0\t4.90e-134\t252\t01_57964\tGTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_2\t974\t320\t337\t317\n+na\tRoot;k__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Pezizaceae;g__Terfezia;s__Terfezia_claveryi\tGU474801_SH104786.07FU_refs_singleton\t100.0\t100.0\t8.56e-142\t266\t01_67063\tGAAGGATCATTACTGAAGAACTATATCGAGTTTTTTTATACCCTTTTGTTTACCTACCCTATTGCTTCCACTGGACAGGTTTCACCTTGTGTGGGTCCTCTCTGGCTTGTGTGAAAAGCACCTGCCAGACAGACGTTGCTGGTGGGAAGAACTATTTACTAAAACTTGATTTTTAAAAAAAAATACAATGTCTGAATAATTTCCTTTAATGAAATAAAACTTTCAACAACGGATCTCTAGGCTCTTGCATCGATGAAGAACGCAGT\tCluster_3\t960\t332\t315\t313\n+na\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Inocybaceae;g__Inocybe;s__Inocybe_sindonia\tUDB015350_SH176685.07FU_refs\t100.0\t100.0\t4.60e-170\t317\t01_80623\tGTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_4\t959\t322\t330\t307\n+na\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Pseudochaete;s__Pseudochaete_subrigidula\tJQ716403_SH219241.07FU_refs\t100.0\t100.0\t7.94e-178\t331\t01_256\tTCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_5\t959\t308\t327\t324\n+na\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii\tUDB002317_SH221025.07FU_refs\t100.0\t100.0\t9.52e-162\t302\t01_54434\tCTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGCTGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGAGGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATTTTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTAAATGATAAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_6\t958\t321\t318\t319\n+na\tRoot;k__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Tuberaceae;g__Tuber;s__Tuber_latisporum\tDQ898183_SH216206.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_44905\tCCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\tCluster_7\t948\t320\t318\t310\n+na\tRoot;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t100.0\t100.0\t4.90e-134\t252\t01_81\tCCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGG'..b'CGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGGAGCGCGTCCTATCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGCGAGGGCTGTCGCTGACTTCAAAGTGCGTGCACGCCGGAGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_1253_FROGS_combined\t8\t2\t5\t1\n+WARNING\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_gentianeus\tKF732310_SH222414.07FU_refs\t80.04\t100.0\t-1\t716\t01_81379_FROGS_combined\tTTGAAATAAACCTGATGAGTTGCTGCTGGCTCTCTTGGGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTAGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTTGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGCTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_2726_FROGS_combined\t13\t1\t6\t6\n+WARNING\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_amnicola\tKF732249_SH136099.07FU_refs_singleton\t79.24\t100.0\t-1\t712\t01_77767_FROGS_combined\tTTGAAATAAACCTGATGAGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACACTCGTCATCTTTGTATATTCACCTGTGCATCTTTTGTAGACCCTTGGGTATCTCTCTGATTGCTTTTAGCACTCAGGATTGAGGATTGACTTCCTGTCTCTTCTTACATTTCCAGGTCTATGTTTCTTAATATACCCTAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAATCTATACAACTTTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATGTGCACACTCGTCATCTTTGTATATTCACCTGTGGCATCTTTTGTAGACCCTTGGGTATCTCTCTGATTGCTTTTAGCACTCAGGATTGAGGATTGACTTCCTGTCTCTTCTTACATTTCCAGGTCTATGTTTCTTAATATACCCTAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_2042_FROGS_combined\t10\t3\t4\t3\n+WARNING\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Strophariaceae;g__Hypholoma;s__Hypholoma_capnoides\tUDB001581_SH219736.07FU_refs\t81.24\t100.0\t-1\t705\t01_7802_FROGS_combined\tTTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTTCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGCAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_2099_FROGS_combined\t9\t4\t3\t2\n+WARNING\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Gamundia;s__Gamundia_leucophylla\tGU234142_SH201120.07FU_refs\t78.84\t100.0\t-1\t698\t01_89678_FROGS_combined\tTTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTCTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\tCluster_4257_FROGS_combined\t8\t3\t1\t4\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/11-affiliation_multihit.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/11-affiliation_multihit.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,87 @@\n+#OTUID\ttaxonomy\tsubject\tevalue\tperc_identity\tperc_query_coverage\taln_length\n+Cluster_1\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Hymenochaete;s__Hymenochaete_longispora\tJQ279537_SH175098.07FU_refs\t0.0\t100.0\t100.0\t337\n+Cluster_2\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_cyathuliformis\tHQ714785_SH330547.07FU_refs\t4.90e-134\t100.0\t100.0\t252\n+Cluster_3\tRoot;k__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Pezizaceae;g__Terfezia;s__Terfezia_claveryi\tGU474801_SH104786.07FU_refs_singleton\t8.56e-142\t100.0\t100.0\t266\n+Cluster_4\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Inocybaceae;g__Inocybe;s__Inocybe_sindonia\tUDB015350_SH176685.07FU_refs\t4.60e-170\t100.0\t100.0\t317\n+Cluster_5\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Pseudochaete;s__Pseudochaete_subrigidula\tJQ716403_SH219241.07FU_refs\t7.94e-178\t100.0\t100.0\t331\n+Cluster_6\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii\tUDB002317_SH221025.07FU_refs\t9.52e-162\t100.0\t100.0\t302\n+Cluster_7\tRoot;k__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Tuberaceae;g__Tuber;s__Tuber_latisporum\tDQ898183_SH216206.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n+Cluster_8\tRoot;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t4.90e-134\t100.0\t100.0\t252\n+Cluster_9\tRoot;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Chaetothyriales;f__Herpotrichiellaceae;g__Exophiala;s__Exophiala_equina\tJF747094_SH197643.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n+Cluster_10\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Paxillaceae;g__Alpova;s__Alpova_alpestris\tHQ714696_SH221416.07FU_refs\t9.98e-172\t100.0\t100.0\t320\n+Cluster_11\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_semisanguifluus\tUDB000320_SH220111.07FU_refs\t1.45e-144\t100.0\t100.0\t271\n+Cluster_12\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Psathyrella;s__Psathyrella_multipedata\tKC992888_SH220378.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n+Cluster_13\tRoot;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_mienum\tJQ621972_SH177703.07FU_refs\t2.32e-137\t100.0\t100.0\t258\n+Cluster_14\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Omphalotaceae;g__Gymnopus;s__Gymnopus_hybridus\tJX536175_SH183774.07FU_refs\t2.39e-142\t100.0\t100.0\t267\n+Cluster_15\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Agaricaceae;g__Lepiota;s__Lepiota_geogenia\tJX179268_SH178540.07FU_refs\t2.53e-152\t100.0\t100.0\t285\n+Cluster_16\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Strophariaceae;g__Hypholoma;s__Hypholoma_capnoides\tUDB001581_SH219736.07FU_refs\t1.97e-153\t100.0\t100.0\t287\n+Cluster_17\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_sp\tEU292260_SH086465.07FU_refs\t3.94e-140\t100.0\t100.0\t263\n+Cluster_18\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Sarcodon;s__Sarcodon_quercophilus\tKM668101_SH491630.07FU_refs_singleton\t3.94e-140\t100.0\t100.0\t263\n+Cluster_19\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_pachyderma\tJX118731_SH218995.07FU_refs\t5.20e-144\t100.0\t100.0\t270\n+Cluster_20\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_aurantiobasis\tJX045670_SH303923.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n+Cluster_21\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_limonius\tUDB001086_SH222381.07FU_refs\t7.59e-168\t100.0\t100.0\t313\n+Cluster_22\tRoot;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__E'..b'erocomus;s__Xerocomus_porophyllus\tKC168089_SH480027.07FU_refs\t-1\t84.03\t100.0\t821\n+Cluster_1179_FROGS_combined\tRoot;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_mienum\tJQ621972_SH177703.07FU_refs\t-1\t77.05\t100.0\t717\n+Cluster_1253_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_semisanguifluus\tUDB000320_SH220111.07FU_refs\t-1\t81.84\t100.0\t744\n+Cluster_1482_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Tricholoma;s__Tricholoma_portentosum\tUDB011569_SH190415.07FU_refs\t-1\t79.4\t100.0\t794\n+Cluster_1736_FROGS_combined\tRoot;k__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Pezizaceae;g__Terfezia;s__Terfezia_claveryi\tGU474801_SH104786.07FU_refs_singleton\t-1\t79.0\t100.0\t712\n+Cluster_2010_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Pseudochaete;s__Pseudochaete_subrigidula\tJQ716403_SH219241.07FU_refs\t-1\t65.87\t100.0\t601\n+Cluster_2042_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_amnicola\tKF732249_SH136099.07FU_refs_singleton\t-1\t79.24\t100.0\t712\n+Cluster_2099_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Strophariaceae;g__Hypholoma;s__Hypholoma_capnoides\tUDB001581_SH219736.07FU_refs\t-1\t81.24\t100.0\t705\n+Cluster_2326_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Paxillaceae;g__Alpova;s__Alpova_alpestris\tHQ714696_SH221416.07FU_refs\t-1\t63.87\t100.0\t601\n+Cluster_2358_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_aurantiobasis\tJX045670_SH303923.07FU_refs\t-1\t81.4\t100.0\t749\n+Cluster_2418_FROGS_combined\tRoot;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Rasamsonia;s__Rasamsonia_emersonii\tJF417478_SH216679.07FU_refs\t-1\t73.85\t100.0\t743\n+Cluster_2726_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_gentianeus\tKF732310_SH222414.07FU_refs\t-1\t80.04\t100.0\t716\n+Cluster_2886_FROGS_combined\tRoot;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_cremeum\tAY737760_SH296378.07FU_refs\t-1\t77.64\t100.0\t716\n+Cluster_3240_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_limonius\tUDB001086_SH222381.07FU_refs\t-1\t82.83\t100.0\t769\n+Cluster_4257_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Gamundia;s__Gamundia_leucophylla\tGU234142_SH201120.07FU_refs\t-1\t78.84\t100.0\t698\n+Cluster_5119_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Omphalotaceae;g__Gymnopus;s__Gymnopus_hybridus\tJX536175_SH183774.07FU_refs\t-1\t84.03\t100.0\t810\n+Cluster_7410_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Sarcodon;s__Sarcodon_quercophilus\tKM668101_SH491630.07FU_refs_singleton\t-1\t80.84\t100.0\t734\n+Cluster_7577_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Psathyrella;s__Psathyrella_sublatispora\tKC992854_SH220410.07FU_refs\t-1\t77.25\t100.0\t724\n+Cluster_8094_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_candidolanata\tJX118682_SH219010.07FU_refs\t-1\t79.24\t100.0\t684\n+Cluster_10102_FROGS_combined\tRoot;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Agaricaceae;g__Lepiota;s__Lepiota_geogenia\tJX179268_SH178540.07FU_refs\t-1\t78.84\t100.0\t766\n+Cluster_12367_FROGS_combined\tRoot;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rodmanii\tEU330948_SH316773.07FU_refs\t-1\t76.45\t100.0\t712\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/11-affiliation_std.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/11-affiliation_std.biom Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_1", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "blast_taxonomy": "Root;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Hymenochaete;s__Hymenochaete_longispora", "seed_id": "01_58367"}}, {"id": "Cluster_2", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_cyathuliformis"], "blast_taxonomy": "Root;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_cyathuliformis", "seed_id": "01_57964"}}, {"id": "Cluster_3", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Pezizaceae", "g__Terfezia", "s__Terfezia_claveryi"], "blast_taxonomy": "Root;k__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Pezizaceae;g__Terfezia;s__Terfezia_claveryi", "seed_id": "01_67063"}}, {"id": "Cluster_4", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Inocybaceae", "g__Inocybe", "s__Inocybe_sindonia"], "blast_taxonomy": "Root;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Inocybaceae;g__Inocybe;s__Inocybe_sindonia", "seed_id": "01_80623"}}, {"id": "Cluster_5", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "blast_taxonomy": "Root;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Pseudochaete;s__Pseudochaete_subrigidula", "seed_id": "01_256"}}, {"id": "Cluster_6", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "blast_taxonomy": "Root;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii", "seed_id": "01_54434"}}, {"id": "Cluster_7", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "blast_taxonomy": "Root;k__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Tuberaceae;g__Tuber;s__Tuber_latisporum", "seed_id": "01_44905"}}, {"id": "Cluster_8", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "blast_taxonomy": "Root;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum", "seed_id": "01_81"}}, {"id": "Cluster_9", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "blast_taxonomy": "Root;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Chaetothyriales;f__Herpotrichiellaceae;g__Exophiala;s__Exophiala_equina", "seed_id": "01_92283"}}, {"id": "Cluster_10", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Paxillaceae", "g__Alpova", "s__Alpova_alpestris"], "blast_taxonomy": "Root;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Paxillaceae;g__Alpova;s__Alpova_alpestris", "seed_id": "01_84442"}}, {"id": "Cluster_11", "metadata": {"comment": "na", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"], "blast_taxonomy": "Root;k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__La'..b'"g__Trichoderma", "s__Trichoderma_rodmanii"], "blast_taxonomy": "Root;k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rodmanii", "seed_id": "02_44718_FROGS_combined"}}], "matrix_element_type": "int", "format": "Biological Observation Matrix 1.0.0", "data": [[0, 0, 339], [0, 1, 318], [0, 2, 345], [1, 0, 320], [1, 1, 337], [1, 2, 317], [2, 0, 332], [2, 1, 315], [2, 2, 313], [3, 0, 322], [3, 1, 330], [3, 2, 307], [4, 0, 308], [4, 1, 327], [4, 2, 324], [5, 0, 321], [5, 1, 318], [5, 2, 319], [6, 0, 320], [6, 1, 318], [6, 2, 310], [7, 0, 284], [7, 1, 322], [7, 2, 341], [8, 0, 320], [8, 1, 302], [8, 2, 323], [9, 0, 329], [9, 1, 305], [9, 2, 320], [10, 0, 300], [10, 1, 312], [10, 2, 331], [11, 0, 334], [11, 1, 308], [11, 2, 299], [12, 0, 319], [12, 1, 321], [12, 2, 300], [13, 0, 326], [13, 1, 287], [13, 2, 326], [14, 0, 312], [14, 1, 302], 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[64, 0, 3], [64, 1, 5], [64, 2, 7], [65, 0, 3], [65, 1, 10], [65, 2, 7], [66, 0, 6], [66, 1, 7], [66, 2, 5], [67, 0, 2], [67, 1, 5], [67, 2, 1], [68, 0, 1], [68, 1, 3], [68, 2, 4], [69, 0, 5], [69, 1, 3], [69, 2, 4], [70, 0, 3], [70, 1, 4], [70, 2, 4], [71, 0, 3], [71, 1, 4], [71, 2, 3], [72, 0, 4], [72, 1, 3], [72, 2, 2], [73, 0, 5], [73, 1, 3], [73, 2, 2], [74, 0, 4], [74, 1, 4], [74, 2, 4], [75, 0, 7], [75, 1, 4], [75, 2, 7], [76, 0, 1], [76, 1, 6], [76, 2, 6], [77, 0, 3], [77, 1, 2], [77, 2, 2], [78, 0, 4], [78, 1, 3], [78, 2, 1], [79, 0, 3], [79, 1, 1], [79, 2, 4], [80, 0, 2], [80, 1, 4], [80, 2, 6], [81, 0, 2], [81, 1, 2], [81, 2, 3], [82, 0, 3], [82, 1, 5], [82, 2, 2], [83, 0, 3], [83, 1, 9], [83, 2, 3], [84, 0, 1], [84, 1, 4], [84, 2, 5], [85, 0, 5], [85, 1, 1], [85, 2, 1]], "generated_by": "swarm", "matrix_type": "sparse", "shape": [86, 3], "format_url": "http://biom-format.org", "date": "2019-02-13T11:13:13", "type": "OTU table", "id": null, "columns": [{"id": "01", "metadata": null}, {"id": "02", "metadata": null}, {"id": "03", "metadata": null}]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/11-biom2stdbiom.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/11-biom2stdbiom.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/biom_to_stdBiom.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/biom_to_stdBiom.py --input-biom res/06-affiliation.biom --output-biom res/11-affiliation_std.biom --output-metadata res/11-affiliation_multihit.tsv --log-file res/11-biom2stdbiom.log + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/12-tsv2biom.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/12-tsv2biom.biom Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "Cluster_346_FROGS_combined", "metadata": {"comment": "WARNING", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_cyathuliformis"], "seed_id": "01_68481_FROGS_combined", "blast_affiliations": [{"perc_identity": "82.4", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_cyathuliformis"], "evalue": "-1", "aln_length": "759", "perc_query_coverage": "100.0", "subject": "HQ714785_SH330547.07FU_refs"}]}}, {"id": "Cluster_2326_FROGS_combined", "metadata": {"comment": "WARNING", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Paxillaceae", "g__Alpova", "s__Alpova_alpestris"], "seed_id": "01_7927_FROGS_combined", "blast_affiliations": [{"perc_identity": "63.87", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Paxillaceae", "g__Alpova", "s__Alpova_alpestris"], "evalue": "-1", "aln_length": "601", "perc_query_coverage": "100.0", "subject": "HQ714696_SH221416.07FU_refs"}]}}, {"id": "Cluster_10102_FROGS_combined", "metadata": {"comment": "WARNING", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "seed_id": "02_32476_FROGS_combined", "blast_affiliations": [{"perc_identity": "78.84", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "evalue": "-1", "aln_length": "766", "perc_query_coverage": "100.0", "subject": "JX179268_SH178540.07FU_refs"}]}}, {"id": "Cluster_3240_FROGS_combined", "metadata": {"comment": "WARNING", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_limonius"], "seed_id": "01_84214_FROGS_combined", "blast_affiliations": [{"perc_identity": "82.83", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_limonius"], "evalue": "-1", "aln_length": "769", "perc_query_coverage": "100.0", "subject": "UDB001086_SH222381.07FU_refs"}]}}, {"id": "Cluster_2418_FROGS_combined", "metadata": {"comment": "WARNING", "blast_taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "seed_id": "01_79704_FROGS_combined", "blast_affiliations": [{"perc_identity": "73.85", "taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "evalue": "-1", "aln_length": "743", "perc_query_coverage": "100.0", "subject": "JF417478_SH216679.07FU_refs"}]}}, {"id": "Cluster_25", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_sinapivelus"], "seed_id": "01_165", "blast_affiliations": [{"perc_identity": "100.0", "taxonomy": ["Root", "k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_sinapivelus"], "evalue": "1.57e-159", "aln_length": "298", "perc_query_coverage": "100.0", "subject": "GQ890305_SH122869.07FU_refs_singleton"}]}}, {"id": "Cluster_24", "metadata": {"comment": "na", "blast_taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "seed_id": "01_59", "blast_affiliations": [{"perc_identity": "100.0", "taxonomy": ["Root", "k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "evalue"'..b'garicomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "evalue": "2.53e-152", "aln_length": "285", "perc_query_coverage": "100.0", "subject": "KC992854_SH220410.07FU_refs"}]}}], "matrix_element_type": "int", "format": "Biological Observation Matrix 1.0.0", "data": [[0, 0, 3], [0, 1, 10], [0, 2, 4], [1, 0, 5], [1, 1, 3], [1, 2, 2], [2, 0, 1], [2, 1, 4], [2, 2, 5], [3, 0, 4], [3, 1, 3], [3, 2, 1], [4, 0, 7], [4, 1, 4], [4, 2, 7], [5, 0, 302], [5, 1, 288], [5, 2, 338], [6, 0, 323], [6, 1, 299], [6, 2, 303], [7, 0, 304], [7, 1, 299], [7, 2, 317], [8, 0, 293], [8, 1, 342], [8, 2, 290], [9, 0, 289], [9, 1, 315], [9, 2, 335], [10, 0, 338], [10, 1, 319], [10, 2, 277], [11, 0, 336], [11, 1, 265], [11, 2, 324], [12, 0, 305], [12, 1, 297], [12, 2, 326], [13, 0, 320], [13, 1, 292], [13, 2, 307], [14, 0, 294], [14, 1, 315], [14, 2, 313], [15, 0, 1], [15, 1, 3], [15, 2, 4], [16, 0, 284], [16, 1, 322], [16, 2, 341], [17, 0, 320], [17, 1, 302], [17, 2, 323], [18, 0, 321], [18, 1, 318], [18, 2, 319], [19, 0, 320], [19, 1, 318], [19, 2, 310], [20, 0, 322], [20, 1, 330], [20, 2, 307], [21, 0, 308], [21, 1, 327], [21, 2, 324], [22, 0, 320], [22, 1, 337], [22, 2, 317], [23, 0, 332], [23, 1, 315], [23, 2, 313], [24, 0, 339], [24, 1, 318], [24, 2, 345], [25, 0, 6], [25, 1, 4], [25, 2, 2], [26, 0, 339], [26, 1, 299], [26, 2, 333], [27, 0, 5], [27, 1, 3], [27, 2, 4], [28, 0, 333], [28, 1, 291], [28, 2, 308], [29, 0, 302], [29, 1, 299], [29, 2, 334], [30, 0, 3], [30, 1, 5], [30, 2, 2], [31, 0, 1], [31, 1, 3], [31, 2, 5], [32, 0, 329], [32, 1, 305], [32, 2, 320], [33, 0, 300], [33, 1, 312], [33, 2, 331], [34, 0, 334], [34, 1, 308], [34, 2, 299], [35, 0, 319], [35, 1, 321], [35, 2, 300], [36, 0, 326], [36, 1, 287], [36, 2, 326], [37, 0, 312], [37, 1, 302], [37, 2, 323], [38, 0, 4], [38, 1, 3], [38, 2, 2], [39, 0, 304], [39, 1, 324], [39, 2, 307], [40, 0, 2], [40, 1, 2], [40, 2, 3], [41, 0, 346], [41, 1, 308], [41, 2, 285], [42, 0, 321], [42, 1, 354], [42, 2, 266], [43, 0, 285], [43, 1, 268], [43, 2, 283], [44, 0, 2], [44, 1, 5], [44, 2, 1], [45, 0, 4], [45, 1, 4], [45, 2, 4], [46, 0, 5], [46, 1, 1], [46, 2, 1], [47, 0, 9], [47, 1, 14], [47, 2, 22], [48, 0, 3], [48, 1, 6], [48, 2, 3], [49, 0, 6], [49, 1, 9], [49, 2, 2], [50, 0, 3], [50, 1, 2], [50, 2, 2], [51, 0, 3], [51, 1, 9], [51, 2, 3], [52, 0, 8], [52, 1, 4], [52, 2, 7], [53, 0, 320], [53, 1, 288], [53, 2, 302], [54, 0, 6], [54, 1, 7], [54, 2, 5], [55, 0, 4], [55, 1, 4], [55, 2, 2], [56, 0, 3], [56, 1, 1], [56, 2, 4], [57, 0, 3], [57, 1, 10], [57, 2, 7], [58, 0, 3], [58, 1, 4], [58, 2, 4], [59, 0, 7], [59, 1, 5], [59, 2, 1], [60, 0, 9], [60, 1, 11], [60, 2, 10], [61, 0, 13], [61, 1, 7], [61, 2, 7], [62, 0, 3], [62, 1, 3], [62, 2, 4], [63, 0, 31], [63, 1, 44], [63, 2, 49], [64, 0, 31], [64, 1, 36], [64, 2, 34], [65, 0, 2], [65, 1, 4], [65, 2, 6], [66, 0, 19], [66, 1, 13], [66, 2, 12], [67, 0, 3], [67, 1, 4], [67, 2, 3], [68, 0, 3], [68, 1, 5], [68, 2, 7], [69, 0, 1], [69, 1, 6], [69, 2, 6], [70, 0, 282], [70, 1, 290], [70, 2, 283], [71, 0, 290], [71, 1, 300], [71, 2, 283], [72, 0, 310], [72, 1, 299], [72, 2, 284], [73, 0, 314], [73, 1, 298], [73, 2, 282], [74, 0, 295], [74, 1, 297], [74, 2, 294], [75, 0, 113], [75, 1, 123], [75, 2, 101], [76, 0, 292], [76, 1, 295], [76, 2, 325], [77, 0, 298], [77, 1, 328], [77, 2, 280], [78, 0, 290], [78, 1, 318], [78, 2, 307], [79, 0, 301], [79, 1, 310], [79, 2, 303], [80, 0, 298], [80, 1, 323], [80, 2, 294], [81, 0, 323], [81, 1, 297], [81, 2, 298], [82, 0, 286], [82, 1, 332], [82, 2, 300], [83, 0, 316], [83, 1, 286], [83, 2, 317], [84, 0, 313], [84, 1, 290], [84, 2, 304], [85, 0, 280], [85, 1, 305], [85, 2, 319]], "generated_by": null, "matrix_type": "sparse", "shape": [86, 3], "format_url": "http://biom-format.org", "date": "2019-02-13T11:14:37", "type": "OTU table", "id": null, "columns": [{"id": "01", "metadata": null}, {"id": "02", "metadata": null}, {"id": "03", "metadata": null}]}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/12-tsv2biom.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/12-tsv2biom.fasta Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,172 @@\n+>Cluster_1\n+CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2\n+GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_3\n+GAAGGATCATTACTGAAGAACTATATCGAGTTTTTTTATACCCTTTTGTTTACCTACCCTATTGCTTCCACTGGACAGGTTTCACCTTGTGTGGGTCCTCTCTGGCTTGTGTGAAAAGCACCTGCCAGACAGACGTTGCTGGTGGGAAGAACTATTTACTAAAACTTGATTTTTAAAAAAAAATACAATGTCTGAATAATTTCCTTTAATGAAATAAAACTTTCAACAACGGATCTCTAGGCTCTTGCATCGATGAAGAACGCAGT\n+>Cluster_4\n+GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_5\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_6\n+CTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGCTGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGAGGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATTTTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTAAATGATAAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_7\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_8\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_9\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_10\n+ATCCGGAGGGGAGATGAAGAGGGAATTTAGTAGGAACCGTAGGCATTGTCGCTGGCCTTTGGAAACAAACGCATGTGCACATCTCGAAAGTCTTACTTAGTACCTCGATCTCTTTCCTTTTGTGAACCCCTTTTCTTACACCTGTGCACCCATTGTAGGTCCCGCGAGGGATCCTATGTCTCTATCTACTCTTAAATGTATGGCCTAGAATGTCTTGAAACGTCGTCCGGCCTGGCTAACGCTTGGTTGGCGGCAGTAAAGAACCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_11\n+TCGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGGAGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_13\n+TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n+>Cluster_12\n+ATGAATATCTATGGCGGTGGTTGTAGCTGGCTTCTAGGAGCATATGTGCACACCCGTCATTCATATCTTTCCACCTGTGAACCTAATGTAGATCTGGATAACTCTCGCTTTCTGAGCGGAAACAGGGATTGCTGTGTCGCAAGGCCAGCTCTCTTTGAATTTCCAGGTCTATGTCCTTTACACACCCCAATTGAATGATGAAGAATGTAGTCAATGGGCTCTAAGCCCATAAAACACAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_14\n+AACTTCTTTGGAGATAGTACTGTTGCTGGCCTTGTAATGAGGTATGTGCACGTTCTATTGCCAATTTATTCATCCACCTGTGCACT'..b'TATTCTCTCTCACACCTGTGCACCCATCGTAGGTCCTCGGAAGAGGATCTATGTTTTCTACATCACACCCATCGCATGTCCATAGAATGTATTACGAACGTCGACCGGCCCCTCTTCGTGGGTCGGACGGTGGGCGAAAGGAATTAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2010_FROGS_combined\n+TCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTTCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACTTATCGATAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_1253_FROGS_combined\n+TCGTACAACATGTGTGAGGCGTGCGAGGGCTGTCGCTGACTTCAAAGTCGTGCACGCCGGAGCGCGTCCTATCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGCGAGGGCTGTCGCTGACTTCAAAGTGCGTGCACGCCGGAGCGCGTCCTCTCACATTAAAATCCATCTCACCCTTTTGTGCACCACCGCGTGGGCACCCTTTTGGGATCGAATCGATCCAGGAGGGGGGCTTGCGTTTTCACACAAACCCCTTTTAAAAAGTGTAGAATGACCCCACTTTGCGATGACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2726_FROGS_combined\n+TTGAAATAAACCTGATGAGTTGCTGCTGGCTCTCTTGGGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTAGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTTGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGCTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2042_FROGS_combined\n+TTGAAATAAACCTGATGAGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACACTCGTCATCTTTGTATATTCACCTGTGCATCTTTTGTAGACCCTTGGGTATCTCTCTGATTGCTTTTAGCACTCAGGATTGAGGATTGACTTCCTGTCTCTTCTTACATTTCCAGGTCTATGTTTCTTAATATACCCTAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAATCTATACAACTTTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATGTGCACACTCGTCATCTTTGTATATTCACCTGTGGCATCTTTTGTAGACCCTTGGGTATCTCTCTGATTGCTTTTAGCACTCAGGATTGAGGATTGACTTCCTGTCTCTTCTTACATTTCCAGGTCTATGTTTCTTAATATACCCTAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_2099_FROGS_combined\n+TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTTCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGCAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n+>Cluster_4257_FROGS_combined\n+TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTCTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/12-tsv2biom.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/12-tsv2biom.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,13 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/tsv_to_biom.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/tsv_to_biom.py --input-tsv res/10-biom2tsv.tsv --input-multi-affi res/10-biom2tsv-affiliation_multihit.tsv --output-biom res/12-tsv2biom.biom --output-fasta res/12-tsv2biom.fasta --log-file res/12-tsv2biom.log + +######################################################################################################## +# Converts a TSV file in Biom. (tsv2biom.py version : 1.1.0) +Command: + tsv2biom.py --input-file res/10-biom2tsv.tsv --input-multihits res/10-biom2tsv-affiliation_multihit.tsv --output-file res/12-tsv2biom.biom --output-fasta res/12-tsv2biom.fasta --fields comment blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length seed_id seed_sequence observation_name --samples-names 01 02 03 + +Execution: + start: 13 Feb 2019 11:14:37 + end: 13 Feb 2019 11:14:37 + |
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| diff -r 000000000000 -r 59bc96331073 test-data/references/13-tree-mafft.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/13-tree-mafft.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,33 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/tree.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/tree.py --nb-cpus 4 --input-otu res/04-filters.fasta --biomfile res/06-affiliation.biom --out-tree res/13-tree-mafft.nwk --html res/13-tree-mafft.html --log-file res/13-tree-mafft.log + +Number of input OTUs sequences: 86 + +######################################################################################################## +# Mafft multiple alignment. (mafft version : v7.407) +Command: + mafft --maxiterate 1000 --globalpair --thread 4 res/04-filters.fasta > res/1550052877.76_4235_mafft_aligned.fasta 2> res/1550052877.76_4235_mafft.stderr + +Execution: + start: 13 Feb 2019 11:14:37 + end: 13 Feb 2019 11:15:14 + +######################################################################################################## +# reconstruction a phylogenetic tree (FastTree version : 2.1.10) +Command: + FastTree -nt -gtr res/1550052877.76_4235_mafft_aligned.fasta > res/1550052877.76_4235_fasttree.nwk 2> res/1550052877.76_4235_fasttree.stderr + +Execution: + start: 13 Feb 2019 11:15:14 + end: 13 Feb 2019 11:15:19 + +######################################################################################################## +# root newick tree with phangorn R package midpoint function. (root_tree.R version : 1.0.0) +Command: + root_tree.R res/1550052877.76_4235_fasttree.nwk res/13-tree-mafft.nwk + +Execution: + start: 13 Feb 2019 11:15:23 + end: 13 Feb 2019 11:15:25 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/14-phylo_import.Rdata |
| b |
| Binary file test-data/references/14-phylo_import.Rdata has changed |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/14-phylo_import.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/14-phylo_import.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,30 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_import_data.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_import_data.py --biomfile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/chaillou.biom --samplefile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/sample_metadata.tsv --treefile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/tree.nwk --rdata res/14-phylo_import.Rdata --html res/14-phylo_import.html --log-file res/14-phylo_import.log + +######################################################################################################## +# Run r_import_data.Rmd (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_import_data.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.html', params=list(biomfile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/chaillou.biom', samplefile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/sample_metadata.tsv', treefile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/tree.nwk', normalization=FALSE, outputRdata='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', ranks='Kingdom Phylum Class Order Family Genus Species', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620116.55_23941_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:02:03 + end: 08 Feb 2019 11:02:13 + +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_import_data.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_import_data.py --biomfile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/chaillou.biom --samplefile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/sample_metadata.tsv --treefile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/tree.nwk --rdata res/14-phylo_import.Rdata --html res/14-phylo_import.html --log-file res/14-phylo_import.log + +######################################################################################################## +# Run r_import_data.Rmd (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_import_data.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.html', params=list(biomfile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/chaillou.biom', samplefile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/sample_metadata.tsv', treefile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/tree.nwk', normalization=FALSE, outputRdata='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', ranks='Kingdom Phylum Class Order Family Genus Species', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623006.35_25404_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:50:09 + end: 08 Feb 2019 11:50:16 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/15-phylo_composition.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/15-phylo_composition.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,30 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_composition.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_composition.py --varExp EnvType --taxaRank1 Kingdom --taxaSet1 Bacteria --taxaRank2 Phylum --numberOfTaxa 9 --rdata res/14-phylo_import.Rdata --html res/15-phylo_composition.html --log-file res/15-phylo_composition.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_composition.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/15-phylo_composition.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',taxaRank1='Kingdom',taxaSet1='Bacteria',taxaRank2='Phylum',numberOfTaxa=9, libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620133.12_23979_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:02:16 + end: 08 Feb 2019 11:02:29 + +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_composition.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_composition.py --varExp EnvType --taxaRank1 Kingdom --taxaSet1 Bacteria --taxaRank2 Phylum --numberOfTaxa 9 --rdata res/14-phylo_import.Rdata --html res/15-phylo_composition.html --log-file res/15-phylo_composition.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_composition.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/15-phylo_composition.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',taxaRank1='Kingdom',taxaSet1='Bacteria',taxaRank2='Phylum',numberOfTaxa=9, libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623016.41_25441_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:50:19 + end: 08 Feb 2019 11:50:31 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/16-phylo_alpha_div.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/16-phylo_alpha_div.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,30 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_alpha_diversity.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_alpha_diversity.py --varExp EnvType --rdata res/14-phylo_import.Rdata --alpha-measures Observed Chao1 Shannon --alpha-out res/16-phylo_alpha_div.tsv --html res/16-phylo_alpha_div.html --log-file res/16-phylo_alpha_div.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_alpha_diversity.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/16-phylo_alpha_div.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', measures='Observed,Chao1,Shannon', varExp='EnvType',fileAlpha='/home/maria/workspace/git/FROGS/FROGS_master/test/res/16-phylo_alpha_div.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620149.26_24026_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:02:32 + end: 08 Feb 2019 11:02:57 + +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_alpha_diversity.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_alpha_diversity.py --varExp EnvType --rdata res/14-phylo_import.Rdata --alpha-measures Observed Chao1 Shannon --alpha-out res/16-phylo_alpha_div.tsv --html res/16-phylo_alpha_div.html --log-file res/16-phylo_alpha_div.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_alpha_diversity.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/16-phylo_alpha_div.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', measures='Observed,Chao1,Shannon', varExp='EnvType',fileAlpha='/home/maria/workspace/git/FROGS/FROGS_master/test/res/16-phylo_alpha_div.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623031.57_25477_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:50:35 + end: 08 Feb 2019 11:50:58 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/16-phylo_alpha_div.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/16-phylo_alpha_div.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,65 @@ + Observed Chao1 se.chao1 Shannon +DLT0.LOT08 210 210 0 2.01603767724795 +DLT0.LOT05 221 254.785714285714 13.3895041926063 1.79800937304124 +DLT0.LOT03 226 226 0 3.45528429286049 +DLT0.LOT07 221 221 0 2.98216090690738 +DLT0.LOT06 278 278 0 3.20952140178085 +DLT0.LOT01 281 281 0 4.10685205650844 +DLT0.LOT04 247 247 0 2.47304361554073 +DLT0.LOT10 236 236 0 3.55173827807196 +MVT0.LOT05 158 158 0 2.34503849832531 +MVT0.LOT01 128 128 0 2.28541492757583 +MVT0.LOT06 157 157 0 3.92479836105885 +MVT0.LOT07 157 157 0 3.75898496293381 +MVT0.LOT03 160 160 0 3.34027078029461 +MVT0.LOT09 122 122 0 3.95221379962838 +MVT0.LOT08 124 124 0 2.30012425431142 +MVT0.LOT10 95 95 0 1.25959560361526 +BHT0.LOT01 103 103 0 2.53131370126125 +BHT0.LOT07 144 144 0 3.15166550279444 +BHT0.LOT06 155 155 0 2.92765820448176 +BHT0.LOT03 153 153 0 2.95001637842565 +BHT0.LOT10 159 159 0 2.7790079222459 +BHT0.LOT05 183 183 0 2.53671816912042 +BHT0.LOT04 209 209 0 3.47635995384084 +BHT0.LOT08 178 178 0 3.09192502544742 +VHT0.LOT02 132 132 0 1.4154609826759 +VHT0.LOT10 134 134 0 1.87555746873306 +VHT0.LOT03 206 206 0 3.51078572003616 +VHT0.LOT01 235 235 0 2.67402666784541 +VHT0.LOT08 157 157 0 3.31989163716182 +VHT0.LOT06 182 182 0 1.88583439498533 +VHT0.LOT07 156 156 0 1.41904291231118 +VHT0.LOT04 193 193 0 2.64373071960283 +SFT0.LOT08 111 165.473684210526 21.5900554349517 1.13874307530455 +SFT0.LOT07 110 110 0 2.96744303252776 +SFT0.LOT06 126 126 0 2.49355558700118 +SFT0.LOT03 119 119 0 2.92356922933234 +SFT0.LOT02 104 104 0 2.47818417340797 +SFT0.LOT05 75 210.125 60.9771168818602 1.33504649810823 +SFT0.LOT04 70 70 0 1.4778600596069 +SFT0.LOT01 117 117 0 1.98786858579725 +FST0.LOT07 150 150 0 2.99751683958306 +FST0.LOT08 152 152 0 3.4863921810005 +FST0.LOT05 156 156 0 3.37246744717753 +FST0.LOT06 165 165 0 3.40841441699795 +FST0.LOT01 149 149 0 2.43179269800015 +FST0.LOT03 168 168 0 2.92905427377967 +FST0.LOT10 186 186 0 3.03616027233611 +FST0.LOT02 179 179 0 3.18742279060019 +FCT0.LOT06 140 140 0 3.08227430433618 +FCT0.LOT10 172 172 0 3.89564247946871 +FCT0.LOT05 166 166 0 1.99860208269453 +FCT0.LOT03 197 197 0 2.70414675332528 +FCT0.LOT08 218 218 0 3.88853679266027 +FCT0.LOT02 195 195 0 2.55307056135657 +FCT0.LOT07 199 199 0 3.50534515553006 +FCT0.LOT01 200 200 0 3.88749477420522 +CDT0.LOT10 125 125 0 1.04948460066206 +CDT0.LOT08 175 175 0 3.25853898017873 +CDT0.LOT05 264 264 0 4.2074225334087 +CDT0.LOT04 269 269 0 4.45683686305649 +CDT0.LOT06 119 119 0 1.23721179294724 +CDT0.LOT09 177 177 0 1.91666097264414 +CDT0.LOT07 161 161 0 3.09013417675057 +CDT0.LOT02 174 174 0 2.42745280040353 |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/17-phylo_beta_div.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/17-phylo_beta_div.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,30 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_beta_diversity.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_beta_diversity.py --varExp EnvType --distance-methods cc,unifrac --rdata res/14-phylo_import.Rdata --matrix-outdir res --html res/17-phylo_beta_div.html --log-file res/17-phylo_beta_div.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_beta_diversity.Rmd',knit_root_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/17-phylo_beta_div.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType', methods='cc,unifrac', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620177.61_24078_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:03:01 + end: 08 Feb 2019 11:03:10 + +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_beta_diversity.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_beta_diversity.py --varExp EnvType --distance-methods cc,unifrac --rdata res/14-phylo_import.Rdata --matrix-outdir res --html res/17-phylo_beta_div.html --log-file res/17-phylo_beta_div.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_beta_diversity.Rmd',knit_root_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/17-phylo_beta_div.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType', methods='cc,unifrac', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623058.33_25515_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:51:01 + end: 08 Feb 2019 11:51:09 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/18-phylo_structure.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/18-phylo_structure.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,30 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py --varExp EnvType --ordination-method MDS --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/18-phylo_structure.html --log-file res/18-phylo_structure.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_structure.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/18-phylo_structure.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620190.28_24114_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:03:14 + end: 08 Feb 2019 11:03:27 + +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py --varExp EnvType --ordination-method MDS --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/18-phylo_structure.html --log-file res/18-phylo_structure.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_structure.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/18-phylo_structure.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623069.52_25554_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:51:12 + end: 08 Feb 2019 11:51:24 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/19-phylo_clustering.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/19-phylo_clustering.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,30 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_clustering.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_clustering.py --varExp EnvType --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/19-phylo_clutering.html --log-file res/19-phylo_clustering.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_clustering.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/19-phylo_clutering.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620207.16_24151_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:03:30 + end: 08 Feb 2019 11:03:37 + +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_clustering.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_clustering.py --varExp EnvType --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/19-phylo_clutering.html --log-file res/19-phylo_clustering.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_clustering.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/19-phylo_clutering.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623084.42_25593_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:51:27 + end: 08 Feb 2019 11:51:34 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/20-phylo_manova.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/20-phylo_manova.log Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,30 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_manova.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_manova.py --varExp "EnvType" --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/20-phylo_manova.html --log-file res/20-phylo_manova.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_manova.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/20-phylo_manova.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620217.55_24189_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:03:41 + end: 08 Feb 2019 11:03:47 + +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_manova.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_manova.py --varExp "EnvType" --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/20-phylo_manova.html --log-file res/20-phylo_manova.log + +######################################################################################################## +# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)" +[1] "Rmarkdown version: 1.10" +[1] "Phyloseq version: 1.19.1") +Command: + Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_manova.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/20-phylo_manova.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623094.2_25631_rmarkdown.stderr + +Execution: + start: 08 Feb 2019 11:51:37 + end: 08 Feb 2019 11:51:43 + |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/Unifrac.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/Unifrac.tsv Thu Feb 28 10:14:49 2019 -0500 |
| b |
| b'@@ -0,0 +1,65 @@\n+\tDLT0.LOT08\tDLT0.LOT05\tDLT0.LOT03\tDLT0.LOT07\tDLT0.LOT06\tDLT0.LOT01\tDLT0.LOT04\tDLT0.LOT10\tMVT0.LOT05\tMVT0.LOT01\tMVT0.LOT06\tMVT0.LOT07\tMVT0.LOT03\tMVT0.LOT09\tMVT0.LOT08\tMVT0.LOT10\tBHT0.LOT01\tBHT0.LOT07\tBHT0.LOT06\tBHT0.LOT03\tBHT0.LOT10\tBHT0.LOT05\tBHT0.LOT04\tBHT0.LOT08\tVHT0.LOT02\tVHT0.LOT10\tVHT0.LOT03\tVHT0.LOT01\tVHT0.LOT08\tVHT0.LOT06\tVHT0.LOT07\tVHT0.LOT04\tSFT0.LOT08\tSFT0.LOT07\tSFT0.LOT06\tSFT0.LOT03\tSFT0.LOT02\tSFT0.LOT05\tSFT0.LOT04\tSFT0.LOT01\tFST0.LOT07\tFST0.LOT08\tFST0.LOT05\tFST0.LOT06\tFST0.LOT01\tFST0.LOT03\tFST0.LOT10\tFST0.LOT02\tFCT0.LOT06\tFCT0.LOT10\tFCT0.LOT05\tFCT0.LOT03\tFCT0.LOT08\tFCT0.LOT02\tFCT0.LOT07\tFCT0.LOT01\tCDT0.LOT10\tCDT0.LOT08\tCDT0.LOT05\tCDT0.LOT04\tCDT0.LOT06\tCDT0.LOT09\tCDT0.LOT07\tCDT0.LOT02\n+DLT0.LOT08\t0\t0.392719389374763\t0.294382689116989\t0.390894424113643\t0.328770053910381\t0.389411250802876\t0.346311420062406\t0.389241305604783\t0.558647350042396\t0.634069916291667\t0.586977876499085\t0.618364439168374\t0.59310690982098\t0.644425105557425\t0.633386627311114\t0.676093271776652\t0.668166275142653\t0.647255138049382\t0.634194437155602\t0.629580000445943\t0.576755603792125\t0.588626884110114\t0.567337706288072\t0.627737130863146\t0.630979925473805\t0.662585829091919\t0.548077006064955\t0.565292617093312\t0.583061634989672\t0.559960446409113\t0.561005582218959\t0.555410973214134\t0.686198206609958\t0.704398980872343\t0.675272727535421\t0.711657734556618\t0.715799775906816\t0.768785445356757\t0.785667248244791\t0.696459130925707\t0.606145374094578\t0.651568775909291\t0.636874887259531\t0.65198384887721\t0.648424320754247\t0.572507853619064\t0.533534738606473\t0.612417013174867\t0.6538120765306\t0.591881312389585\t0.619093998659405\t0.585895717589353\t0.548200617493159\t0.594002797632857\t0.586013673904125\t0.585980145595343\t0.651109623648418\t0.62720674623346\t0.532414786060701\t0.547377296717564\t0.695399519089384\t0.602389412681498\t0.651285257071645\t0.625692860559332\n+DLT0.LOT05\t0.392719389374763\t0\t0.334665743823981\t0.352189924174674\t0.342174777989704\t0.389749555645828\t0.290240347963101\t0.390007860403765\t0.533242142441534\t0.598457283793849\t0.534095626389918\t0.595630244132359\t0.563155315513785\t0.627301946703866\t0.62362079028169\t0.676679178026565\t0.661442446324936\t0.607174222014807\t0.627098405326444\t0.611311880024972\t0.595770697120776\t0.579339730768954\t0.553223124743228\t0.610516542648508\t0.666088798070038\t0.657587079833307\t0.576069019426189\t0.556446826887928\t0.600775747996288\t0.5911490693311\t0.616992581263469\t0.601616192130504\t0.651100765662097\t0.681452439239435\t0.635746166689655\t0.656251161738522\t0.660748149236051\t0.718117436370543\t0.745868841494258\t0.651811755169484\t0.583079458698659\t0.611335962879801\t0.60471232308416\t0.626317689189847\t0.620601501298686\t0.555908156452842\t0.533249165381552\t0.574427223549588\t0.609466674526089\t0.554013286087225\t0.591520342983099\t0.578096390189169\t0.520647115926058\t0.532256954612006\t0.559759285330547\t0.567759482939216\t0.594543966139689\t0.566565902699841\t0.553655484607033\t0.540051048491254\t0.650961029981557\t0.575509994600553\t0.624808022531917\t0.595884187417361\n+DLT0.LOT03\t0.294382689116989\t0.334665743823981\t0\t0.372786534310374\t0.327187118252722\t0.359513238833913\t0.339907385955891\t0.38492662266766\t0.552498990377251\t0.589114989880665\t0.542041154505155\t0.59613025240974\t0.552461963400675\t0.617844578077283\t0.604774998121854\t0.664017875696736\t0.648793735381351\t0.622368182568259\t0.620604700459984\t0.591910414837232\t0.566744912701015\t0.561672474315041\t0.556623781014959\t0.59265696724107\t0.632841968867748\t0.66421462312413\t0.569031394968335\t0.538210280024464\t0.583964660155039\t0.555481448289844\t0.59213139931072\t0.579064617903163\t0.677073030113301\t0.679856615483388\t0.659776066311386\t0.671077096490443\t0.673953708382158\t0.753757865966224\t0.744905299647077\t0.669777464567699\t0.594953408905372\t0.594885764729724\t0.591809685788661\t0.623526170876335\t0.633556125967904\t0.563161599049313\t0.558391672795279\t0.58499884389222\t0.658968009415742\t0.598607385198043\t0.618132787151034\t0.591293863217907\t0.548709240291208\t0.589473963654829\t0.562723847684429\t0.5904743'..b'\t0.722926571406701\t0.688716587074794\t0.685695663618906\t0.662023385683372\t0.67171887301095\t0.661637888388034\t0.675884693159838\t0.718056925126289\t0.654689380709201\t0.68223217716672\t0.653431565041232\t0.668030013340577\t0.685721750598227\t0.664857249588266\t0.689007839280897\t0.657620741452954\t0.653159907372082\t0.6911709832662\t0.683048323863822\t0.62760665087889\t0.668064647721933\t0.657719412509422\t0.65224952356914\t0.668623077011986\t0.628907107332197\t0.39806333112609\t0.418710436434128\t0.493956484929211\t0.481853960906529\t0\t0.366581982149745\t0.33459366247948\t0.385617526833289\n+CDT0.LOT09\t0.602389412681498\t0.575509994600553\t0.603788346166801\t0.591747048678134\t0.590911650223996\t0.591128709519011\t0.596211588106372\t0.57104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|
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/normalisation.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/normalisation.log Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,34 @@ +## Application +Software: normalisation.py (version: 3.1) +Command: ./../app/normalisation.py -n 100 -f res/04-filters.fasta -i res/06-affiliation.biom -s res/normalisation_report.html -l res/normalisation.log + +Application start: 13 Feb 2019 11:24:00 + +#Normalisation calculation + start: 13 Feb 2019 11:24:00 +######################################################################################################## +# Random sampling in each sample. (biomTools.py version : 0.10.1) +Command: + biomTools.py sampling --nb-sampled 100 --input-file res/06-affiliation.biom --output-file abundance.biom + +Execution: + start: 13 Feb 2019 11:24:00 + end: 13 Feb 2019 11:24:00 + + end: 13 Feb 2019 11:24:00 + +######################################################################################################## +# Update fasta file based on sequence in biom file (biomFastaUpdate.py version : 1.0.1) +Command: + biomFastaUpdate.py --input-biom abundance.biom --input-fasta res/04-filters.fasta --output-file sequence.fasta --log 1550053440.26_4588_tmp_fasta_update.log + +Execution: + start: 13 Feb 2019 11:24:00 + end: 13 Feb 2019 11:24:00 + + +#Summarise + start: 13 Feb 2019 11:24:00 + end: 13 Feb 2019 11:24:00 + +Application end: 13 Feb 2019 11:24:00 |
| b |
| diff -r 000000000000 -r 59bc96331073 test-data/references/normalisation_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/normalisation_report.html Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| b'@@ -0,0 +1,434 @@\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<html>\n+\t<head>\n+\t\t<title>FROGS Abundance Normalisation</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="1.0.1">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\tul.nav-tabs {\n+\t\t\t\tmargin-bottom: 30px;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover:enabled{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t\tcursor:pointer !important;\n+\t\t\t}\n+\t\t\t\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t\n+\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n+\t\t\t.container {\n+\t\t\t\tposition: relative;\n+\t\t\t\tpadding-left: 35px;\n+\t\t\t\tmargin-bottom: 12px;\n+\t\t\t\tcursor: pointer;\n+\t\t\t\t-webkit-user-select: none;\n+\t\t\t\t-moz-user-select: none;\n+\t\t\t\t-ms-user-select: none;\n+\t\t\t\tuser-select: none;\n+\t\t\t}\n+\n+\t\t\t/* Hide the browser\'s default checkbox */\n+\t\t\t.container input {\n+\t\t\t\tposition: absolute;\n+\t\t\t\topacity: 0;\n+\t\t\t\tcursor: pointer;\n+\t\t\t}\n+\n+\t\t\t/* Create a custom checkbox */\n+\t\t\t.checkmark {\n+\t\t\t\tposition: absolute;\n+\t\t\t\ttop: 0;\n+\t\t\t\tleft: 0;\n+\t\t\t\theight: 25px;\n+\t\t\t\twidth: 25px;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-radius: 5px;\n+\t\t\t\topacity:0.65;\n+\t\t\t}\n+\n+\t\t\t/* On mouse-over, add a grey background color */\n+\t\t\t.container:hover input ~ .checkmark {\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\n+\t\t\t/* When the checkbox is checked, add a blue background */\n+\t\t\t.container input:checked ~ .checkmark {\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\topacity:1;\n+\t\t\t}\n+\n+\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n+\t\t\t.checkmark:after {\n+\t\t\t\tcontent: "";\n+\t\t\t\tposition: absolute;\n+\t\t\t\tdisplay: none;\n+\t\t\t}\n+\n+\t\t\t/* Show the checkmark when checked */\n+\t\t\t.container input:checked ~ .checkmark:after {\n+\t\t\t\tdisplay: block;\n+\t\t\t}\n+\n+\t\t\t/* Style the checkmark/indicator */\n+\t\t\t.container .checkmark:after {\n+\t\t\t\tleft: 9px;\n+\t\t\t\ttop: 5px;\n+\t\t\t\twidth: 5px;\n+\t\t\t\theight: 10px;\n+\t\t\t\tborder: solid white;\n+\t\t\t\tborder-width: 0 3px 3px 0;\n+\t\t\t\t-webkit-transform:'..b'riped table-bordered">\\n\' + table_header + table_body + "</table>\\n" ;\n+\t\t\t}\n+\t\t\t\n+\t\t\tvar histogram_param = function( pTitle, pYTitle, pCategories, pSeries, unity ) {\n+\t\t\t\t\n+\t\t\t\t\n+\t\t\t\tvar param = {\n+\t\t\t\t\tchart: {\n+\t\t\t\t\t\ttype: \'column\'\n+\t\t\t\t\t},\n+\t\t\t\t\ttitle: {\n+\t\t\t\t\t\ttext: pTitle\n+\t\t\t\t\t},\n+\t\t\t\t\texporting:{buttons: {contextButton: { symbol: \'download\' }}},\n+\t\t\t\t\txAxis: {\n+\t\t\t\t\t\tcategories: pCategories,\n+\t\t\t\t\t\tcrosshair: true\n+\t\t\t\t\t},\n+\t\t\t\t\tyAxis: {\n+\t\t\t\t\t\tmin: 0,\n+\t\t\t\t\t\ttitle: {\n+\t\t\t\t\t\t\ttext: pYTitle\n+\t\t\t\t\t\t}\n+\t\t\t\t\t},\n+\t\t\t\t\ttooltip: {\n+\t\t\t\t\t\theaderFormat: \'<span style="font-size:10px">{point.key}</span><table>\',\n+\t\t\t\t\t\tpointFormat: \'<tr><td style="color:{series.color};padding:0">{series.name}: </td>\' +\n+\t\t\t\t\t\t\t\'<td style="padding:0"><b>{point.y} \' + unity + \'</b></td></tr>\',\n+\t\t\t\t\t\tfooterFormat: \'</table>\',\n+\t\t\t\t\t\tshared: true,\n+\t\t\t\t\t\tuseHTML: true\n+\t\t\t\t\t},\n+\t\t\t\t\tplotOptions: {\n+ column: {\n+\t\t\t\t\t\t\tstacking: \'normal\',\n+\t\t\t\t\t\t\tdataLabels: {\n+\t\t\t\t\t\t\t\tenabled: true,\n+\t\t\t\t\t\t\t\tstyle: {\n+\t\t\t\t\t\t\t\t\ttextShadow: false,\n+\t\t\t\t\t\t\t\t\tcolor: (Highcharts.theme && Highcharts.theme.textColor) || \'white\'\n+\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t},\n+ pointPadding: 0.2,\n+ borderWidth: 0\n+ }\n+ },\n+\t\t\t\t\tcredits: {\n+\t\t\t\t\t\tenabled: false\n+\t\t\t\t\t},\n+\t\t\t\t\texporting:{buttons: {contextButton: { symbol: \'download\' }}},\n+\t\t\t\t\tbuttons: {contextButton: {menuItems: [\'downloadPNG\', \'downloadSVG\']}},\n+\t\t\t\t\tseries: pSeries,\n+\t\t\t\t\tnavigation: {\n+\t\t\t\t\t\t\tbuttonOptions: {\n+\t\t\t\t\t\t\t\ttheme: {\n+\t\t\t\t\t\t\t\t\tr: 4,\n+\t\t\t\t\t\t\t\t\tfill:\'#8EADAC\',\n+\t\t\t\t\t\t\t\t\tstates: {\n+\t\t\t\t\t\t\t\t\t\thover: {\n+\t\t\t\t\t\t\t\t\t\t\tfill: \'rgb(100, 138, 137)\',\n+\t\t\t\t\t\t\t\t\t\t\tstroke:\'#8EADAC\'\n+\t\t\t\t\t\t\t\t\t\t},\n+\t\t\t\t\t\t\t\t\t\tselect: {\n+\t\t\t\t\t\t\t\t\t\t\tstroke: \'#8EADAC\',\n+\t\t\t\t\t\t\t\t\t\t\tfill: \'rgb(100, 138, 137)\',\n+\t\t\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t}\n+\t\t\t\t};\n+\t\t\t\t\n+\t\t\t\treturn param ;\n+\t\t\t}\n+\t\t\t\n+\t\t\t$(function() {\n+\t\t\t\tvar categories = ["Nb OTU before normalisation", "Nb OTU after normalisation"] ;\n+\t\t\t\tvar histogram_series = [86, 53] ;\n+\t\t\t\tvar series_by_sample = [{"data": [86, 53], "name": "01"}, {"data": [86, 53], "name": "02"}, {"data": [86, 53], "name": "03"}] ;\n+\t\t\t\t\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Display summary\n+\t\t\t\tvar global_series = [{ name: \'All samples\', data: histogram_series }];\n+\t\t\t\t$(\'#filter-summary\').highcharts( histogram_param(\'Composition summary\', \'Nb OTUs\', categories, global_series, \'otu\') );\n+\t\t\t\t\n+\t\t\t\t// Display data by sample\n+\t\t\t\tvar table_categories = categories.slice() ;\n+\t\t\t\ttable_categories.unshift( "Sample" );\n+\t\t\t\tvar table_series = new Array();\n+\t\t\t\tfor( var spl_idx = 0 ; spl_idx < series_by_sample.length ; spl_idx++ ){\n+\t\t\t\t\tvar nb_by_step = series_by_sample[spl_idx][\'data\'].slice() ;\n+\t\t\t\t\tnb_by_step.unshift( series_by_sample[spl_idx][\'name\'] );\n+\t\t\t\t\ttable_series.push( nb_by_step );\n+\t\t\t\t};\n+\t\t\t\t$(\'#filter-log\').append( table("Composition by sample", table_categories, table_series) );\n+\t\t\t\t$(\'#filter-log table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#filter-log table\').DataTable({\n+\t\t\t\t\tdom: \t"<\'#details-csv-export\'><\'row\'<\'col-sm-5\'l><\'col-sm-7\'f>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-12\'tr>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-5\'i><\'col-sm-7\'p>>"\n+\t\t\t\t});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n+\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n+\t\t\t\t$(\'#details-csv-export\').datatableExport({\n+\t\t\t\t\t\'table_id\': "details-table"\n+\t\t\t\t});\n+\t\t\t});\n+\t\t</script>\n+\t</head>\n+\t<body>\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t<div id="content" class="hidden">\n+\t\t\t<div id="filter-summary"></div>\n+\t\t\t<div id="filter-log"></div>\n+\t\t</div>\n+\t</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 59bc96331073 tool-data/HVL_db.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/HVL_db.loc.sample Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,31 @@ +# Copyright (C) 2014 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_affiliations_postprocess to solve +#inclusive amplicon sequence by selecting the smallest reference among multihit +#You will need to create or download exact amplicon sequence reference fasta file +#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL_reference +#Finally you will need to create HVL_db.loc file similar to this one.The HVL_db.loc file has this format (longer white space characters are +#TAB characters): +# +#<unique_database_name> <name> <file_path> +# +#First column will be the visible name in galaxy. +#So, for example, if you have UNITE 7.1 ITS1 (only!) stored +#in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta +#then the HVL_db.loc entry would look like this: +# +#UNITE_7.1_ITS1 UNITE 7.1 ITS1 <FROGS-wrappers>/test-data/databases/HVL_db_data/Unite_extract_ITS1.fasta |
| b |
| diff -r 000000000000 -r 59bc96331073 tool-data/frogs_db.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/frogs_db.loc.sample Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,52 @@ +# Copyright (C) 2014 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_affiliations_OTU to use taxonomy database for +#taxonomy affiliation. You will need to create or download Blast+ index and train your database +#for RDP classifier these data files. +#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation +#Finally you will need to create frogs_db.loc file similar to this one. +#The frogs_db.loc file has this format (longer white space characters are +#TAB characters): +# +#<unique_database_name> <printed_database_name> <file_path> +# +#Second column will be the visible name in galaxy. +#So, for example, if you had 16S silva 128 indexed stored in +#/galaxy_databanks/16S/silva_128/ +#then the frogs_db.loc entry would look like this: +# +#silva_128_16S silva 128 16S /galaxy_databanks/16S/silva_128/silva_128_16S.fasta +# +#and your /galaxy_databanks/16S/silva_128/ directory +#would contain index files: +# +#-rw-r--r-- 1 mbernard FROGS 8097966 5 déc. 16:56 bergeyTrainingTree.xml +#-rw-r--r-- 1 mbernard FROGS 1572981589 5 déc. 16:56 genus_wordConditionalProbList.txt +#-rw-r--r-- 1 mbernard FROGS 1654 5 déc. 16:56 LICENCE.txt +#-rw-r--r-- 1 mbernard FROGS 1072228 5 déc. 16:56 logWordPrior.txt +#-rw-r--r-- 1 mbernard FROGS 940834335 5 déc. 16:56 silva_128_16S.fasta +#-rw-r--r-- 1 mbernard FROGS 152606489 5 déc. 16:56 silva_128_16S.fasta.nhr +#-rw-r--r-- 1 mbernard FROGS 6918588 5 déc. 16:56 silva_128_16S.fasta.nin +#-rw-r--r-- 1 mbernard FROGS 205320030 5 déc. 16:56 silva_128_16S.fasta.nsq +#-rw-r--r-- 1 mbernard FROGS 281 5 déc. 16:56 silva_128_16S.fasta.properties +#-rw-r--r-- 1 mbernard FROGS 3420464 5 déc. 16:56 silva_128_16S.tax +#-rw-r--r-- 1 mbernard FROGS 964048 5 déc. 16:57 wordConditionalProbIndexArr.txt +# +# +#<value> <name> <file_path> +# +#ITS_test ITS1 extract <FROGS-wrappers>/test-data/databases/frogs_db_data/ITS1.rdp.fasta |
| b |
| diff -r 000000000000 -r 59bc96331073 tool-data/phiX_db.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/phiX_db.loc.sample Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,41 @@ +# Copyright (C) 2014 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_filters to identify phix contaminant. You will #need to create or download Blast+ index. +#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants +#Finally you will need to create phiX_db.loc file similar to this one.The phiX_db.loc file has this format (longer white space characters are +#TAB characters): +# +#<unique_database_name> <printed_database_name> <file_path> +# +#Second column will be the visible name in galaxy. +#So, for example, if you had phix Blast+ indexed stored in +#/galaxy_databanks/phiX/ +#then the phiX_db.loc entry would look like this: +# +#phiX phiX /galaxy_databanks/phiX/phi.fa +# +#and your /galaxy_databanks/phiX/ directory +#would contain index files: +# +#-rwxrwxr-x 1 gpascal FROGS 5535 16 sept. 2015 phi.fa +#-rw-rwxr-- 1 gpascal FROGS 132 16 sept. 2015 phi.fa.nhr +#-rw-rwxr-- 1 gpascal FROGS 88 16 sept. 2015 phi.fa.nin +#-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq +# +#<value> <name> <file_path> +# +#phiX phiX <FROGS-wrappers>/test-data/databases/phiX_db_data/phi.fa |
| b |
| diff -r 000000000000 -r 59bc96331073 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,15 @@ +<tables> + <!-- Location of frogs database files --> + <table name="frogs_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/tool-data/frogs_db.loc" /> + </table> + <table name="HVL_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/tool-data/HVL_db.loc" /> + </table> + <table name="phiX_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/tool-data/phiX_db.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 59bc96331073 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,15 @@ +<tables> + <!-- Location of frogs database files --> + <table name="frogs_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/databases/frogs_db.loc" /> + </table> + <table name="HVL_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/databases/HVL_db.loc" /> + </table> + <table name="phiX_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/databases/phiX_db.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 59bc96331073 tree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tree.xml Thu Feb 28 10:14:49 2019 -0500 |
| b |
| @@ -0,0 +1,126 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_Tree" name="FROGS Tree" version="3.1"> + <description>Reconstruction of phylogenetic tree </description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command>tree.py + --input-otu $input_otu + --biomfile $biomfile + --nb-cpus \${GALAXY_SLOTS:-1} + --out-tree $out_tree + --html $html + </command> + <inputs> + <!-- Files --> + <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false"> + <validator type="empty_field" message="This parameter is required." /> + </param> + </inputs> + <outputs> + <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/> + <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="input_otu" value="references/04-filters.fasta"/> + <param name="biomfile" value="references/06-affiliation.biom"/> + <!--output name="out_tree" value="references/13-tree-mafft.nwk"/--> + <!--output name="html" value="references/13-tree-mafft.html"/--> + <output name="html"> + <assert_contents> + <has_text_matching expression="FROGS\sTree" /> + <has_text_matching expression="abundance_removed.*:\s0" /> + <has_text_matching expression="abundance_kept.*:\s45574" /> + <has_text_matching expression="otu_removed.*:\s0" /> + <has_text_matching expression="otu_kept.*:\s86" /> + </assert_contents> + </output> + </test> + </tests> + <help> +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Creation of a multiple alignment of OTUs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_. +And creation of a rooted phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_ and `Phangorn R package <https://cran.r-project.org/web/packages/phangorn/index.html>`_. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**OTUs fasta file**: + +The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). +Careful: FROGS Tree works only with less than 10 000 sequences! + + .. image:: static/images/frogs_images/frogs_tree_otufile.png + +**OTUs biom file**: + +The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). +This file can be obtained in particular with the FROGS pipeline. + +.. class:: h3 + +Outputs + +**Newick file** (tree.nwk): + +The phylogenetic tree in Newick format (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_). + + .. image:: static/images/frogs_images/nwk_treefile.png + +**Html file** (summary.html): + +The summary file describing which OTUs are contained or not in the phylogenetic tree. + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
| b |
| diff -r 000000000000 -r 59bc96331073 tsv_to_biom.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tsv_to_biom.xml Thu Feb 28 10:14:49 2019 -0500 |
| [ |
| @@ -0,0 +1,142 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2016 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="3.1"> + <description>Converts a TSV file in a BIOM file.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + tsv_to_biom.py + --input-tsv $tsv_file + --output-biom $biom_file + #if $multi_affi_file + --input-multi-affi $multi_affi_file + #end if + #if $extract_fasta + --output-fasta $sequence_file + #end if + </command> + <inputs> + <!-- Files --> + <param format="tabular" name="tsv_file" type="data" label="Abundance TSV File" help="Your FROGS abundance TSV file. Take care to keep original column names." optional="false"/> + <param format="tabular" name="multi_affi_file" type="data" label="Multi_hits TSV File" help="TSV file describing multi_hit blast results." optional="true" /> + <!-- Parameters --> + <param name="extract_fasta" type="boolean" label="Extract seeds in FASTA file" help="If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file." /> + </inputs> + <outputs> + <data format="biom1" name="biom_file" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" /> + <data format="fasta" name="sequence_file" label="${tool.name}: sequences.fasta" from_work_dir="seed.fasta" > + <filter>extract_fasta</filter> + </data> + </outputs> + <tests> + <test> + <param name="tsv_file" value="references/10-biom2tsv.tsv" /> + <param name="multi_affi_file" value="references/10-biom2tsv-affiliation_multihit.tsv" /> + <param name="extract_fasta" value="true"/> + <output name="biom_file" file="references/12-tsv2biom.biom" compare="sim_size" delta="0"/> + <output name="sequence_file" file="references/12-tsv2biom.fasta" /> + </test> + </tests> + <help> +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +This tool converts a TSV file in a BIOM file. + +.. class:: h3 + +Inputs + +**Abundance file**: + +The table with abundances each cluster in each sample and other details conerning the cluster (format TSV). + +Authorised column names : rdp_tax_and_bootstrap, blast_taxonomy, blast_subject, blast_perc_identity, blast_perc_query_coverage, blast_evalue, blast_aln_length, seed_id, seed_sequence, observation_name, observation_sum + +**Multiple affiliation file**: + +The file that stores the multiple blast hits. + +.. class:: h3 + +Outputs + +**Abundance file**: + + The abundance of each cluster in each sample and their metadata (format `BIOM <http://biom-format.org/>`_). + +**Sequence file [optional]**: + + By checking the "Extract seed FASTA file" option, the sequences will be extract from TSV to create a file in `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_ format. + For this option, be sure that your TSV file contains the seed_sequence column. + + +.. class:: infomark page-header h2 + +How it works + +FROGS TSV_to_BIOM detects any metadata (columns before "observation_name") and names of samples (columns after "observation_sum"). + +Then it reconstructs the BIOM abundance file : for each "observation_name" it adds the associated metadata and the count of samples. + +If blast_taxonomy is included in metadata and if blast_subject is equal to "multi-subject", it parses multi_hit TSV file. Then it extracts the list of blast_affiliations that contains the non ambiguous blast_taxonomy. + + + +.. class:: infomark page-header h2 + +Advices + +This tool is usefull if you have modified your abundance TSV file and that you want to generate rarefaction curve or sunburst with the FROGS affiliation_stat tool. + +If you modify your abundance TSV file + + * -do not modify column names + * -do not remove columns + * -take care to choose a taxonomy available in your multi_hit TSV file + * -if you delete lines of the multi_hit file, take care to not remove a complete cluster whithout removing all "multi tags" in you abundance TSV file. + * -if you want to rename a taxon level (ex : genus "Ruminiclostridium 5;" to genus "Ruminiclostridium;"), do not forget to modify also your multi_hit TSV file. + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool> |
