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Commit message:
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.3 commit fb1bb0bebef3a4f756718905088b2b50c93cb50e" |
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modified:
README.md RELEASE_NOTE.md affiliation_OTU.xml affiliation_filters.xml affiliation_postprocess.xml affiliations_stat.xml biom_to_stdBiom.xml biom_to_tsv.xml clustering.xml clusters_stat.xml demultiplex.xml deseq2_preprocess.xml deseq2_visualisation.xml itsx.xml normalisation.xml otu_filters.xml phyloseq_alpha_diversity.xml phyloseq_beta_diversity.xml phyloseq_clustering.xml phyloseq_composition.xml phyloseq_import_data.xml phyloseq_manova.xml phyloseq_structure.xml preprocess.xml remove_chimera.xml static/images/FROGS_DESeq2_html_MA_plot.png static/images/FROGS_DESeq2_html_Volcano_plot.png static/images/FROGS_DESeq2_html_pieChart.png static/images/FROGS_DESeq2_html_table.png test-data/references/01-prepro-flash.html test-data/references/01-prepro-vsearch.html test-data/references/02-clustering_denoising.biom test-data/references/02-clustering_fastidious.biom test-data/references/03-chimera.biom test-data/references/03-chimera.html test-data/references/04-filters.biom test-data/references/04-filters.html test-data/references/05-itsx.biom test-data/references/05-itsx.html test-data/references/06-affiliation.biom test-data/references/06-affiliation.html test-data/references/07-affiliation_deleted.biom test-data/references/07-affiliation_deleted.html test-data/references/07-affiliation_masked.biom test-data/references/07-affiliation_masked.html test-data/references/08-affiliation_postprocessed.biom test-data/references/09-normalisation.biom test-data/references/09-normalisation.fasta test-data/references/09-normalisation.html test-data/references/10-clustersStat.html test-data/references/11-affiliationsStat.html test-data/references/12-biom2tsv.tsv test-data/references/13-affiliation_multihit.tsv test-data/references/13-affiliation_std.biom test-data/references/14-tsv2biom.biom test-data/references/14-tsv2biom.fasta test-data/references/15-tree-mafft.html test-data/references/15-tree-mafft.nwk test-data/references/16-phylo_import.Rdata test-data/references/19-phylo_beta_div.nb.html test-data/references/21-phylo_clustering.nb.html test-data/references/23-deseq2_preprocess.Rdata test-data/references/24-deseq2_visualisation.nb.html tool-data/frogs_contaminant_db.loc.sample tree.xml tsv_to_biom.xml |
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test-data/references/16-phylo_import.nb.html test-data/references/18-phylo_alpha_div.nb.html test-data/references/22-phylo_manova.nb.html |
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conda_toolshed_frogs planemo_test.sh planemo_test/deseq2_preprocess.test.log shedSave.yml test-data/references/01-prepro-flash.log test-data/references/01-prepro-vsearch.log test-data/references/02-clustering_denoising.log test-data/references/02-clustering_fastidious.log test-data/references/03-chimera.log test-data/references/04-filters.log test-data/references/05-itsx.log test-data/references/06-affiliation.log test-data/references/06-affiliation2.biom test-data/references/06-affiliation2.html test-data/references/06-affiliation2.log test-data/references/07-affiliation_filter_delMode.log test-data/references/07-affiliation_filter_maskMode.log test-data/references/08-affiliation_postprocessed.log test-data/references/09-normalisation.log test-data/references/10-clustersStat.log test-data/references/11-affiliationsStat.log test-data/references/12-biom2tsv.log test-data/references/13-biom2stdbiom.log test-data/references/14-tsv2biom.log test-data/references/15-tree-mafft.log test-data/references/16-phylo_import.log test-data/references/17-phylo_composition.log test-data/references/18-phylo_alpha_div.log test-data/references/19-phylo_beta_div.log test-data/references/20-phylo_structure.log test-data/references/21-phylo_clustering.log test-data/references/22-phylo_manova.log test-data/references/23-deseq2_preprocess.log test-data/references/24-deseq2_visualisation.log test-data/references/demultiplex.log |
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| diff -r 834843ebe569 -r 2ed857799fd5 README.md --- a/README.md Thu Apr 08 14:30:48 2021 +0000 +++ b/README.md Fri Jun 04 14:56:24 2021 +0000 |
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| b'@@ -6,7 +6,7 @@\n \n Visit our web site : http://frogs.toulouse.inrae.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+[](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@@ -52,39 +52,39 @@\n ```\n <section id="FROGS" name="FROGS" version="">\n \n- <label id="FROGS_OTU_toolshed_3.2.2" text="OTUs reconstruction" version="" />\n+ <label id="FROGS_OTU_toolshed_3.2.3" text="OTUs reconstruction" version="" />\n \n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.2" /> \n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/3.2.2" />\n- <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/3.2.2" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_demultiplex/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clustering/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.3" /> \n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_postprocess/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_stdBiom/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_biom_to_tsv/3.2.3" />\n+ <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_tsv_to_biom/3.2.3" />\n \n- <la'..b'and composition analysis" version="3_2_3" />\n+ <tool id="FROGSSTAT_Phyloseq_Import_Data_3_2_3" />\n+ <tool id="FROGSSTAT_Phyloseq_Composition_Visualisation_3_2_3" />\n+ <tool id="FROGSSTAT_Phyloseq_Alpha_Diversity_3_2_3" />\n+ <tool id="FROGSSTAT_Phyloseq_Beta_Diversity_3_2_3" />\n+ <tool id="FROGSSTAT_Phyloseq_Sample_Clustering_3_2_3" />\n+ <tool id="FROGSSTAT_Phyloseq_Structure_Visualisation_3_2_3" />\n+ <tool id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance_3_2_3" />\n+ <label id="frogsstat_deseq_3_2_3" text="Differential abundance analysis" version="_3_2_3" />\n+ <tool id="FROGSSTAT_DESeq2_Preprocess_3_2_3" />\n+ <tool id="FROGSSTAT_DESeq2_Visualisation_3_2_3" />\n </section>\n ```\n \n@@ -299,25 +299,25 @@\n You need to uncomment `sanitize_whitelist_file` line in `<Galaxy_Dir>/config/galaxy.ini`, create the corresponding `<Galaxy_Dir>/config/sanitize_whitelist.txt` file if not already done, and add the following lines in it. You may also manage it from the Admin interface of Galaxy in the `Manage Allowlist` section.\n \n ```\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Preprocess/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.2\n-toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.2\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Preprocess/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_DESeq2_Visualisation/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Alpha_Diversity/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Beta_Diversity/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Composition_Visualisation/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Import_Data/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Sample_Clustering/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGSSTAT_Phyloseq_Structure_Visualisation/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_OTU_filters/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_Tree/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_OTU/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliation_filters/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_affiliations_stat/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_clusters_stat/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_itsx/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_normalisation/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_preprocess/3.2.3\n+toolshed.g2.bx.psu.edu/repos/frogs/frogs/FROGS_remove_chimera/3.2.3\n \n ```\n \n' |
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| diff -r 834843ebe569 -r 2ed857799fd5 RELEASE_NOTE.md --- a/RELEASE_NOTE.md Thu Apr 08 14:30:48 2021 +0000 +++ b/RELEASE_NOTE.md Fri Jun 04 14:56:24 2021 +0000 |
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| @@ -1,3 +1,13 @@ +# v3.2.3 [2021-06] + +## Modifications: + +* Affiliation_OTU : add a taxonomic rank parameter to correctly take into account taxonomy not defined on commonly used 7 ranks. +* Update R and package dependencies to version 4.0.5 (because of trouble installing DESeq2 version 1.26). +* Rename OTU FIlter and Affiliation Filter output files. + + + # v3.2.2 [2021-04] ### Tools added: |
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| diff -r 834843ebe569 -r 2ed857799fd5 affiliation_OTU.xml --- a/affiliation_OTU.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/affiliation_OTU.xml Fri Jun 04 14:56:24 2021 +0000 |
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| @@ -15,57 +15,52 @@ # 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_OTU" name="FROGS Affiliation OTU" version="3.2.2"> - <description>Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description> - <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> +<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="3.2.3"> + <description>Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description> + <requirements> + <requirement type="package" version="3.2.3">frogs</requirement> <requirement type="package" version="2.10">blast</requirement> <requirement type="package" version="6.6.0">emboss</requirement> <requirement type="package" version="2.0.3">rdptools</requirement> </requirements> - <command detect_errors="exit_code"> - #set $reference_filename = str( $ref_file.fields.path ) - affiliation_OTU.py - --reference '${reference_filename}' - --input-biom $biom_abundance - --input-fasta $fasta_sequences - --output-biom $biom_affiliation - --summary $summary - --nb-cpus \${GALAXY_SLOTS:-1} - --java-mem $mem - #if $rdp - --rdp - #end if - </command> - <inputs> - <!-- JOB Parameter --> - <param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param> - <!-- Database Choice --> - <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> - <options from_data_table="frogs_db"></options> - <validator type="no_options" message="A built-in database is not available" /> - </param> - <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)" /> + <command detect_errors="exit_code"> + #set $reference_filename = str( $ref_file.fields.path ) + affiliation_OTU.py + --reference '${reference_filename}' + --taxonomy-ranks $taxonomic_ranks + --input-biom $biom_abundance + --input-fasta $fasta_sequences + --output-biom $biom_affiliation + --summary $summary + --nb-cpus \${GALAXY_SLOTS:-1} + --java-mem $mem + #if $rdp + --rdp + #end if + </command> + <inputs> + <!-- JOB Parameter --> + <param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param> + <!-- Database Choice --> + <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> + <options from_data_table="frogs_db"></options> + <validator type="no_options" message="A built-in database is not available" /> + </param> + <param name="rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allow you to perform it also with RDP classifier (default No)" /> + <param name="taxonomic_ranks" type="text" label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in the taxonomical reference. Each rank is separated by one space." optional="false" value="Domain Phylum Class Order Family Genus Species" size="80" /> <!-- Files --> <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/> <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="OTU abundances (format: BIOM)."/> - </inputs> - <outputs> - <data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom" /> - <data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/> - </outputs> + </inputs> + <outputs> + <data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom" /> + <data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/> + </outputs> <tests> <test> <param name="ref_file" value="ITS1_test"/> <param name="fasta_sequences" value="references/04-filters.fasta"/> <param name="biom_abundance" value="references/04-filters.biom"/> - <output name="biom_affiliation" file="references/06-affiliation2.biom" compare="sim_size" delta="0" /> - <output name="summary" file="references/06-affiliation2.html" compare="diff" lines_diff="0"/> - </test> - <test> - <param name="ref_file" value="ITS1_test"/> - <param name="fasta_sequences" value="references/04-filters.fasta"/> - <param name="biom_abundance" value="references/04-filters.biom"/> <param name="rdp" value="true"/> <output name="biom_affiliation" file="references/06-affiliation.biom" compare="sim_size" delta="5" /> <output name="summary" file="references/06-affiliation.html" compare="diff" lines_diff="0"/> @@ -73,7 +68,7 @@ </tests> - <help> + <help> .. image:: static/images/FROGS_logo.png :height: 144 @@ -167,10 +162,10 @@ For the precedent use cases we will obtain: * Case 1: 16S V3V4 overlapped sequence - % sequenced bases identity = 400 matches / 400 bp = 100% + % sequenced bases identity = 400 matches / 400 bp = 100% * Case 2: very large ITS1 “FROGS combined” shorter than the real sequence - % sequenced bases identity = (250 + 250 ) / (600 - 100) = 100% + % sequenced bases identity = (250 + 250 ) / (600 - 100) = 100% This calculation allows to return 100% of identity on sequenced bases for “FROGS combined” 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. @@ -196,5 +191,5 @@ Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. <https://doi.org/10.1093/bioinformatics/btx791>`_ - </help> + </help> </tool> |
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| diff -r 834843ebe569 -r 2ed857799fd5 affiliation_filters.xml --- a/affiliation_filters.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/affiliation_filters.xml Fri Jun 04 14:56:24 2021 +0000 |
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| @@ -15,10 +15,10 @@ # 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_filters" name="FROGS Affiliation Filters" version="3.2.2"> +<tool id="FROGS_affiliation_filters" name="FROGS Affiliation Filters" version="3.2.3"> <description>Filters OTUs on several affiliation criteria.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -106,8 +106,8 @@ </inputs> <outputs> - <data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" /> - <data format="fasta" name="output_fasta" label="${tool.name}: sequences.fasta" from_work_dir="sequences.fasta"> + <data format="biom1" name="output_biom" label="${tool.name}: affiFilter_abundance.biom" from_work_dir="affiFilter_abundance.biom" /> + <data format="fasta" name="output_fasta" label="${tool.name}: affiFilter_sequences.fasta" from_work_dir="affiFilter_sequences.fasta"> <filter> conditional_mode['mode'] == 'delete'</filter> </data> <data format="tabular" name="output_impacted" label="${tool.name}: impacted_OTU.tsv" from_work_dir="impacted.tsv" /> |
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| diff -r 834843ebe569 -r 2ed857799fd5 affiliation_postprocess.xml --- a/affiliation_postprocess.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/affiliation_postprocess.xml Fri Jun 04 14:56:24 2021 +0000 |
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| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="3.2.3"> <description>Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 affiliations_stat.xml --- a/affiliations_stat.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/affiliations_stat.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="3.2.3"> <description>Process some metrics on taxonomies.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 biom_to_stdBiom.xml --- a/biom_to_stdBiom.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/biom_to_stdBiom.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="3.2.3"> <description>Converts a FROGS BIOM in fully compatible BIOM.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 biom_to_tsv.xml --- a/biom_to_tsv.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/biom_to_tsv.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="3.2.3"> <description>Converts a BIOM file in TSV file.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 clustering.xml --- a/clustering.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/clustering.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_clustering" name="FROGS Clustering swarm" version="3.2.3"> <description>Single-linkage clustering on sequences</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> <requirement type="package" version="3.0.0">swarm</requirement> </requirements> <stdio> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 clusters_stat.xml --- a/clusters_stat.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/clusters_stat.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="3.2.3"> <description>Process some metrics on clusters.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 conda_toolshed_frogs --- a/conda_toolshed_frogs Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,136 +0,0 @@ -#################################################### - -1) construction prerelease FROGS -2) recette conda sur channel conda perso -3) ( fork bioconda ) / ( creation branche frogs ) / ajout/update recette frogs / pull request -4) planemo test -5) construction prerelease FROGS-wrappers -6) planemo shed_create --shed_target testtoolshed (update FROGS-wrappers/.shed.yml compte owner oinizan + version et URL de répo) - ==> planemo shed_update --shed_target testtoolshed si update -7) planemo shed_create --shed_target toolshed (update FROGS-wrappers/.shed.yml compte owner frogs) - -#################################################### - - - - - Comment faire un paquet conda (doc sur github bioconda) - -init: - fork de bioconda-recipes (github bioconda) - git clone https://github.com/mariabernard/bioconda-recipes.git - # pour mettre à jour le fork (upstream), avec le code de bioconda (origin) - git pull origin - ajout de ton recette conda - tester avec la chaine d'intégration circleci (cf github bioconda-recipes : https://bioconda.github.io/contrib-setup.htm) -ou - conda-build ==> conda build / conda-build n'est pas fourni par défaut.==> faire un environnement conda spécifique à conda-build et faire le build dans l'env. - si test ok alors pullrequest via interface github à partir de la page du fork. - si souhait de faire test sur un channel perso alors anaconda upload (indiqué en commentaire à la fin) ==> à condition d'avoir paramétrer conda pour indiquer sur quel channel écrire. - -mise à jour: - faire un fetch de son fork - puis modif - -recette conda: - meta.yaml = liste des dépendances - build.sh = script d'install, autrement dit gestion de l'arborescence/ creation de liens symboliques - - -1 check package dans conda (ex : ITSx) - ajout dans meta.yaml - - si paquet n'existe pas, alors il faut le créer. meta.yaml quasi vide, build.sh permet de faire le download et les compilation si necessaire. - - - - Utiliser conda - -# pour lister les environnements disponibles - -~/miniconda3/bin/conda env list - -# pour installer un environnement - # pour ajouter un channel (ici vmarcon) - -~/miniconda3/bin/conda config --add channels vmarcon - - # pour installer en précisant la version (@3.0.0) - -~/miniconda3/bin/conda create -n __frogs@3.1.0 frogs=3.1.0 - -# pour charger un environnement (see env list) - -source ~/miniconda3/bin/activate <envName>@<version> - -# pour quitter - -source deactivate - -# pour supprimer un environnement - - conda env remove -n <envName> - -# pour upgrade un env - conda env upgrade -n <envName> - - Comment déposer sur le toolshed - -le github FROGS_wrapper doit contenir un dossier test-data qui correspond au dossier pour la section test des wrappers -contient les fichiers loc - - -1) Ajout dans les wrappers : - des requirements - des codes de sortie - section test - - -2) Test des wrappers avec planemo - - - installer planemo !!! avec Ubuntu c'est cool - - # creation d'un environnement virtuel - virtualenv .planemo - # activation de l'environnement - . ~/.planemo/bin/activate - # installation avec pip (>= 7) - pip install planemo - # upgrade - pip install -U planemo - - - Utilisation de planemo - -# activation de l'environnement -. ~/planemo/bin/activate - -test de la structure et la dispo des dépendances sous conda: - planemo lint --conda_requirements <tool>.xml - - failed si pas de citation alors que ce n'est qu'un warning. - -test de la création de l'environnement - planemo conda_install <tool>.xml - ==> cela va créer un env __<dependency_tool>@<version> - -test la section tests - planemo test <tool>.xml (note: lors du premier test il fait un install de Galaxy) - -# tant que la recette conda n'est pas sur bioconda, il faut ajouter le channel de test" - planemo test <tool>.xml --conda_channels "vmarcon,defaults,bioconda,conda-forge" - - # option utile - --no_cleanup Do not cleanup temp files created for and by Galaxy. - -publication sur toolshed - via l'interface - via planemo - créer un .shed.yaml - définition d'un catégorie (check sur le web) - du owner - description - planemo shed_init # à compléter - planemo shed_create --shed_target testtoolshed # premier dépôt : dépôt frogs (sans nom de version a été créé lors de la mise en ligne de la version 3.2.1) - planemo shed_update --shed_target testtoolshed # nouvelle release : pour toutes les prochaines release il suffit de faire un update - -Dans .planemo.yml définition des login de compte toolshed, l'idée est de partager une clé pour pouvoir pousser à plusieurs. |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 demultiplex.xml --- a/demultiplex.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/demultiplex.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,11 +15,11 @@ # 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_demultiplex" name="FROGS Demultiplex reads" version="3.2.2"> +<tool id="FROGS_demultiplex" name="FROGS Demultiplex reads" version="3.2.3"> <description>Attribute reads to samples in function of inner barcode.</description> <requirements> <requirement type="binary">perl</requirement> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 deseq2_preprocess.xml --- a/deseq2_preprocess.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/deseq2_preprocess.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,14 +15,14 @@ # 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 DESeq2 Preprocess" id="FROGSSTAT_DESeq2_Preprocess" version="3.2.2"> +<tool name="FROGSSTAT DESeq2 Preprocess" id="FROGSSTAT_DESeq2_Preprocess" version="3.2.3"> <description>import a Phyloseq object and prepare it for DESeq2 differential abundance analysis </description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> - <requirement type="package" version="1.26.0">bioconductor-deseq2</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="1.30.1">bioconductor-deseq2</requirement> <requirement type="package" version="1.6.6">r-optparse</requirement> </requirements> <stdio> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 deseq2_visualisation.xml --- a/deseq2_visualisation.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/deseq2_visualisation.xml Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| @@ -15,15 +15,15 @@ # 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="FROGSTAT Deseq2 Visualisation" id="FROGSSTAT_DESeq2_Visualisation" version="3.2.2"> +<tool name="FROGSTAT Deseq2 Visualisation" id="FROGSSTAT_DESeq2_Visualisation" version="3.2.3"> <description>to extract and visualise differentially abundant OTUs</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> - <requirement type="package" version="1.26.0">bioconductor-deseq2</requirement> - <requirement type="package" version="0.17">r-dt</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="1.30.1">bioconductor-deseq2</requirement> + <requirement type="package" version="0.18">r-dt</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -83,21 +83,15 @@ <output name="html"> <assert_contents> <has_text text="FROGSSTAT DESeq2: Visualisation" /> - <has_text text="Phyloseq 1.30.0" /> <has_text text='["otu_01582",' /> - <!-- HTML caracter not authorized, search for value only --> - <!-- baseMean value of otu_01582, - <has_text text='["\<span style=\"display: block; padding: 0 4px; border-radius: 4px; background-color: #fffcfd\">52.445511' /> --> + <!-- baseMean value of otu_01582 --> <has_text text='52.445510949046' /> - <!-- Log2 FC of otu_01582 - <has_text text='["\<span style=\"color: red\">21.662506' /> --> - <has_text text='21.6625060651457' /> - <!-- lfcSE of otu_01582 - <has_text text='["\<span style=\"display: block; padding: 0 4px; border-radius: 4px; background-color: #c9e5ee\">2.2089268' /> --> - <has_text text='2.20892675663989' /> - <!-- pvalue otu_01582 - <has_text text='["\<span style=\"display: block; padding: 0 4px; border-radius: 4px; background-color: #add8e6\">1.052520e-22' /> --> - <has_text text='1.0525195975273e-22' /> + <!-- Log2 FC of otu_01582 --> + <has_text text='21.6622901050859' /> + <!-- lfcSE of otu_01582 --> + <has_text text='2.20892675384734' /> + <!-- pvalue otu_01582 --> + <has_text text='1.0535393782052e-22' /> </assert_contents> </output> </test> @@ -138,31 +132,31 @@ The html file contains Table, Pie Chart, MA plot, Volcano plot and Heatmap plot. If the experimental variable is qualitative, only samples corresponding to the 2 compared conditions are shown in the Heatmap. Otherwise, samples are sorted in increasing order of the experimental variable. -Table containing the differentially abundant OTUs. +* Table containing the differentially abundant OTUs. .. image:: static/images/FROGS_DESeq2_html_table.png - :height: 354 - :width: 1153 + :height: 216 + :width: 789 -Pie Chart, MA plot and Volcano plot +* Pie Chart, MA plot and Volcano plot .. image:: static/images/FROGS_DESeq2_html_pieChart.png - :height: 391 - :width: 563 + :height: 576 + :width: 768 .. image:: static/images/FROGS_DESeq2_html_MA_plot.png - :height: 324 - :width: 525 + :height: 480 + :width: 672 .. image:: static/images/FROGS_DESeq2_html_Volcano_plot.png - :height: 576 - :width: 720 + :height: 506 + :width: 633 -Heatmap plot corresponding to the differentially abundant OTUs. +* Heatmap plot corresponding to the differentially abundant OTUs. .. image:: static/images/FROGS_DESeq2_html_heatmap_plot.png - :height: 576 - :width: 720 + :height: 576 + :width: 768 .. class:: infomark page-header h2 |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 itsx.xml --- a/itsx.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/itsx.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_itsx" name="FROGS ITSx" version="3.2.3"> <description>Extract the highly variable ITS1 and ITS2 subregions from ITS sequences.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> <requirement type="package" version="1.1.2">itsx</requirement> </requirements> <stdio> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 normalisation.xml --- a/normalisation.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/normalisation.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="3.2.3"> <description>Normalise OTUs abundance.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 otu_filters.xml --- a/otu_filters.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/otu_filters.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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_OTU_filters" name="FROGS OTU Filters" version="3.2.2"> +<tool id="FROGS_OTU_filters" name="FROGS OTU Filters" version="3.2.3"> <description>Filters OTUs on several criteria.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> <requirement type="package" version="2.9.0">blast</requirement> </requirements> <stdio> @@ -114,8 +114,8 @@ </conditional> </inputs> <outputs> - <data format="fasta" name="output_fasta" label="${tool.name}: sequences.fasta" from_work_dir="sequences.fasta" /> - <data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" /> + <data format="biom1" name="output_biom" label="${tool.name}: otuFilter_abundance.biom" from_work_dir="otuFilter_abundance.biom" /> + <data format="fasta" name="output_fasta" label="${tool.name}: otuFilter_sequences.fasta" from_work_dir="otuFilter_sequences.fasta" /> <data format="tabular" name="output_excluded" label="${tool.name}: excluded.tsv" from_work_dir="excluded.tsv" /> <data format="html" name="output_summary" label="${tool.name}: report.html" from_work_dir="report.html" /> </outputs> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 phyloseq_alpha_diversity.xml --- a/phyloseq_alpha_diversity.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/phyloseq_alpha_diversity.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,13 +15,13 @@ # 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="3.2.2"> +<tool name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.2.3"> <description>with richness plot</description> <requirements> <requirement type="package" version="3.2.">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> <!-- <requirement type="package" version="1.1">r-markdown</requirement> <requirement type="package" version="2.11.4">pandoc</requirement> --> @@ -66,6 +66,7 @@ <param name="varExp" value="EnvType" /> <param name="measures" value="Observed,Chao1,Shannon" /> <output name="alphaD" file="references/18-phylo_alpha_div.tsv" compare="diff" lines_diff="0" /> + <output name="html" value="references/18-phylo_alpha_div.nb.html" compare="diff" lines_diff="0"/> </test> </tests> <help> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 phyloseq_beta_diversity.xml --- a/phyloseq_beta_diversity.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/phyloseq_beta_diversity.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,13 +15,13 @@ # 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="3.2.2"> +<tool name="FROGSSTAT Phyloseq Beta Diversity" id="FROGSSTAT_Phyloseq_Beta_Diversity" version="3.2.3"> <description>distance matrix</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> <requirement type="package" version="2.3">r-gridextra</requirement> </requirements> <stdio> @@ -72,13 +72,7 @@ <param name="data" value="references/16-phylo_import.Rdata" /> <param name="varExp" value="EnvType" /> <param name="methods" value="cc,unifrac" /> - <!-- <output name="html" file="references/19-phylo_beta_div.nb.html" compare="diff" lines_diff="0" /> --> - <output name="html"> - <assert_contents> - <has_text text='FROGS Phyloseq: Beta Diversity Visualisation' /> - <has_text text='Phyloseq 1.30.0' /> - </assert_contents> - </output> + <output name="html" file="references/19-phylo_beta_div.nb.html" compare="diff" lines_diff="0" /> </test> </tests> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 phyloseq_clustering.xml --- a/phyloseq_clustering.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/phyloseq_clustering.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,13 +15,13 @@ # 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="3.2.2"> +<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.2.3"> <description>of samples using different linkage methods</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -54,12 +54,7 @@ <param name="data" value="references/16-phylo_import.Rdata"/> <param name="varExp" value="EnvType"/> <param name="method" value="references/unifrac.tsv"/> - <output name="html"> - <assert_contents> - <has_text text='FROGS Phyloseq: Sample clustering using different linkage method' /> - <has_text text='Phyloseq 1.30.0' /> - </assert_contents> - </output> + <output name="html" file="references/21-phylo_clustering.nb.html" compare="diff" lines_diff="0"/> </test> </tests> <help> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 phyloseq_composition.xml --- a/phyloseq_composition.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/phyloseq_composition.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,13 +15,13 @@ # 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="3.2.2"> +<tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="3.2.3"> <description>with bar plot and composition plot</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> <requirement type="package" version="4.9.3">r-plotly</requirement> </requirements> <stdio> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 phyloseq_import_data.xml --- a/phyloseq_import_data.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/phyloseq_import_data.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,13 +15,13 @@ # 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="3.2.2"> +<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.2.3"> <description>from 3 files: biomfile, samplefile, treefile </description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -66,6 +66,7 @@ <param name="samplefile" value="input/sample_metadata.tsv"/> <param name="treefile" value="input/tree.nwk"/> <output name="data" value="references/16-phylo_import.Rdata" compare="sim_size" delta="10"/> + <output name="html" value="references/16-phylo_import.nb.html" compare="diff" lines_diff="0"/> </test> </tests> <help> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 phyloseq_manova.xml --- a/phyloseq_manova.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/phyloseq_manova.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,13 +15,13 @@ # 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="3.2.2"> +<tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="3.2.3"> <description>perform Multivariate Analysis of Variance (MANOVA)</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -54,14 +54,7 @@ <param name="data" value="references/16-phylo_import.Rdata"/> <param name="varExp" value="EnvType"/> <param name="method" value="references/unifrac.tsv"/> - - <output name="html"> - <assert_contents> - <has_text_matching expression="EnvType 7 7.6565 1.09379 13.699 0.63132 1e-04 \*\*\*" /> - <has_text_matching expression="Residuals 56 4.4713 0.07984 0.36868 " /> - <has_text_matching expression="Total 63 12.1278 1.00000 " /> - </assert_contents> - </output> + <output name="html" value="references/22-phylo_manova.nb.html" compare="diff" lines_diff="0"/> </test> </tests> <help> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 phyloseq_structure.xml --- a/phyloseq_structure.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/phyloseq_structure.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,13 +15,13 @@ # 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="3.2.2"> +<tool name="FROGSSTAT Phyloseq Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="3.2.3"> <description>with heatmap plot and ordination plot</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="3.6">r-essentials</requirement> - <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement> <requirement type="package" version="4.9.3">r-plotly</requirement> </requirements> <stdio> @@ -73,7 +73,7 @@ </tests> <help> -.. image:: static/images/FROGS_logo.png +.. image:: static/images/FROGS_logo.png :height: 144 :width: 110 @@ -111,6 +111,12 @@ :height: 343 :width: 450 +.. class:: warningmark + +**Percentages on axis may be interpreted similarly as the percentages on a PCA, but are not percentage of explained variance.** +These percentages will be computed for MDS/PCoA and DPCoA ordination methods as a percentage of explained beta diversity variation. +For NMDS there is not simple equivalent notion. + .. image:: static/images/FROGS_Phyloseq_plot_heatmap_red.png :height: 343 :width: 450 |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 planemo_test.sh --- a/planemo_test.sh Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,42 +0,0 @@ -#!/bin/sh - -mkdir -p planemo_test - -####################################################################################################### -# TEST LA STRUCTURE -for i in *.xml -do - echo $i - planemo lint $i > planemo_test/`basename $i |sed 's/\.xml//'`.lint.log 2>&1 -done - -grep Failed planemo_test/*.lint.log - -####################################################################################################### -# VALIDE L'EXECUTION -for i in ` ls *.xml | grep -vE 'demultiplexe|preprocess|clustering|remove_chimera'` -do - echo $i - planemo test --no_cleanup $i > planemo_test/`basename $i |sed 's/\.xml//'`.test.log 2>&1 -done - -grep FAILED planemo_test/*test.log - - -grep "test(s) executed passed" planemo_test/*test.log - -# planemo_test/preprocess.test.log:All 2 test(s) executed passed. - - -# remote: warning: File test-data/references/01-prepro-flash.fasta is 95.81 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB -# remote: error: File test-data/references/02-clustering_fastidious.fasta is 109.85 MB; this exceeds GitHub's file size limit of 100.00 MB -# remote: error: File test-data/references/01-prepro-vsearch.fasta is 121.32 MB; this exceeds GitHub's file size limit of 100.00 MB -# remote: error: File test-data/references/02-clustering_denoising.fasta is 108.50 MB; this exceeds GitHub's file size limit of 100.00 MB -# remote: error: File test-data/references/03-chimera.fasta is 109.85 MB; this exceeds GitHub's file size limit of 100.00 MB - - -####################################################################################################### -# TEST SOUS GALAXY - -####################################################################################################### -# SOUMISSION AU TOOLSHED \ No newline at end of file |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 planemo_test/deseq2_preprocess.test.log --- a/planemo_test/deseq2_preprocess.test.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,704 +0,0 @@\n-git --git-dir /home/maria/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/maria/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/maria/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/maria/.planemo/gx_repo /tmp/tmpf6w1rwu5/galaxy-dev\n-Clonage dans \'/tmp/tmpf6w1rwu5/galaxy-dev\'...\n-error: object file ./objects/1d/3b5b4b0610a48d6950fbf2a3c49559fc28f85e is empty\n-fait.\n-Extraction des fichiers: 71% (3877/5411) \rExtraction des fichiers: 72% (3896/5411) \rExtraction des fichiers: 73% (3951/5411) \rExtraction des fichiers: 74% (4005/5411) \rExtraction des fichiers: 75% (4059/5411) \rExtraction des fichiers: 76% (4113/5411) \rExtraction des fichiers: 77% (4167/5411) \rExtraction des fichiers: 78% (4221/5411) \rExtraction des fichiers: 79% (4275/5411) \rExtraction des fichiers: 80% (4329/5411) \rExtraction des fichiers: 81% (4383/5411) \rExtraction des fichiers: 82% (4438/5411) \rExtraction des fichiers: 83% (4492/5411) \rExtraction des fichiers: 84% (4546/5411) \rExtraction des fichiers: 85% (4600/5411) \rExtraction des fichiers: 86% (4654/5411) \rExtraction des fichiers: 87% (4708/5411) \rExtraction des fichiers: 88% (4762/5411) \rExtraction des fichiers: 89% (4816/5411) \rExtraction des fichiers: 90% (4870/5411) \rExtraction des fichiers: 91% (4925/5411) \rExtraction des fichiers: 92% (4979/5411) \rExtraction des fichiers: 93% (5033/5411) \rExtraction des fichiers: 94% (5087/5411) \rExtraction des fichiers: 95% (5141/5411) \rExtraction des fichiers: 96% (5195/5411) \rExtraction des fichiers: 97% (5249/5411) \rExtraction des fichiers: 98% (5303/5411) \rExtraction des fichiers: 99% (5357/5411) \rExtraction des fichiers: 100% (5411/5411) \rExtraction des fichiers: 100% (5411/5411), fait.\n-if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/maria/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/maria/planemo/bin/virtualenv -p /home/maria/planemo/bin/python3 $GALAXY_VIRTUAL_ENV; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && COMMON_STARTUP_ARGS=; $(grep -q \'skip-venv\' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}" && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/maria/.planemo/gx_venv_3\n-Set COMMON_STARTUP_ARGS to --dev-wheels\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/maria/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=8.1 in /home/maria/.planemo/gx_venv_3/lib/python3.8/site-packages (21.0.1)\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple\n-Ignoring importlib-metadata: markers \'python_version < "3.8"\' don\'t match your environment\n-Ignoring importlib-resources: markers \'python_version < "3.7"\' don\'t match your environment\n-Ignoring pathlib2: markers \'python_version < "3.6"\' don\'t match your environment\n-Ignoring ruamel.yaml.clib: markers \'platform_python_implementation == "CPython" and python_version < "3.8"\' don\'t match your environment\n-Ignoring typing: markers \'python_version < "3.5"\' don\'t match your environment\n-Ignoring zipp: markers \'python_version < "3.8"\''..b'8bf93fc86139ca\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/maria/miniconda3/bin/activate\' \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/maria/miniconda3/bin/activate\' \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/maria/miniconda3/bin/activate\' \'/home/maria/miniconda3/envs/mulled-v1-7476be2a9781bd0543b5f892f93d3256e374f4f9a123fcba2c8bf93fc86139ca\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; deseq2_preprocess.py --data /tmp/tmpf6w1rwu5/files/0/a/3/dataset_0a3efe28-a7d2-496a-b6f6-aae5fb4287e5.dat --var EnvType --out-Rdata /tmp/tmpf6w1rwu5/files/2/8/a/dataset_28ac11fe-96b4-4b27-9ec4-c2bc4ef7e731.dat]\n-ok\n-\n-----------------------------------------------------------------------\n-XML: /tmp/tmpf6w1rwu5/xunit.xml\n-----------------------------------------------------------------------\n-Ran 1 test in 1264.958s\n-\n-OK\n-2021-04-08 16:09:58,055 INFO [test_driver] Shutting down\n-2021-04-08 16:09:58,056 INFO [test_driver] Shutting down embedded galaxy web server\n-2021-04-08 16:09:58,058 INFO [test_driver] Embedded web server galaxy stopped\n-2021-04-08 16:09:58,058 INFO [test_driver] Stopping application galaxy\n-2021-04-08 16:09:58,430 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task.\n-2021-04-08 16:09:58,483 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2021-04-08 16:09:58,483 INFO [galaxy.jobs.handler] job handler queue stopped\n-2021-04-08 16:09:58,483 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads\n-2021-04-08 16:09:58,483 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...\n-2021-04-08 16:09:58,484 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly\n-2021-04-08 16:09:58,484 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads\n-2021-04-08 16:09:58,484 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown...\n-2021-04-08 16:09:58,484 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly\n-2021-04-08 16:09:58,484 INFO [galaxy.jobs.handler] sending stop signal to worker thread\n-2021-04-08 16:09:58,485 INFO [galaxy.jobs.handler] job handler stop queue stopped\n-2021-04-08 16:09:58,485 INFO [test_driver] Application galaxy stopped.\n-Testing complete. HTML report is in "/home/maria/workspace/FROGS-wrappers_dev/tool_test_output.html".\n-All 1 test(s) executed passed.\n-FROGSSTAT_DESeq2_Preprocess (Test #1): passed\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 preprocess.xml --- a/preprocess.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/preprocess.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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_preprocess" name="FROGS Pre-process" version="3.2.2"> +<tool id="FROGS_preprocess" name="FROGS Pre-process" version="3.2.3"> <description>merging, denoising and dereplication.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> <requirement type="package" version="2.17.0">vsearch</requirement> <requirement type="package" version="1.2.11">flash</requirement> <requirement type="package" version="2.10">cutadapt</requirement> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 remove_chimera.xml --- a/remove_chimera.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/remove_chimera.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="3.2.3"> <description>Remove PCR chimera in each sample.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> <requirement type="package" version="2.15.1">vsearch</requirement> </requirements> <stdio> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 shedSave.yml --- a/shedSave.yml Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -categories: -- Metagenomics -description: Suite for metabarcoding analysis -long_description: | - This is FROGS version 3.2.2 Galaxy Wrappers - FROGS: Find Rapidly OTUs through Galaxy Solution - FROGS is a workflow designed to produce an OTU count matrix from high depth sequencing amplicon data. - Adviced : - reorder integrated_tool_panel.xml as indicated here : https://github.com/geraldinepascal/FROGS-wrappers#simplest-way -name: frogs -owner: oinizan #TestToolshed -homepage_url: https://github.com/geraldinepascal/FROGS-wrappers -remote_repository_url: https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 static/images/FROGS_DESeq2_html_MA_plot.png |
| b |
| Binary file static/images/FROGS_DESeq2_html_MA_plot.png has changed |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 static/images/FROGS_DESeq2_html_Volcano_plot.png |
| b |
| Binary file static/images/FROGS_DESeq2_html_Volcano_plot.png has changed |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 static/images/FROGS_DESeq2_html_pieChart.png |
| b |
| Binary file static/images/FROGS_DESeq2_html_pieChart.png has changed |
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| diff -r 834843ebe569 -r 2ed857799fd5 static/images/FROGS_DESeq2_html_table.png |
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| Binary file static/images/FROGS_DESeq2_html_table.png has changed |
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| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/01-prepro-flash.html --- a/test-data/references/01-prepro-flash.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/01-prepro-flash.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Pre-process</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <!-- CSS --> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/01-prepro-flash.log --- a/test-data/references/01-prepro-flash.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,331 +0,0 @@\n-## Application\n-Software: preprocess.py (version: 3.2.2)\n-Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/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 1 --mismatch-rate 0.15 --keep-unmerged --input-archive /home/maria/miniconda3/envs/frogs@3.2.2/bin/test/data/test_dataset2.tar.gz --output-dereplicated res_3.2.2//01-prepro-flash.fasta --output-count res_3.2.2//01-prepro-flash.tsv --summary res_3.2.2//01-prepro-flash.html --log-file res_3.2.2//01-prepro-flash.log\n-\n-## Application\n-Software: preprocess.py (version: 3.2.2)\n-Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/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 2 --mismatch-rate 0.15 --keep-unmerged --input-archive data/test_dataset2.tar.gz --output-dereplicated res_3.2.2/01-prepro-flash.fasta --output-count res_3.2.2/01-prepro-flash.tsv --summary res_3.2.2/01-prepro-flash.html --log-file res_3.2.2/01-prepro-flash.log\n-\n-\n-##Sample\n-R1 : res_3.2.2/1617285415.591807_15700_01_subsample_R1.fastq.gz\n-R2 : res_3.2.2/1617285415.591807_15700_01_subsample_R2.fastq.gz\n-Sample name : 01_subsample\n-nb seq before process : 50000\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_3.2.2/1617285415.591807_15700_01_subsample_R1.fastq.gz res_3.2.2/1617285415.591807_15700_01_subsample_R2.fastq.gz --output-directory res_3.2.2 --output-prefix 1617285416.0384917_15702_01_subsample_flash 2> res_3.2.2/1617285416.0384917_15702_01_subsample_flash.stderr\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:56:56\n-\tend: 01 Apr 2021 15:57:01\n-\n-Results:\n-\tnb seq paired-end assembled: 29070\n-########################################################################################################\n-# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10)\n-Command:\n-\tcutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.2/1617285416.0384917_15702_01_subsample_flash.extendedFrags.fastq.gz > res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_5prim_log.txt 2> res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_5prim_err.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:02\n-\tend: 01 Apr 2021 15:57:05\n-\n-Results:\n-\tnb seq with 5' primer : 29070\n-########################################################################################################\n-# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10)\n-Command:\n-\tcutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt.fastq.gz res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_3prim_log.txt 2> res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt_3prim_err.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:05\n-\tend: 01 Apr 2021 15:57:09\n-\n-Results:\n-\tnb seq with 3' primer : 29070\n-########################################################################################################\n-# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0)\n-Command:\n-\tfilterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.2/1617285416.0384917_15702_01_subsample_cutadapt.fast"..b' and 3\' primer and removes primer sequence. (cutadapt version : 2.10)\n-Command:\n-\tcutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.2/1617285447.6133468_15702_03_subsample_flash.notCombined_1.fastq.gz res_3.2.2/1617285447.6133468_15702_03_subsample_flash.notCombined_2.fastq.gz > res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_err.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:38\n-\tend: 01 Apr 2021 15:57:41\n-\n-Results:\n-\tnb seq with 5\' primer : 20851\n-\tnb seq with 3\' primer : 20851\n-########################################################################################################\n-# Concatenate paired reads. (combine_and_split.py version : 1.0.0)\n-Command:\n-\tcombine_and_split.py --reads1 res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.2/1617285447.6133468_15702_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.2/1617285447.6133468_15702_03_subsample_artificial_combined.fastq.gz\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:41\n-\tend: 01 Apr 2021 15:57:48\n-\n-########################################################################################################\n-# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0)\n-Command:\n-\tfilterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.2/1617285447.6133468_15702_03_subsample_artificial_combined.fastq.gz --output-file res_3.2.2/1617285447.6133468_15702_03_subsample_art_N_filter.fasta --log-file res_3.2.2/1617285447.6133468_15702_03_subsample_art_N_filter_log.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:48\n-\tend: 01 Apr 2021 15:57:48\n-\n-Results:\n-\tnb seq with expected length : 20851\n-\tnb seq without N : 20851\n-########################################################################################################\n-# Replace join tag. (combine_and_split.py version : 1.0.0)\n-Command:\n-\tcombine_and_split.py --reads1 res_3.2.2/1617285447.6133468_15702_03_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.2/1617285447.6133468_15702_03_subsample_art_XtoN.fasta\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:48\n-\tend: 01 Apr 2021 15:57:49\n-\n-########################################################################################################\n-# Dereplicates sample sequences. (derepSamples.py version : 1.6.1)\n-Command:\n-\tderepSamples.py --sequences-files res_3.2.2/1617285447.6133468_15702_03_subsample_N_and_length_filter.fasta res_3.2.2/1617285447.6133468_15702_03_subsample_art_XtoN.fasta --dereplicated-file res_3.2.2/1617285415.591807_15700_03_subsample_filtered.fasta --count-file res_3.2.2/1617285447.6133468_15702_03_subsample_derep_count.tsv\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:49\n-\tend: 01 Apr 2021 15:57:51\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 2 --size-separator \';size=\' --samples-ref res_3.2.2/1617285415.591807_15700_derep_inputs.tsv --dereplicated-file res_3.2.2/01-prepro-flash.fasta --count-file res_3.2.2/01-prepro-flash.tsv\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:51\n-\tend: 01 Apr 2021 15:57:55\n-\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/01-prepro-vsearch.html --- a/test-data/references/01-prepro-vsearch.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/01-prepro-vsearch.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Pre-process</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <!-- CSS --> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/01-prepro-vsearch.log --- a/test-data/references/01-prepro-vsearch.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,327 +0,0 @@\n-## Application\n-Software: preprocess.py (version: 3.2.2)\n-Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/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 2 --mismatch-rate 0.15 --keep-unmerged --input-archive data/test_dataset2.tar.gz --output-dereplicated res_3.2.2/01-prepro-vsearch.fasta --output-count res_3.2.2/01-prepro-vsearch.tsv --summary res_3.2.2/01-prepro-vsearch.html --log-file res_3.2.2/01-prepro-vsearch.log\n-\n-\n-##Sample\n-R1 : res_3.2.2/1617285475.3604712_15868_01_subsample_R1.fastq.gz\n-R2 : res_3.2.2/1617285475.3604712_15868_01_subsample_R2.fastq.gz\n-Sample name : 01_subsample\n-nb seq before process : 50000\n-##Commands\n-########################################################################################################\n-# join overlapping paired reads (vsearch version : v2.17.0_linux_x86_64)\n-Command:\n-\tvsearch --threads 1 --fastq_mergepairs res_3.2.2/1617285475.3604712_15868_01_subsample_R1.fastq.gz --reverse res_3.2.2/1617285475.3604712_15868_01_subsample_R2.fastq.gz --fastqout res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.assembled.fastq --fastqout_notmerged_fwd res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.unassembled_R1.fastq --fastqout_notmerged_rev res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.unassembled_R2.fastq --fastq_allowmergestagger --fastq_ascii 33 --fastq_maxdiffpct 15.0 --fastq_minovlen 43 2> res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.log\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:56\n-\tend: 01 Apr 2021 15:57:58\n-\n-Results:\n-\tnb seq paired-end assembled: 24402\n-########################################################################################################\n-# Removes reads without the 5' primer and removes primer sequence. (cutadapt version : 2.10)\n-Command:\n-\tcutadapt -g GGCGVACGGGTGAGTAA --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 16 -o res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_5prim_trim.fastq.gz res_3.2.2/1617285475.569636_15869_01_subsample_vsearch.assembled.fastq > res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_5prim_log.txt 2> res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_5prim_err.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:57:58\n-\tend: 01 Apr 2021 15:58:00\n-\n-Results:\n-\tnb seq with 5' primer : 24402\n-########################################################################################################\n-# Removes reads without the 3' primer and removes primer sequence. (cutadapt version : 2.10)\n-Command:\n-\tcutadapt -a GTGCCAGCNGCNGCGG --error-rate 0.1 --discard-untrimmed --match-read-wildcards --overlap 15 -o res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt.fastq.gz res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_5prim_trim.fastq.gz > res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_3prim_log.txt 2> res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt_3prim_err.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:58:00\n-\tend: 01 Apr 2021 15:58:03\n-\n-Results:\n-\tnb seq with 3' primer : 24402\n-########################################################################################################\n-# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0)\n-Command:\n-\tfilterSeq.py --force-fasta --max-N 0 --min-length 11 --max-length 457 --input-file res_3.2.2/1617285475.569636_15869_01_subsample_cutadapt.fastq.gz --output-file res_3.2.2/1617285475.569636_15869_01_subsample_N_and_length_filter.fasta --log-file res_3.2.2/1617285475.569636_15869_01_subsample_N_and_length_filter_log.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:58:03\n-\tend: 01 Apr 2021 15:58:04\n-\n-Results:\n-\tnb seq with expected length : 24402\n-\tnb seq without N : 24402\n-########################################################################################################\n-# Removes read pa"..b'\' primer and removes primer sequence. (cutadapt version : 2.10)\n-Command:\n-\tcutadapt -g "GGCGVACGGGTGAGTAA;min_overlap=16" -G "CCGCNGCNGCTGGCAC;min_overlap=15" --error-rate 0.1 --discard-untrimmed --match-read-wildcards --pair-filter=any -o res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz -p res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz res_3.2.2/1617285503.8445683_15869_03_subsample_vsearch.unassembled_R1.fastq res_3.2.2/1617285503.8445683_15869_03_subsample_vsearch.unassembled_R2.fastq > res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_log.txt 2> res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_err.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:58:31\n-\tend: 01 Apr 2021 15:58:35\n-\n-Results:\n-\tnb seq with 5\' primer : 25457\n-\tnb seq with 3\' primer : 25457\n-########################################################################################################\n-# Concatenate paired reads. (combine_and_split.py version : 1.0.0)\n-Command:\n-\tcombine_and_split.py --reads1 res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_trim_R1.fastq.gz --reads2 res_3.2.2/1617285503.8445683_15869_03_subsample_uncomb_cutadapt_paired_trim_R2.fastq.gz -c XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX --combined-output res_3.2.2/1617285503.8445683_15869_03_subsample_artificial_combined.fastq.gz\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:58:35\n-\tend: 01 Apr 2021 15:58:44\n-\n-########################################################################################################\n-# Filters amplicons without primers by length and N count. (filterSeq.py version : 1.6.0)\n-Command:\n-\tfilterSeq.py --force-fasta --max-N 0 --min-length 267 --input-file res_3.2.2/1617285503.8445683_15869_03_subsample_artificial_combined.fastq.gz --output-file res_3.2.2/1617285503.8445683_15869_03_subsample_art_N_filter.fasta --log-file res_3.2.2/1617285503.8445683_15869_03_subsample_art_N_filter_log.txt\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:58:44\n-\tend: 01 Apr 2021 15:58:44\n-\n-Results:\n-\tnb seq with expected length : 25457\n-\tnb seq without N : 25457\n-########################################################################################################\n-# Replace join tag. (combine_and_split.py version : 1.0.0)\n-Command:\n-\tcombine_and_split.py --reads1 res_3.2.2/1617285503.8445683_15869_03_subsample_art_N_filter.fasta -s XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -c NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --combined-output res_3.2.2/1617285503.8445683_15869_03_subsample_art_XtoN.fasta\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:58:45\n-\tend: 01 Apr 2021 15:58:46\n-\n-########################################################################################################\n-# Dereplicates sample sequences. (derepSamples.py version : 1.6.1)\n-Command:\n-\tderepSamples.py --sequences-files res_3.2.2/1617285503.8445683_15869_03_subsample_N_and_length_filter.fasta res_3.2.2/1617285503.8445683_15869_03_subsample_art_XtoN.fasta --dereplicated-file res_3.2.2/1617285475.3604712_15868_03_subsample_filtered.fasta --count-file res_3.2.2/1617285503.8445683_15869_03_subsample_derep_count.tsv\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:58:46\n-\tend: 01 Apr 2021 15:58:48\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 2 --size-separator \';size=\' --samples-ref res_3.2.2/1617285475.3604712_15868_derep_inputs.tsv --dereplicated-file res_3.2.2/01-prepro-vsearch.fasta --count-file res_3.2.2/01-prepro-vsearch.tsv\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:58:48\n-\tend: 01 Apr 2021 15:58:52\n-\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/02-clustering_denoising.biom --- a/test-data/references/02-clustering_denoising.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/02-clustering_denoising.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T16:00:42", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_22"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_103"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_94"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_108"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_60934"}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_13", "metadata": {"comment": [], "seed_id": "01_85419"}}, {"id": "Cluster_14", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_15", "metadata": {"comment": [], "seed_id": "01_66997"}}, {"id": "Cluster_16", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_17", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_18", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_96725"}}, {"id": "Cluster_20", "metadata": {"comment": [], "seed_id": "01_71661"}}, {"id": "Cluster_21", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_201"}}, {"id": "Cluster_23", "metadata": {"comment": [], "seed_id": "01_76"}}, {"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_10"}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_97506"}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_190"}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_30", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_31", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_155"}}, {"id": "Cluster_34", "metadata": {"comment": [], "seed_id": "01_54706"}}, {"id": "Cluster_35", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_51488"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_40"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_151"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_76743"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_54589"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_101"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_67"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_66"}}, {"id": "Cluster_48_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_50", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": 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"sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/02-clustering_denoising.log --- a/test-data/references/02-clustering_denoising.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,69 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/clustering.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/clustering.py --distance 3 --denoising --input-fasta res_3.2.2/01-prepro-vsearch.fasta --input-count res_3.2.2/01-prepro-vsearch.tsv --output-biom res_3.2.2/02-clustering_denoising.biom --output-fasta res_3.2.2/02-clustering_denoising.fasta --output-compo res_3.2.2/02-clustering_denoising_compo.tsv --log-file res_3.2.2/02-clustering_denoising.log --nb-cpus 2 - -######################################################################################################## -# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0) -Command: - sortAbundancies.py --size-separator ';size=' --input-file res_3.2.2/01-prepro-vsearch.fasta --output-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted.fasta - -Execution: - start: 01 Apr 2021 15:59:16 - end: 01 Apr 2021 15:59:19 - -repalce 100 N tags by 50A-50C in: res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted.fasta out : res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted_NtoA.fasta -######################################################################################################## -# Clustering sequences. (swarm version : 3.0.0) -Command: - swarm --differences 1 --threads 2 --log res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_log.txt --output-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_composition.txt res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted_NtoA.fasta - -Execution: - start: 01 Apr 2021 15:59:20 - end: 01 Apr 2021 15:59:22 - -######################################################################################################## -# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1) -Command: - extractSwarmsFasta.py --input-fasta res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_composition.txt --output-fasta res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_seeds.fasta - -Execution: - start: 01 Apr 2021 15:59:22 - end: 01 Apr 2021 15:59:24 - -######################################################################################################## -# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0) -Command: - sortAbundancies.py --size-separator '_' --input-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_resizedSeeds.fasta --output-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_sortedSeeds.fasta - -Execution: - start: 01 Apr 2021 15:59:26 - end: 01 Apr 2021 15:59:28 - -######################################################################################################## -# Clustering sequences. (swarm version : 3.0.0) -Command: - swarm --differences 3 --threads 2 --log res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_swarm_log.txt --output-file res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_swarmD3_composition.txt res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_sortedSeeds.fasta - -Execution: - start: 01 Apr 2021 15:59:28 - end: 01 Apr 2021 16:00:42 - -######################################################################################################## -# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0) -Command: - swarm2biom.py --clusters-file res_3.2.2/02-clustering_denoising_compo.tsv --count-file res_3.2.2/01-prepro-vsearch.tsv --output-file res_3.2.2/02-clustering_denoising.biom - -Execution: - start: 01 Apr 2021 16:00:42 - end: 01 Apr 2021 16:00:44 - -######################################################################################################## -# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1) -Command: - extractSwarmsFasta.py --input-fasta res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_denoising_sortedSeeds.fasta --input-swarms res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_swarmD3_composition.txt --output-fasta res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_final_seeds.fasta - -Execution: - start: 01 Apr 2021 16:00:45 - end: 01 Apr 2021 16:00:46 - -replace 50A-50C tags by N. in: res_3.2.2/1617285556.5923936_16017_01-prepro-vsearch_final_seeds.fasta out : res_3.2.2/02-clustering_denoising.fasta |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/02-clustering_fastidious.biom --- a/test-data/references/02-clustering_fastidious.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/02-clustering_fastidious.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
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newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/02-clustering_fastidious.log --- a/test-data/references/02-clustering_fastidious.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,42 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/clustering.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/clustering.py --distance 1 --fastidious --input-fasta res_3.2.2/01-prepro-vsearch.fasta --input-count res_3.2.2/01-prepro-vsearch.tsv --output-biom res_3.2.2/02-clustering_fastidious.biom --output-fasta res_3.2.2/02-clustering_fastidious.fasta --output-compo res_3.2.2/02-clustering_fastidious_compo.tsv --log-file res_3.2.2/02-clustering_fastidious.log --nb-cpus 2 - -######################################################################################################## -# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0) -Command: - sortAbundancies.py --size-separator ';size=' --input-file res_3.2.2/01-prepro-vsearch.fasta --output-file res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted.fasta - -Execution: - start: 01 Apr 2021 15:58:52 - end: 01 Apr 2021 15:58:55 - -repalce 100 N tags by 50A-50C in: res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted.fasta out : res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted_NtoA.fasta -######################################################################################################## -# Clustering sequences. (swarm version : 3.0.0) -Command: - swarm --differences 1 --fastidious --threads 2 --log res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_swarm_log.txt --output-file res_3.2.2/02-clustering_fastidious_compo.tsv res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted_NtoA.fasta - -Execution: - start: 01 Apr 2021 15:58:56 - end: 01 Apr 2021 15:59:10 - -######################################################################################################## -# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0) -Command: - swarm2biom.py --clusters-file res_3.2.2/02-clustering_fastidious_compo.tsv --count-file res_3.2.2/01-prepro-vsearch.tsv --output-file res_3.2.2/02-clustering_fastidious.biom - -Execution: - start: 01 Apr 2021 15:59:10 - end: 01 Apr 2021 15:59:13 - -######################################################################################################## -# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1) -Command: - extractSwarmsFasta.py --input-fasta res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res_3.2.2/02-clustering_fastidious_compo.tsv --output-fasta res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_final_seeds.fasta - -Execution: - start: 01 Apr 2021 15:59:13 - end: 01 Apr 2021 15:59:14 - -replace 50A-50C tags by N. in: res_3.2.2/1617285532.398339_15994_01-prepro-vsearch_final_seeds.fasta out : res_3.2.2/02-clustering_fastidious.fasta |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/03-chimera.biom --- a/test-data/references/03-chimera.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/03-chimera.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22"}}, {"id": "Cluster_13", "metadata": {"comment": [], "seed_id": "01_94"}}, {"id": "Cluster_14", "metadata": {"comment": [], "seed_id": "01_76"}}, {"id": "Cluster_15", "metadata": {"comment": [], "seed_id": "01_60934"}}, {"id": "Cluster_16", "metadata": {"comment": [], "seed_id": "01_85419"}}, {"id": "Cluster_17", "metadata": {"comment": [], "seed_id": "01_54589"}}, {"id": "Cluster_18", "metadata": {"comment": [], "seed_id": "01_40"}}, {"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_66"}}, {"id": "Cluster_20", "metadata": {"comment": [], "seed_id": "01_51488"}}, {"id": "Cluster_21", "metadata": {"comment": [], "seed_id": "01_54706"}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_155"}}, {"id": "Cluster_23", "metadata": {"comment": [], "seed_id": "01_101"}}, {"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_10"}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_97506"}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_151"}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_108"}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661"}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id": "01_201"}}, {"id": "Cluster_30", "metadata": {"comment": [], "seed_id": "01_66997"}}, {"id": "Cluster_31", "metadata": {"comment": [], "seed_id": "01_190"}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_96725"}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_103"}}, {"id": "Cluster_34", "metadata": {"comment": [], "seed_id": "01_67"}}, {"id": "Cluster_35", "metadata": {"comment": [], "seed_id": "01_76743"}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_48", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": {"comment": [], 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newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/03-chimera.html --- a/test-data/references/03-chimera.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/03-chimera.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Remove Chimera</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <!-- CSS --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/03-chimera.log --- a/test-data/references/03-chimera.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,49 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/remove_chimera.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/remove_chimera.py --input-fasta res_3.2.2/02-clustering_fastidious.fasta --input-biom res_3.2.2/02-clustering_fastidious.biom --non-chimera res_3.2.2/03-chimera.fasta --out-abundance res_3.2.2/03-chimera.biom --summary res_3.2.2/03-chimera.html --log-file res_3.2.2/03-chimera.log --nb-cpus 2 - -######################################################################################################## -# Removes PCR chimera by samples. (parallelChimera.py version : 0.7.2 [vsearch v2.17.0_linux_x86_64]) -Command: - parallelChimera.py --lenient-filter --nb-cpus 2 --sequences res_3.2.2/02-clustering_fastidious.fasta --biom res_3.2.2/02-clustering_fastidious.biom --non-chimera res_3.2.2/03-chimera.fasta --out-abundance res_3.2.2/03-chimera.biom --summary res_3.2.2/1617285647.872855_16058_03-chimera.fasta_summary.tsv --log-file res_3.2.2/1617285647.872855_16058_03-chimera.fasta_tmp.log - -Execution: - start: 01 Apr 2021 16:00:47 - end: 01 Apr 2021 16:02:01 - - - -##Sample : 01_subsample -## Vsearch command: vsearch --uchime_denovo res_3.2.2/1617285648.0228698_16063_01_subsample.fasta.tmp --nonchimeras res_3.2.2/1617285648.0228698_16063_01_subsample.fasta --uchimeout res_3.2.2/1617285648.0228698_16063_01_subsample.fasta.log -##Results -sample_name: 01_subsample -nb_chimera: 0 -chimera_abun: 0 -max_chimera_abun: 0 -nb_non_chimera: 25127 -non_chimera_abun: 50000 - -##Sample : 02_subsample -## Vsearch command: vsearch --uchime_denovo res_3.2.2/1617285648.0228698_16063_02_subsample.fasta.tmp --nonchimeras res_3.2.2/1617285648.0228698_16063_02_subsample.fasta --uchimeout res_3.2.2/1617285648.0228698_16063_02_subsample.fasta.log -##Results -sample_name: 02_subsample -nb_chimera: 1 -chimera_abun: 1 -max_chimera_abun: 1 -nb_non_chimera: 24947 -non_chimera_abun: 49999 - -##Sample : 03_subsample -## Vsearch command: vsearch --uchime_denovo res_3.2.2/1617285648.0228698_16063_03_subsample.fasta.tmp --nonchimeras res_3.2.2/1617285648.0228698_16063_03_subsample.fasta --uchimeout res_3.2.2/1617285648.0228698_16063_03_subsample.fasta.log -##Results -sample_name: 03_subsample -nb_chimera: 1 -chimera_abun: 1 -max_chimera_abun: 1 -nb_non_chimera: 24960 -non_chimera_abun: 49999 - - -## Removes the chimera observation from BIOM. - - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/04-filters.biom --- a/test-data/references/04-filters.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/04-filters.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22"}}, {"id": "Cluster_13", "metadata": {"comment": [], "seed_id": "01_94"}}, {"id": "Cluster_14", "metadata": {"comment": [], "seed_id": "01_76"}}, {"id": "Cluster_15", "metadata": {"comment": [], "seed_id": "01_60934"}}, {"id": "Cluster_16", "metadata": {"comment": [], "seed_id": "01_85419"}}, {"id": "Cluster_17", "metadata": {"comment": [], "seed_id": "01_54589"}}, {"id": "Cluster_18", "metadata": {"comment": [], "seed_id": "01_40"}}, {"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_66"}}, {"id": "Cluster_20", "metadata": {"comment": [], "seed_id": "01_51488"}}, {"id": "Cluster_21", "metadata": {"comment": [], "seed_id": "01_54706"}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_155"}}, {"id": "Cluster_23", "metadata": {"comment": [], "seed_id": "01_101"}}, {"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_10"}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_97506"}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_151"}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_108"}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661"}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id": "01_201"}}, {"id": "Cluster_30", "metadata": {"comment": [], "seed_id": "01_66997"}}, {"id": "Cluster_31", "metadata": {"comment": [], "seed_id": "01_190"}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_96725"}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_103"}}, {"id": "Cluster_34", "metadata": {"comment": [], "seed_id": "01_67"}}, {"id": "Cluster_35", "metadata": {"comment": [], "seed_id": "01_76743"}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_48", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": {"comment": [], "seed_id"'..b'er_36", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_48", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": {"comment": [], "seed_id": "01_1953"}}, {"id": "Cluster_53", "metadata": {"comment": [], "seed_id": "01_4641"}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904"}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609"}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 484], [7, 2, 513], [8, 0, 526], [8, 1, 494], [8, 2, 551], [9, 0, 511], [9, 1, 529], [9, 2, 479], [10, 0, 469], [10, 1, 520], [10, 2, 516], [11, 0, 542], [11, 1, 531], [11, 2, 537], [12, 0, 527], [12, 1, 543], [12, 2, 506], [13, 0, 495], [13, 1, 511], [13, 2, 528], [14, 0, 508], [14, 1, 527], [14, 2, 530], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 508], [16, 1, 504], [16, 2, 490], [17, 0, 490], [17, 1, 531], [17, 2, 495], [18, 0, 499], [18, 1, 490], [18, 2, 476], [19, 0, 526], [19, 1, 498], [19, 2, 494], [20, 0, 514], [20, 1, 507], [20, 2, 499], [21, 0, 504], [21, 1, 483], [21, 2, 536], [22, 0, 510], [22, 1, 472], [22, 2, 518], [23, 0, 515], [23, 1, 500], [23, 2, 515], [24, 0, 491], [24, 1, 506], [24, 2, 533], [25, 0, 494], [25, 1, 513], [25, 2, 509], [26, 0, 536], [26, 1, 490], [26, 2, 547], [27, 0, 545], [27, 1, 507], [27, 2, 493], [28, 0, 498], [28, 1, 515], [28, 2, 524], [29, 0, 525], [29, 1, 530], [29, 2, 510], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 509], [31, 1, 522], [31, 2, 515], [32, 0, 508], [32, 1, 544], [32, 2, 545], [33, 0, 480], [33, 1, 504], [33, 2, 515], [34, 0, 525], [34, 1, 499], [34, 2, 483], [35, 0, 536], [35, 1, 534], [35, 2, 521], [36, 0, 499], [36, 1, 538], [36, 2, 539], [37, 0, 473], [37, 1, 528], [37, 2, 524], [38, 0, 518], [38, 1, 508], [38, 2, 486], [39, 0, 534], [39, 1, 524], [39, 2, 514], [40, 0, 518], [40, 1, 517], [40, 2, 494], [41, 0, 540], [41, 1, 524], [41, 2, 516], [42, 0, 497], [42, 1, 505], [42, 2, 514], [43, 0, 511], [43, 1, 518], [43, 2, 502], [44, 0, 530], [44, 1, 513], [44, 2, 541], [45, 0, 507], [45, 1, 530], [45, 2, 498], [46, 0, 499], [46, 1, 513], [46, 2, 520], [47, 0, 177], [47, 1, 203], [47, 2, 164], [48, 0, 80], [48, 1, 83], [48, 2, 82], [49, 0, 526], [49, 1, 518], [49, 2, 553], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/04-filters.html --- a/test-data/references/04-filters.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/04-filters.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS OTU Filters</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/04-filters.log --- a/test-data/references/04-filters.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,26 +0,0 @@ -## Application -Software: otu_filters.py (version: 3.2.2) -Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/otu_filters.py --min-abundance 0.00005 --min-sample-presence 3 --contaminant data/phi.fa --nb-cpus 2 --input-biom res_3.2.2/03-chimera.biom --input-fasta res_3.2.2/03-chimera.fasta --output-fasta res_3.2.2/04-filters.fasta --output-biom res_3.2.2/04-filters.biom --excluded res_3.2.2/04-filters.excluded --summary res_3.2.2/04-filters.html --log-file res_3.2.2/04-filters.log - -######################################################################################################## -# Removes contaminant sequences. (removeConta.py version : 1.0) -Command: - removeConta.py --nb-cpus 2 --word-size 40 --min-identity 0.8 --min-coverage 0.8 --input-fasta res_3.2.2/03-chimera.fasta --contaminant-db data/phi.fa --input-biom res_3.2.2/03-chimera.biom --clean-fasta res_3.2.2/1617285721.9659483_16080_cleaned_sequences.fasta --clean-biom res_3.2.2/1617285721.9659483_16080_cleaned_abundance.biom --conta-fasta res_3.2.2/1617285721.9659483_16080_contaminated_sequences.fasta --log-file res_3.2.2/1617285721.9659483_16080_clean.log - -Execution: - start: 01 Apr 2021 16:02:05 - end: 01 Apr 2021 16:02:31 - -Results: - number of processed sequences: 74920 - 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_3.2.2/04-filters.biom --input-fasta res_3.2.2/03-chimera.fasta --output-file res_3.2.2/04-filters.fasta --log res_3.2.2/1617285721.9659483_16080_update_fasta_log.txt - -Execution: - start: 01 Apr 2021 16:02:32 - end: 01 Apr 2021 16:02:32 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/05-itsx.biom --- a/test-data/references/05-itsx.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/05-itsx.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22"}}, {"id": "Cluster_13", "metadata": {"comment": [], "seed_id": "01_94"}}, {"id": "Cluster_14", "metadata": {"comment": [], "seed_id": "01_76"}}, {"id": "Cluster_15", "metadata": {"comment": [], "seed_id": "01_60934"}}, {"id": "Cluster_16", "metadata": {"comment": [], "seed_id": "01_85419"}}, {"id": "Cluster_17", "metadata": {"comment": [], "seed_id": "01_54589"}}, {"id": "Cluster_18", "metadata": {"comment": [], "seed_id": "01_40"}}, {"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_66"}}, {"id": "Cluster_20", "metadata": {"comment": [], "seed_id": "01_51488"}}, {"id": "Cluster_21", "metadata": {"comment": [], "seed_id": "01_54706"}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_155"}}, {"id": "Cluster_23", "metadata": {"comment": [], "seed_id": "01_101"}}, {"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_10"}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_97506"}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_151"}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_108"}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661"}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id": "01_201"}}, {"id": "Cluster_30", "metadata": {"comment": [], "seed_id": "01_66997"}}, {"id": "Cluster_31", "metadata": {"comment": [], "seed_id": "01_190"}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_96725"}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_103"}}, {"id": "Cluster_34", "metadata": {"comment": [], "seed_id": "01_67"}}, {"id": "Cluster_35", "metadata": {"comment": [], "seed_id": "01_76743"}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_48", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": {"comment": [], "seed_id"'..b'er_36", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_48", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": {"comment": [], "seed_id": "01_1953"}}, {"id": "Cluster_53", "metadata": {"comment": [], "seed_id": "01_4641"}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904"}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609"}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 484], [7, 2, 513], [8, 0, 526], [8, 1, 494], [8, 2, 551], [9, 0, 511], [9, 1, 529], [9, 2, 479], [10, 0, 469], [10, 1, 520], [10, 2, 516], [11, 0, 542], [11, 1, 531], [11, 2, 537], [12, 0, 527], [12, 1, 543], [12, 2, 506], [13, 0, 495], [13, 1, 511], [13, 2, 528], [14, 0, 508], [14, 1, 527], [14, 2, 530], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 508], [16, 1, 504], [16, 2, 490], [17, 0, 490], [17, 1, 531], [17, 2, 495], [18, 0, 499], [18, 1, 490], [18, 2, 476], [19, 0, 526], [19, 1, 498], [19, 2, 494], [20, 0, 514], [20, 1, 507], [20, 2, 499], [21, 0, 504], [21, 1, 483], [21, 2, 536], [22, 0, 510], [22, 1, 472], [22, 2, 518], [23, 0, 515], [23, 1, 500], [23, 2, 515], [24, 0, 491], [24, 1, 506], [24, 2, 533], [25, 0, 494], [25, 1, 513], [25, 2, 509], [26, 0, 536], [26, 1, 490], [26, 2, 547], [27, 0, 545], [27, 1, 507], [27, 2, 493], [28, 0, 498], [28, 1, 515], [28, 2, 524], [29, 0, 525], [29, 1, 530], [29, 2, 510], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 509], [31, 1, 522], [31, 2, 515], [32, 0, 508], [32, 1, 544], [32, 2, 545], [33, 0, 480], [33, 1, 504], [33, 2, 515], [34, 0, 525], [34, 1, 499], [34, 2, 483], [35, 0, 536], [35, 1, 534], [35, 2, 521], [36, 0, 499], [36, 1, 538], [36, 2, 539], [37, 0, 473], [37, 1, 528], [37, 2, 524], [38, 0, 518], [38, 1, 508], [38, 2, 486], [39, 0, 534], [39, 1, 524], [39, 2, 514], [40, 0, 518], [40, 1, 517], [40, 2, 494], [41, 0, 540], [41, 1, 524], [41, 2, 516], [42, 0, 497], [42, 1, 505], [42, 2, 514], [43, 0, 511], [43, 1, 518], [43, 2, 502], [44, 0, 530], [44, 1, 513], [44, 2, 541], [45, 0, 507], [45, 1, 530], [45, 2, 498], [46, 0, 499], [46, 1, 513], [46, 2, 520], [47, 0, 177], [47, 1, 203], [47, 2, 164], [48, 0, 80], [48, 1, 83], [48, 2, 82], [49, 0, 526], [49, 1, 518], [49, 2, 553], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/05-itsx.html --- a/test-data/references/05-itsx.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/05-itsx.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS ITSx</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/05-itsx.log --- a/test-data/references/05-itsx.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,35 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/itsx.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/itsx.py --input-fasta res_3.2.2/04-filters.fasta --input-biom res_3.2.2/04-filters.biom --region ITS1 --nb-cpus 2 --out-abundance res_3.2.2/05-itsx.biom --summary res_3.2.2/05-itsx.html --log-file res_3.2.2/05-itsx.log --out-fasta res_3.2.2/05-itsx.fasta --out-removed res_3.2.2/05-itsx-excluded.fasta - -######################################################################################################## -# identifies ITS sequences and extracts the ITS region (parallelITSx.py version : 1.0.0 [ITSx 1.1.2]) -Command: - parallelITSx.py -f res_3.2.2/04-filters.fasta -b res_3.2.2/04-filters.biom --nb-cpus 2 --its ITS1 --organism-groups F -o res_3.2.2/05-itsx.fasta -m res_3.2.2/05-itsx-excluded.fasta -a res_3.2.2/05-itsx.biom --log-file res_3.2.2/1617285755.6009042_16135_ITSx.log - -Execution: - start: 01 Apr 2021 16:02:35 - end: 01 Apr 2021 16:02:43 - -Results: - -# split res_3.2.2/04-filters.fasta in 1 fasta files -Results - Wrote 55 records to res_3.2.2/1617285755.838389_16140_04-filters.fasta_0 - -## Input file : 1617285755.838389_16140_04-filters.fasta_0 -## in working directory: res_3.2.2/1617285755.838389_16140_1617285755.838389_16140_04-filters.fasta_0 -## ITSx command: ITSx -i /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285755.838389_16140_04-filters.fasta_0 -o 1617285755.838389_16140_04-filters --preserve T -t F --save_regions all -##Results - nb LSU (removed): 0 - nb 5_8S (removed): 0 - nb SSU (removed): 1 - nb full (removed): 0 - nb no_detections (removed): 0 - nb ITS2 (removed): 0 - nb ITS1 (kept): 55 - - -## Removes the observations after ITSx. - - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/06-affiliation.biom --- a/test-data/references/06-affiliation.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/06-affiliation.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54", "blast_affiliations": [{"subject": "JF747094_SH197643.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546", "blast_affiliations": [{"subject": "DQ898183_SH216206.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59", "blast_affiliations": [{"subject": "JN711441_SH022548.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "evalue": "8.06e-132", "aln_length": 248, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81", "blast_affiliations": [{"subject": "AF456924_SH097201.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "evalue": "4.90e-134", "aln_length": 252, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25", "blast_affiliations": [{"subject": "JX399009_SH268556.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed'..b' 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904", "blast_affiliations": [{"subject": "UDB016470_SH189377.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "evalue": "1.70e-128", "aln_length": 242, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609", "blast_affiliations": [{"subject": "UDB011541_SH194446.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "evalue": "6.09e-128", "aln_length": 241, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 484], [7, 2, 513], [8, 0, 526], [8, 1, 494], [8, 2, 551], [9, 0, 511], [9, 1, 529], [9, 2, 479], [10, 0, 469], [10, 1, 520], [10, 2, 516], [11, 0, 542], [11, 1, 531], [11, 2, 537], [12, 0, 527], [12, 1, 543], [12, 2, 506], [13, 0, 495], [13, 1, 511], [13, 2, 528], [14, 0, 508], [14, 1, 527], [14, 2, 530], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 508], [16, 1, 504], [16, 2, 490], [17, 0, 490], [17, 1, 531], [17, 2, 495], [18, 0, 499], [18, 1, 490], [18, 2, 476], [19, 0, 526], [19, 1, 498], [19, 2, 494], [20, 0, 514], [20, 1, 507], [20, 2, 499], [21, 0, 504], [21, 1, 483], [21, 2, 536], [22, 0, 510], [22, 1, 472], [22, 2, 518], [23, 0, 515], [23, 1, 500], [23, 2, 515], [24, 0, 491], [24, 1, 506], [24, 2, 533], [25, 0, 494], [25, 1, 513], [25, 2, 509], [26, 0, 536], [26, 1, 490], [26, 2, 547], [27, 0, 545], [27, 1, 507], [27, 2, 493], [28, 0, 498], [28, 1, 515], [28, 2, 524], [29, 0, 525], [29, 1, 530], [29, 2, 510], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 509], [31, 1, 522], [31, 2, 515], [32, 0, 508], [32, 1, 544], [32, 2, 545], [33, 0, 480], [33, 1, 504], [33, 2, 515], [34, 0, 525], [34, 1, 499], [34, 2, 483], [35, 0, 536], [35, 1, 534], [35, 2, 521], [36, 0, 499], [36, 1, 538], [36, 2, 539], [37, 0, 473], [37, 1, 528], [37, 2, 524], [38, 0, 518], [38, 1, 508], [38, 2, 486], [39, 0, 534], [39, 1, 524], [39, 2, 514], [40, 0, 518], [40, 1, 517], [40, 2, 494], [41, 0, 540], [41, 1, 524], [41, 2, 516], [42, 0, 497], [42, 1, 505], [42, 2, 514], [43, 0, 511], [43, 1, 518], [43, 2, 502], [44, 0, 530], [44, 1, 513], [44, 2, 541], [45, 0, 507], [45, 1, 530], [45, 2, 498], [46, 0, 499], [46, 1, 513], [46, 2, 520], [47, 0, 177], [47, 1, 203], [47, 2, 164], [48, 0, 80], [48, 1, 83], [48, 2, 82], [49, 0, 526], [49, 1, 518], [49, 2, 553], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/06-affiliation.html --- a/test-data/references/06-affiliation.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/06-affiliation.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <!-- CSS --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/06-affiliation.log --- a/test-data/references/06-affiliation.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,106 +0,0 @@ -## Application -Software: affiliation_OTU.py (version: 3.2.2) -Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_OTU.py --reference data/ITS1.rdp.fasta --input-fasta res_3.2.2/04-filters.fasta --input-biom res_3.2.2/04-filters.biom --output-biom res_3.2.2/06-affiliation.biom --summary res_3.2.2/06-affiliation.html --log-file res_3.2.2/06-affiliation.log --nb-cpus 2 --java-mem 2 --rdp - -Nb seq : 55 - with nb seq artificially combined :1 - -######################################################################################################## -# split res_3.2.2/04-filters.fasta in smaller fasta files -Results - Wrote 55 records to res_3.2.2/1617285763.8139765_17240_04-filters.fasta_0 -######################################################################################################## -# Split on tag. (combine_and_split.py version : 1.0.0) -Command: - combine_and_split.py --reads1 res_3.2.2/1617285763.8139765_17240_04-filters.fasta_FROGS_combined -s NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --split-output1 res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R1.fasta --split-output2 res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R2.fasta - -Execution: - start: 01 Apr 2021 16:02:46 - end: 01 Apr 2021 16:02:46 - -######################################################################################################## -# blast taxonomic affiliation (blastn version : 2.10.1+) -Command: - blastn -num_threads 2 -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_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R1.fasta -out res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R1.fasta.blast -db data/ITS1.rdp.fasta - -Execution: - start: 01 Apr 2021 16:02:46 - end: 01 Apr 2021 16:02:46 - -######################################################################################################## -# blast taxonomic affiliation (blastn version : 2.10.1+) -Command: - blastn -num_threads 2 -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_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R2.fasta -out res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R2.fasta.blast -db data/ITS1.rdp.fasta - -Execution: - start: 01 Apr 2021 16:02:46 - end: 01 Apr 2021 16:02:46 - -######################################################################################################## -# Reduced reference fasta file based on R1 and R2 100 best score blast alignment (reduce_ref_for_needleall.py version : 1.0) -Command: - reduce_ref_for_needleall.py -r data/ITS1.rdp.fasta --query-blast-R1 res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R1.fasta.blast --query-blast-R2 res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_R2.fasta.blast -f res_3.2.2/1617285763.8139765_17240_reduced_ITS1.rdp.fasta -l res_3.2.2/1617285763.8139765_17240_reduced_ITS1.rdp.fasta.log - -Execution: - start: 01 Apr 2021 16:02:46 - end: 01 Apr 2021 16:02:46 - - # Parsing blast alignment results to reduce reference databse - Reducing reference databases from 102 to 32 sequences - - -######################################################################################################## -# split res_3.2.2/1617285763.8139765_17240_04-filters.fasta_FROGS_combined in smaller fasta files -Results - Generate -1 fasta files of 10 reads - Generate 1 fasta file of 1 reads - -######################################################################################################## -# rdp taxonomic affiliation (classifier.jar version : unknown) -Command: - java -Xmx2g -jar /home/maria/miniconda3/envs/frogs@3.2.2/bin/classifier.jar classify -c 0.0 -t data/ITS1.rdp.fasta.properties -o res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_0.rdp res_3.2.2/1617285763.8139765_17240_04-filters.fasta_0 - -Execution: - start: 01 Apr 2021 16:02:43 - end: 01 Apr 2021 16:02:46 - - -######################################################################################################## -# Perform global alignment (needleall version : EMBOSS:6.6.0.0) -Command: - needleall -asequence res_3.2.2/1617285763.8139765_17240_reduced_ITS1.rdp.fasta -bsequence res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0 -outfile res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.sam -aformat3 sam -gapopen 10.0 -gapextend 0.5 -errfile res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.log - -Execution: - start: 01 Apr 2021 16:02:47 - end: 01 Apr 2021 16:02:47 - -######################################################################################################## -# convert NeedleAll Sam output in blast like tsv output sorted by bitscore (needleallSam_to_tsv.py version : 1.0.0) -Command: - needleallSam_to_tsv.py -n res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.sam -r res_3.2.2/1617285763.8139765_17240_reduced_ITS1.rdp.fasta -b res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.blast_like - -Execution: - start: 01 Apr 2021 16:02:47 - end: 01 Apr 2021 16:02:47 - - -######################################################################################################## -# blast taxonomic affiliation (blastn version : 2.10.1+) -Command: - blastn -num_threads 2 -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_3.2.2/1617285763.8139765_17240_04-filters.fasta_FROGS_full_length -out res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_full_length.blast -db data/ITS1.rdp.fasta - -Execution: - start: 01 Apr 2021 16:02:47 - end: 01 Apr 2021 16:02:47 - - - -######################################################################################################## -# Add Blast and/or RDP affiliation to biom (addAffiliation2biom.py version : 2.3.0) -Command: - addAffiliation2biom.py -f data/ITS1.rdp.fasta -i res_3.2.2/04-filters.biom -o res_3.2.2/06-affiliation.biom -b res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_full_length.blast res_3.2.2/_1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_FROGS_combined_0.needleall.blast_like -r res_3.2.2/1617285763.8139765_17240_1617285763.8139765_17240_04-filters.fasta_0.rdp - -Execution: - start: 01 Apr 2021 16:02:48 - end: 01 Apr 2021 16:02:48 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/06-affiliation2.biom --- a/test-data/references/06-affiliation2.biom Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2021-04-01T15:59:10", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54", "blast_affiliations": [{"subject": "JF747094_SH197643.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"]}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546", "blast_affiliations": [{"subject": "DQ898183_SH216206.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"]}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59", "blast_affiliations": [{"subject": "JN711441_SH022548.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "evalue": "8.06e-132", "aln_length": 248, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"]}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81", "blast_affiliations": [{"subject": "AF456924_SH097201.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "evalue": "4.90e-134", "aln_length": 252, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"]}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_25", "blast_affiliations": [{"subject": "JX399009_SH268556.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"]}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803", "blast_affiliations": [{"subject": "KM668101_SH491630.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "evalue": "3.94e-140", "aln_length": 263, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"]}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_38", "blast_affiliations": [{"subject": "JF417478_SH216679.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "evalue": "1.75e-133", "aln_length": 251, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"]}}, {"id": "'..b'SH177722.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rhododendri"], "evalue": "1.70e-128", "aln_length": 242, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rhododendri"]}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904", "blast_affiliations": [{"subject": "UDB016470_SH189377.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "evalue": "1.70e-128", "aln_length": 242, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"]}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609", "blast_affiliations": [{"subject": "UDB011541_SH194446.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "evalue": "6.09e-128", "aln_length": 241, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 484], [7, 2, 513], [8, 0, 526], [8, 1, 494], [8, 2, 551], [9, 0, 511], [9, 1, 529], [9, 2, 479], [10, 0, 469], [10, 1, 520], [10, 2, 516], [11, 0, 542], [11, 1, 531], [11, 2, 537], [12, 0, 527], [12, 1, 543], [12, 2, 506], [13, 0, 495], [13, 1, 511], [13, 2, 528], [14, 0, 508], [14, 1, 527], [14, 2, 530], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 508], [16, 1, 504], [16, 2, 490], [17, 0, 490], [17, 1, 531], [17, 2, 495], [18, 0, 499], [18, 1, 490], [18, 2, 476], [19, 0, 526], [19, 1, 498], [19, 2, 494], [20, 0, 514], [20, 1, 507], [20, 2, 499], [21, 0, 504], [21, 1, 483], [21, 2, 536], [22, 0, 510], [22, 1, 472], [22, 2, 518], [23, 0, 515], [23, 1, 500], [23, 2, 515], [24, 0, 491], [24, 1, 506], [24, 2, 533], [25, 0, 494], [25, 1, 513], [25, 2, 509], [26, 0, 536], [26, 1, 490], [26, 2, 547], [27, 0, 545], [27, 1, 507], [27, 2, 493], [28, 0, 498], [28, 1, 515], [28, 2, 524], [29, 0, 525], [29, 1, 530], [29, 2, 510], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 509], [31, 1, 522], [31, 2, 515], [32, 0, 508], [32, 1, 544], [32, 2, 545], [33, 0, 480], [33, 1, 504], [33, 2, 515], [34, 0, 525], [34, 1, 499], [34, 2, 483], [35, 0, 536], [35, 1, 534], [35, 2, 521], [36, 0, 499], [36, 1, 538], [36, 2, 539], [37, 0, 473], [37, 1, 528], [37, 2, 524], [38, 0, 518], [38, 1, 508], [38, 2, 486], [39, 0, 534], [39, 1, 524], [39, 2, 514], [40, 0, 518], [40, 1, 517], [40, 2, 494], [41, 0, 540], [41, 1, 524], [41, 2, 516], [42, 0, 497], [42, 1, 505], [42, 2, 514], [43, 0, 511], [43, 1, 518], [43, 2, 502], [44, 0, 530], [44, 1, 513], [44, 2, 541], [45, 0, 507], [45, 1, 530], [45, 2, 498], [46, 0, 499], [46, 1, 513], [46, 2, 520], [47, 0, 177], [47, 1, 203], [47, 2, 164], [48, 0, 80], [48, 1, 83], [48, 2, 82], [49, 0, 526], [49, 1, 518], [49, 2, 553], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/06-affiliation2.html --- a/test-data/references/06-affiliation2.html Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,548 +0,0 @@\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="3.2.2">\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' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/06-affiliation2.log --- a/test-data/references/06-affiliation2.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,92 +0,0 @@ -## Application -Software: affiliation_OTU.py (version: 3.2.2) -Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_OTU.py --reference data/ITS1.rdp.fasta --input-fasta res_3.2.2/04-filters.fasta --input-biom res_3.2.2/04-filters.biom --output-biom res_3.2.2/06-affiliation2.biom --summary res_3.2.2/06-affiliation2.html --log-file res_3.2.2/06-affiliation2.log --nb-cpus 2 --java-mem 2 - -Nb seq : 55 - with nb seq artificially combined :1 - -######################################################################################################## -# Split on tag. (combine_and_split.py version : 1.0.0) -Command: - combine_and_split.py --reads1 res_3.2.2/1617285768.1955829_17320_04-filters.fasta_FROGS_combined -s NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --split-output1 res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R1.fasta --split-output2 res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R2.fasta - -Execution: - start: 01 Apr 2021 16:02:48 - end: 01 Apr 2021 16:02:48 - -######################################################################################################## -# blast taxonomic affiliation (blastn version : 2.10.1+) -Command: - blastn -num_threads 2 -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_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R1.fasta -out res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R1.fasta.blast -db data/ITS1.rdp.fasta - -Execution: - start: 01 Apr 2021 16:02:48 - end: 01 Apr 2021 16:02:48 - -######################################################################################################## -# blast taxonomic affiliation (blastn version : 2.10.1+) -Command: - blastn -num_threads 2 -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_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R2.fasta -out res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R2.fasta.blast -db data/ITS1.rdp.fasta - -Execution: - start: 01 Apr 2021 16:02:48 - end: 01 Apr 2021 16:02:48 - -######################################################################################################## -# Reduced reference fasta file based on R1 and R2 100 best score blast alignment (reduce_ref_for_needleall.py version : 1.0) -Command: - reduce_ref_for_needleall.py -r data/ITS1.rdp.fasta --query-blast-R1 res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R1.fasta.blast --query-blast-R2 res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_R2.fasta.blast -f res_3.2.2/1617285768.1955829_17320_reduced_ITS1.rdp.fasta -l res_3.2.2/1617285768.1955829_17320_reduced_ITS1.rdp.fasta.log - -Execution: - start: 01 Apr 2021 16:02:48 - end: 01 Apr 2021 16:02:48 - - # Parsing blast alignment results to reduce reference databse - Reducing reference databases from 102 to 32 sequences - - -######################################################################################################## -# split res_3.2.2/1617285768.1955829_17320_04-filters.fasta_FROGS_combined in smaller fasta files -Results - Generate -1 fasta files of 10 reads - Generate 1 fasta file of 1 reads - -######################################################################################################## -# Perform global alignment (needleall version : EMBOSS:6.6.0.0) -Command: - needleall -asequence res_3.2.2/1617285768.1955829_17320_reduced_ITS1.rdp.fasta -bsequence res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0 -outfile res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.sam -aformat3 sam -gapopen 10.0 -gapextend 0.5 -errfile res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.log - -Execution: - start: 01 Apr 2021 16:02:48 - end: 01 Apr 2021 16:02:48 - -######################################################################################################## -# convert NeedleAll Sam output in blast like tsv output sorted by bitscore (needleallSam_to_tsv.py version : 1.0.0) -Command: - needleallSam_to_tsv.py -n res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.sam -r res_3.2.2/1617285768.1955829_17320_reduced_ITS1.rdp.fasta -b res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.blast_like - -Execution: - start: 01 Apr 2021 16:02:49 - end: 01 Apr 2021 16:02:49 - - -######################################################################################################## -# blast taxonomic affiliation (blastn version : 2.10.1+) -Command: - blastn -num_threads 2 -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_3.2.2/1617285768.1955829_17320_04-filters.fasta_FROGS_full_length -out res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_full_length.blast -db data/ITS1.rdp.fasta - -Execution: - start: 01 Apr 2021 16:02:49 - end: 01 Apr 2021 16:02:49 - - - -######################################################################################################## -# Add Blast and/or RDP affiliation to biom (addAffiliation2biom.py version : 2.3.0) -Command: - addAffiliation2biom.py -f data/ITS1.rdp.fasta -i res_3.2.2/04-filters.biom -o res_3.2.2/06-affiliation2.biom -b res_3.2.2/1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_full_length.blast res_3.2.2/_1617285768.1955829_17320_1617285768.1955829_17320_04-filters.fasta_FROGS_combined_0.needleall.blast_like - -Execution: - start: 01 Apr 2021 16:02:49 - end: 01 Apr 2021 16:02:49 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/07-affiliation_deleted.biom --- a/test-data/references/07-affiliation_deleted.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/07-affiliation_deleted.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "FROGS_affiliation_filters", "date": "2021-04-01T16:02:50", "rows": [{"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_10", "blast_affiliations": [{"subject": "UDB003291_SH182302.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "evalue": "7.05e-153", "aln_length": 286, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_97506", "blast_affiliations": [{"subject": "KC992854_SH220410.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "evalue": "2.53e-152", "aln_length": 285, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_151", "blast_affiliations": [{"subject": "JX179268_SH178540.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "evalue": "2.53e-152", "aln_length": 285, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_108", "blast_affiliations": [{"subject": "KF732310_SH222414.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "evalue": "5.49e-154", "aln_length": 288, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661", "blast_affiliations": [{"subject": "UDB001581_SH219736.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "evalue": "1.97e-153", "aln_length": 287, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id"'..b'idiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485", "blast_affiliations": [{"subject": "JQ716403_SH219241.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "evalue": "7.94e-178", "aln_length": 331, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410", "blast_affiliations": [{"subject": "EU623745_SH215851.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "evalue": "0.0", "aln_length": 390, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined", "blast_affiliations": [{"subject": "JF419897_SH181470.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "evalue": "-1", "aln_length": 1017, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 515], [0, 1, 500], [0, 2, 515], [1, 0, 491], [1, 1, 506], [1, 2, 533], [2, 0, 494], [2, 1, 513], [2, 2, 509], [3, 0, 536], [3, 1, 490], [3, 2, 547], [4, 0, 545], [4, 1, 507], [4, 2, 493], [5, 0, 498], [5, 1, 515], [5, 2, 524], [6, 0, 525], [6, 1, 530], [6, 2, 510], [7, 0, 511], [7, 1, 550], [7, 2, 469], [8, 0, 509], [8, 1, 522], [8, 2, 515], [9, 0, 508], [9, 1, 544], [9, 2, 545], [10, 0, 480], [10, 1, 504], [10, 2, 515], [11, 0, 525], [11, 1, 499], [11, 2, 483], [12, 0, 536], [12, 1, 534], [12, 2, 521], [13, 0, 499], [13, 1, 538], [13, 2, 539], [14, 0, 473], [14, 1, 528], [14, 2, 524], [15, 0, 518], [15, 1, 508], [15, 2, 486], [16, 0, 534], [16, 1, 524], [16, 2, 514], [17, 0, 518], [17, 1, 517], [17, 2, 494], [18, 0, 540], [18, 1, 524], [18, 2, 516], [19, 0, 497], [19, 1, 505], [19, 2, 514], [20, 0, 511], [20, 1, 518], [20, 2, 502], [21, 0, 530], [21, 1, 513], [21, 2, 541], [22, 0, 507], [22, 1, 530], [22, 2, 498], [23, 0, 499], [23, 1, 513], [23, 2, 520], [24, 0, 526], [24, 1, 518], [24, 2, 553]], "shape": [25, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/07-affiliation_deleted.html --- a/test-data/references/07-affiliation_deleted.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/07-affiliation_deleted.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation Filters</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/07-affiliation_filter_delMode.log --- a/test-data/references/07-affiliation_filter_delMode.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,26 +0,0 @@ -## Application -Software: affiliation_filters.py (version: 3.2.2) -Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_filters.py --input-biom res_3.2.2/06-affiliation.biom --input-fasta res_3.2.2/04-filters.fasta --output-biom res_3.2.2/07-affiliation_deleted.biom --output-fasta res_3.2.2/07-affiliation_deleted.fasta --summary res_3.2.2/07-affiliation_deleted.html --impacted res_3.2.2/07-impacted_OTU_deleted.tsv --impacted-multihit res_3.2.2/07-impacted_OTU_deleted_multihit.tsv --log-file res_3.2.2/07-affiliation_filter_delMode.log --min-rdp-bootstrap Species:0.8 --min-blast-length 150 --min-blast-identity 1.0 --min-blast-coverage 1.0 --max-blast-evalue 1e-150 --ignore-blast-taxa "g__Sarcodon" "s__Trichoderma" --delete --taxonomic-ranks Domain Phylum Class Order Family Genus Species - -Identify OTU with : - - Blast evalue > 1e-150 : 30 - - Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma : 6 - - Blast identity < 1.0 : 1 -######################################################################################################## -# Convert a biom file into tsv file (biom_to_tsv.py version : 3.2.2) -Command: - biom_to_tsv.py --input-biom res_3.2.2/1617285770.1797566_17379_impacted.biom --input-fasta res_3.2.2/04-filters.fasta --output-tsv res_3.2.2/07-impacted_OTU_deleted.tsv --output-multi-affi res_3.2.2/07-impacted_OTU_deleted_multihit.tsv --log-file res_3.2.2/1617285770.1797566_17379_impacted.biom2tsv.log - -Execution: - start: 01 Apr 2021 16:02:50 - end: 01 Apr 2021 16:02:50 - -######################################################################################################## -# Updates fasta file based on sequence in biom file. (biomFastaUpdate.py version : 1.0.1) -Command: - biomFastaUpdate.py --input-biom res_3.2.2/07-affiliation_deleted.biom --input-fasta res_3.2.2/04-filters.fasta --output-file res_3.2.2/07-affiliation_deleted.fasta --log res_3.2.2/1617285770.1797566_17379_update_fasta_log.txt - -Execution: - start: 01 Apr 2021 16:02:50 - end: 01 Apr 2021 16:02:50 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/07-affiliation_filter_maskMode.log --- a/test-data/references/07-affiliation_filter_maskMode.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,17 +0,0 @@ -## Application -Software: affiliation_filters.py (version: 3.2.2) -Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_filters.py --input-biom res_3.2.2/06-affiliation.biom --input-fasta res_3.2.2/04-filters.fasta --output-biom res_3.2.2/07-affiliation_masked.biom --summary res_3.2.2/07-affiliation_masked.html --impacted res_3.2.2/07-impacted_OTU_masked.tsv --impacted-multihit res_3.2.2/07-impacted_OTU_masked_multihit.tsv --log-file res_3.2.2/07-affiliation_filter_maskMode.log --min-rdp-bootstrap Species:0.8 --min-blast-length 150 --min-blast-identity 1.0 --min-blast-coverage 1.0 --max-blast-evalue 1e-150 --ignore-blast-taxa "g__Sarcodon" "s__Trichoderma" --mask --taxonomic-ranks Domain Phylum Class Order Family Genus Species - -Identify OTU with : - - Blast evalue > 1e-150 : 30 - - Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma : 6 - - Blast identity < 1.0 : 1 -######################################################################################################## -# Convert a biom file into tsv file (biom_to_tsv.py version : 3.2.2) -Command: - biom_to_tsv.py --input-biom res_3.2.2/1617285769.6536694_17365_impacted.biom --input-fasta res_3.2.2/04-filters.fasta --output-tsv res_3.2.2/07-impacted_OTU_masked.tsv --output-multi-affi res_3.2.2/07-impacted_OTU_masked_multihit.tsv --log-file res_3.2.2/1617285769.6536694_17365_impacted.biom2tsv.log - -Execution: - start: 01 Apr 2021 16:02:49 - end: 01 Apr 2021 16:02:50 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/07-affiliation_masked.biom --- a/test-data/references/07-affiliation_masked.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/07-affiliation_masked.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "FROGS_affiliation_filters", "date": "2021-04-01T16:02:49", "rows": [{"id": "Cluster_1", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_54", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_2", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_92546", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_3", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_59", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_4", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_81", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_5", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_25", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_6", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_74803", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_7", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_38", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_8", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_90", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Suillaceae", "g__Truncocolumella", "s__Truncocolumella_rubra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_9", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_97858", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_mienum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_10", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_259", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_cyathuliformis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.99]}}, {"id": "Cluster_11", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_90304", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__A'..b'dp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_52", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_1953", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_53", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_4641", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rhododendri"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_54", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_3904", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_55", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_67609", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 484], [7, 2, 513], [8, 0, 526], [8, 1, 494], [8, 2, 551], [9, 0, 511], [9, 1, 529], [9, 2, 479], [10, 0, 469], [10, 1, 520], [10, 2, 516], [11, 0, 542], [11, 1, 531], [11, 2, 537], [12, 0, 527], [12, 1, 543], [12, 2, 506], [13, 0, 495], [13, 1, 511], [13, 2, 528], [14, 0, 508], [14, 1, 527], [14, 2, 530], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 508], [16, 1, 504], [16, 2, 490], [17, 0, 490], [17, 1, 531], [17, 2, 495], [18, 0, 499], [18, 1, 490], [18, 2, 476], [19, 0, 526], [19, 1, 498], [19, 2, 494], [20, 0, 514], [20, 1, 507], [20, 2, 499], [21, 0, 504], [21, 1, 483], [21, 2, 536], [22, 0, 510], [22, 1, 472], [22, 2, 518], [23, 0, 515], [23, 1, 500], [23, 2, 515], [24, 0, 491], [24, 1, 506], [24, 2, 533], [25, 0, 494], [25, 1, 513], [25, 2, 509], [26, 0, 536], [26, 1, 490], [26, 2, 547], [27, 0, 545], [27, 1, 507], [27, 2, 493], [28, 0, 498], [28, 1, 515], [28, 2, 524], [29, 0, 525], [29, 1, 530], [29, 2, 510], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 509], [31, 1, 522], [31, 2, 515], [32, 0, 508], [32, 1, 544], [32, 2, 545], [33, 0, 480], [33, 1, 504], [33, 2, 515], [34, 0, 525], [34, 1, 499], [34, 2, 483], [35, 0, 536], [35, 1, 534], [35, 2, 521], [36, 0, 499], [36, 1, 538], [36, 2, 539], [37, 0, 473], [37, 1, 528], [37, 2, 524], [38, 0, 518], [38, 1, 508], [38, 2, 486], [39, 0, 534], [39, 1, 524], [39, 2, 514], [40, 0, 518], [40, 1, 517], [40, 2, 494], [41, 0, 540], [41, 1, 524], [41, 2, 516], [42, 0, 497], [42, 1, 505], [42, 2, 514], [43, 0, 511], [43, 1, 518], [43, 2, 502], [44, 0, 530], [44, 1, 513], [44, 2, 541], [45, 0, 507], [45, 1, 530], [45, 2, 498], [46, 0, 499], [46, 1, 513], [46, 2, 520], [47, 0, 177], [47, 1, 203], [47, 2, 164], [48, 0, 80], [48, 1, 83], [48, 2, 82], [49, 0, 526], [49, 1, 518], [49, 2, 553], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/07-affiliation_masked.html --- a/test-data/references/07-affiliation_masked.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/07-affiliation_masked.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation Filters</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/08-affiliation_postprocessed.biom --- a/test-data/references/08-affiliation_postprocessed.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/08-affiliation_postprocessed.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "FROGS_aggregate_affiliated_otu", "date": "2021-04-01T16:02:51", "rows": [{"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_74803", "blast_affiliations": [{"subject": "KM668101_SH491630.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "evalue": "3.94e-140", "aln_length": 263, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22", "blast_affiliations": [{"subject": "JX118731_SH218995.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "evalue": "5.20e-144", "aln_length": 270, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_103", "blast_affiliations": [{"subject": "HG007976_SH219743.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Pholiota", "s__Pholiota_highlandensis"], "evalue": "1.22e-160", "aln_length": 300, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Pholiota", "s__Pholiota_highlandensis"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Pholiota", "s__Pholiota_highlandensis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined", "blast_affiliations": [{"subject": "JF419897_SH181470.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "evalue": "-1", "aln_length": 1017, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222", "blast_affiliations": [{"subject": "UDB002317_SH221025.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "evalue": "9.52e-162", "aln_length": 302, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_boots'..b' 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_54", "metadata": {"comment": [], "seed_id": "01_3904", "blast_affiliations": [{"subject": "UDB016470_SH189377.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "evalue": "1.70e-128", "aln_length": 242, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_55", "metadata": {"comment": [], "seed_id": "01_67609", "blast_affiliations": [{"subject": "UDB011541_SH194446.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "evalue": "6.09e-128", "aln_length": 241, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 574], [0, 2, 545], [1, 0, 542], [1, 1, 531], [1, 2, 537], [2, 0, 508], [2, 1, 544], [2, 2, 545], [3, 0, 526], [3, 1, 518], [3, 2, 553], [4, 0, 536], [4, 1, 534], [4, 2, 521], [5, 0, 530], [5, 1, 513], [5, 2, 541], [6, 0, 540], [6, 1, 524], [6, 2, 516], [7, 0, 527], [7, 1, 543], [7, 2, 506], [8, 0, 499], [8, 1, 538], [8, 2, 539], [9, 0, 536], [9, 1, 490], [9, 2, 547], [10, 0, 534], [10, 1, 524], [10, 2, 514], [11, 0, 526], [11, 1, 494], [11, 2, 551], [12, 0, 508], [12, 1, 527], [12, 2, 530], [13, 0, 525], [13, 1, 530], [13, 2, 510], [14, 0, 503], [14, 1, 515], [14, 2, 546], [15, 0, 535], [15, 1, 512], [15, 2, 517], [16, 0, 512], [16, 1, 515], [16, 2, 534], [17, 0, 508], [17, 1, 512], [17, 2, 536], [18, 0, 514], [18, 1, 502], [18, 2, 534], [19, 0, 509], [19, 1, 522], [19, 2, 515], [20, 0, 545], [20, 1, 507], [20, 2, 493], [21, 0, 521], [21, 1, 550], [21, 2, 473], [22, 0, 498], [22, 1, 515], [22, 2, 524], [23, 0, 507], [23, 1, 530], [23, 2, 498], [24, 0, 495], [24, 1, 511], [24, 2, 528], [25, 0, 509], [25, 1, 492], [25, 2, 532], [26, 0, 499], [26, 1, 513], [26, 2, 520], [27, 0, 511], [27, 1, 518], [27, 2, 502], [28, 0, 515], [28, 1, 500], [28, 2, 515], [29, 0, 491], [29, 1, 506], [29, 2, 533], [30, 0, 511], [30, 1, 550], [30, 2, 469], [31, 0, 518], [31, 1, 517], [31, 2, 494], [32, 0, 473], [32, 1, 528], [32, 2, 524], [33, 0, 526], [33, 1, 484], [33, 2, 513], [34, 0, 504], [34, 1, 483], [34, 2, 536], [35, 0, 514], [35, 1, 507], [35, 2, 499], [36, 0, 511], [36, 1, 529], [36, 2, 479], [37, 0, 526], [37, 1, 498], [37, 2, 494], [38, 0, 490], [38, 1, 531], [38, 2, 495], [39, 0, 494], [39, 1, 513], [39, 2, 509], [40, 0, 497], [40, 1, 505], [40, 2, 514], [41, 0, 518], [41, 1, 508], [41, 2, 486], [42, 0, 525], [42, 1, 499], [42, 2, 483], [43, 0, 469], [43, 1, 520], [43, 2, 516], [44, 0, 508], [44, 1, 504], [44, 2, 490], [45, 0, 510], [45, 1, 472], [45, 2, 518], [46, 0, 480], [46, 1, 504], [46, 2, 515], [47, 0, 499], [47, 1, 490], [47, 2, 476], [48, 0, 177], [48, 1, 203], [48, 2, 164], [49, 0, 80], [49, 1, 83], [49, 2, 82], [50, 0, 22], [50, 1, 28], [50, 2, 33], [51, 0, 26], [51, 1, 16], [51, 2, 17], [52, 0, 17], [52, 1, 12], [52, 2, 16], [53, 0, 9], [53, 1, 13], [53, 2, 15], [54, 0, 2], [54, 1, 6], [54, 2, 2]], "shape": [55, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/08-affiliation_postprocessed.log --- a/test-data/references/08-affiliation_postprocessed.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ -## Application -Software: affiliation_postprocess.py (version: 3.2.2) -Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliation_postprocess.py --input-biom res_3.2.2/06-affiliation.biom --input-fasta res_3.2.2/04-filters.fasta --reference data/Unite_extract_ITS1.fasta --output-biom res_3.2.2/08-affiliation_postprocessed.biom --output-compo res_3.2.2/08-affiliation_postprocessed.compo.tsv --output-fasta res_3.2.2/08-affiliation_postprocessed.fasta --log-file res_3.2.2/08-affiliation_postprocessed.log - -######################################################################################################## -# Select smallest reference as affiliation. (select_inclusive_amplicon.py version : 1.0) -Command: - select_inclusive_amplicon.py --ITS-reference data/Unite_extract_ITS1.fasta -b res_3.2.2/06-affiliation.biom -o res_3.2.2/1617285770.775001_17397_06-affiliation.biom_resolve_inclusiv_its.biom --log-file res_3.2.2/1617285770.775001_17397_06-affiliation.biom_resolve_inclusiv_its.log - -Execution: - start: 01 Apr 2021 16:02:50 - end: 01 Apr 2021 16:02:50 - - # nb OTU : 55 - # 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 : 1.0.0) -Command: - aggregate_affiliated_otus.py -b res_3.2.2/1617285770.775001_17397_06-affiliation.biom_resolve_inclusiv_its.biom -f res_3.2.2/04-filters.fasta --identity 99.0 --coverage 99.0 --output-biom res_3.2.2/08-affiliation_postprocessed.biom --output-compo res_3.2.2/08-affiliation_postprocessed.compo.tsv --output-fasta res_3.2.2/08-affiliation_postprocessed.fasta --log-file res_3.2.2/1617285770.775001_17397_06-affiliation.biom_aggregation.log - -Execution: - start: 01 Apr 2021 16:02:51 - end: 01 Apr 2021 16:02:51 - - # nb OTU in : 55 - # nb OTU out : 55 - # nb OTU aggregated : 0 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/09-normalisation.biom --- a/test-data/references/09-normalisation.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/09-normalisation.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "Sampling 100 elements by sample from res_3.2.2/08-affiliation_postprocessed.biom", "date": "2021-04-01T16:02:51", "rows": [{"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_66", "blast_affiliations": [{"subject": "JX118682_SH219010.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_candidolanata"], "evalue": "5.05e-139", "aln_length": 261, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_candidolanata"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_candidolanata"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_22", "blast_affiliations": [{"subject": "JX118731_SH218995.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "evalue": "5.20e-144", "aln_length": 270, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_155", "blast_affiliations": [{"subject": "UDB000320_SH220111.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"], "evalue": "1.45e-144", "aln_length": 271, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410", "blast_affiliations": [{"subject": "EU623745_SH215851.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "evalue": "0.0", "aln_length": 390, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222", "blast_affiliations": [{"subject": "UDB002317_SH221025.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "evalue": "9.52e-162", "aln_length": 302, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_bootstrap":'..b'"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_19", "blast_affiliations": [{"subject": "JQ320113_SH190746.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Entolomataceae", "g__Entoloma", "s__Entoloma_sp"], "evalue": "2.66e-162", "aln_length": 303, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Entolomataceae", "g__Entoloma", "s__Entoloma_sp"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Entolomataceae", "g__Entoloma", "s__Entoloma_sp"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_85242", "blast_affiliations": [{"subject": "HQ714699_SH221418.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Paxillaceae", "g__Alpova", "s__Alpova_corsicus"], "evalue": "1.69e-174", "aln_length": 325, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Paxillaceae", "g__Alpova", "s__Alpova_corsicus"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Paxillaceae", "g__Alpova", "s__Alpova_corsicus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_52", "metadata": {"comment": [], "seed_id": "01_1953", "blast_affiliations": [{"subject": "EF669607_SH109271.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "evalue": "4.75e-129", "aln_length": 243, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 4], [0, 2, 1], [1, 0, 2], [1, 1, 6], [1, 2, 3], [2, 0, 2], [2, 1, 2], [2, 2, 3], [3, 0, 3], [3, 1, 1], [3, 2, 1], [4, 0, 2], [4, 1, 2], [4, 2, 2], [5, 0, 4], [5, 1, 2], [5, 2, 5], [6, 0, 3], [6, 1, 2], [7, 0, 5], [7, 1, 2], [7, 2, 2], [8, 0, 3], [8, 1, 1], [9, 0, 3], [9, 1, 3], [10, 0, 6], [11, 0, 2], [11, 1, 2], [11, 2, 2], [12, 0, 2], [12, 1, 1], [12, 2, 3], [13, 0, 2], [13, 1, 3], [13, 2, 3], [14, 0, 2], [14, 1, 3], [15, 0, 3], [15, 1, 2], [15, 2, 5], [16, 0, 4], [16, 1, 4], [16, 2, 2], [17, 0, 4], [17, 1, 2], [18, 0, 2], [18, 1, 3], [18, 2, 1], [19, 0, 5], [19, 1, 3], [19, 2, 1], [20, 0, 3], [20, 1, 3], [21, 0, 5], [21, 1, 2], [21, 2, 3], [22, 0, 2], [22, 1, 3], [22, 2, 2], [23, 0, 1], [23, 1, 3], [23, 2, 2], [24, 0, 2], [24, 1, 1], [24, 2, 5], [25, 0, 1], [25, 1, 4], [25, 2, 1], [26, 0, 2], [26, 1, 7], [26, 2, 1], [27, 0, 3], [27, 1, 3], [27, 2, 1], [28, 0, 2], [28, 1, 1], [28, 2, 3], [29, 0, 1], [29, 1, 1], [29, 2, 3], [30, 0, 3], [30, 1, 2], [30, 2, 1], [31, 0, 1], [31, 1, 1], [32, 0, 1], [32, 1, 2], [32, 2, 1], [33, 0, 1], [33, 1, 3], [33, 2, 3], [34, 0, 1], [34, 1, 3], [35, 0, 1], [35, 1, 2], [35, 2, 3], [36, 0, 1], [36, 2, 2], [37, 0, 2], [37, 2, 3], [38, 0, 1], [38, 2, 1], [39, 0, 1], [39, 2, 1], [40, 0, 1], [40, 1, 1], [40, 2, 5], [41, 0, 1], [41, 1, 2], [41, 2, 1], [42, 1, 1], [42, 2, 3], [43, 1, 2], [43, 2, 4], [44, 1, 1], [44, 2, 1], [45, 1, 5], [45, 2, 3], [46, 1, 1], [46, 2, 4], [47, 1, 1], [48, 1, 1], [48, 2, 4], [49, 2, 2], [50, 2, 2], [51, 2, 1]], "shape": [52, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/09-normalisation.fasta --- a/test-data/references/09-normalisation.fasta Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/09-normalisation.fasta Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -98,3 +98,7 @@ TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC >Cluster_50_FROGS_combined R1_desc:reference=JF419897_SH181470.07FU_refs position=1..250;R2_desc=R2_desc=reference=JF419897_SH181470.07FU_refs position=1..250 GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC +>Cluster_51 reference=AJ786644_SH470265.07FU_refs_singleton position=1..243 errors=78%G +CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC +>Cluster_52 reference=EF669607_SH109271.07FU_refs_singleton position=1..243 +CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/09-normalisation.html --- a/test-data/references/09-normalisation.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/09-normalisation.html Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Abundance Normalisation</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <!-- CSS --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> @@ -383,8 +383,8 @@ $(function() { var categories = ["Nb OTU before normalisation", "Nb OTU after normalisation"] ; - var histogram_series = [55, 50] ; - var series_by_sample = [{"name": "01_subsample", "data": [55, 41]}, {"name": "02_subsample", "data": [55, 42]}, {"name": "03_subsample", "data": [55, 42]}] ; + var histogram_series = [55, 52] ; + var series_by_sample = [{"name": "01_subsample", "data": [55, 42]}, {"name": "02_subsample", "data": [55, 43]}, {"name": "03_subsample", "data": [55, 42]}] ; // Remove alert $('#js-alert').remove(); |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/09-normalisation.log --- a/test-data/references/09-normalisation.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,34 +0,0 @@ -## Application -Software: normalisation.py (version: 3.2.2) -Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/normalisation.py -n 100 --input-biom res_3.2.2/08-affiliation_postprocessed.biom --input-fasta res_3.2.2/08-affiliation_postprocessed.fasta --output-biom res_3.2.2/09-normalisation.biom --output-fasta res_3.2.2/09-normalisation.fasta --summary res_3.2.2/09-normalisation.html --log-file res_3.2.2/09-normalisation.log - -Application start: 01 Apr 2021 16:02:51 - -#Normalisation calculation - start: 01 Apr 2021 16:02:51 -######################################################################################################## -# Random sampling in each sample. (biomTools.py version : 0.10.1) -Command: - biomTools.py sampling --nb-sampled 100 --input-file res_3.2.2/08-affiliation_postprocessed.biom --output-file res_3.2.2/09-normalisation.biom - -Execution: - start: 01 Apr 2021 16:02:51 - end: 01 Apr 2021 16:02:51 - - end: 01 Apr 2021 16:02:51 - -######################################################################################################## -# Update fasta file based on sequence in biom file (biomFastaUpdate.py version : 1.0.1) -Command: - biomFastaUpdate.py --input-biom res_3.2.2/09-normalisation.biom --input-fasta res_3.2.2/08-affiliation_postprocessed.fasta --output-file res_3.2.2/09-normalisation.fasta --log res_3.2.2/1617285771.1815455_17407_tmp_fasta_update.log - -Execution: - start: 01 Apr 2021 16:02:51 - end: 01 Apr 2021 16:02:51 - - -#Summarise - start: 01 Apr 2021 16:02:51 - end: 01 Apr 2021 16:02:51 - -Application end: 01 Apr 2021 16:02:51 |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/10-clustersStat.html --- a/test-data/references/10-clustersStat.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/10-clustersStat.html Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Cluster stat</title> <meta charset="UTF-8"> - <meta name="version" content="3.2.2"> + <meta name="version" content="3.2.3"> <!-- CSS --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> @@ -838,14 +838,14 @@ // Data // /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - var clusters_sizes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13] ; + var clusters_sizes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11] ; var series = [{ 'name': "All", - 'data': [1, 1, 5, 8, 4, 13, 6, 7, 1, 2, 1, 1] + 'data': [2, 6, 1, 5, 8, 14, 5, 3, 2, 4, 2] }]; var sum_series = new Array() ; - var samples_distrib = {"01_subsample": {"shared_seq": 99, "shared_observations": 40, "own_seq": 1, "own_observations": 1}, "02_subsample": {"shared_seq": 100, "shared_observations": 42, "own_seq": 0, "own_observations": 0}, "03_subsample": {"shared_seq": 100, "shared_observations": 42, "own_seq": 0, "own_observations": 0}} ; - var newick = "((03_subsample,(01_subsample,02_subsample):0.400):0.425);" ; + var samples_distrib = {"01_subsample": {"shared_seq": 94, "shared_observations": 41, "own_seq": 6, "own_observations": 1}, "02_subsample": {"shared_seq": 99, "shared_observations": 42, "own_seq": 1, "own_observations": 1}, "03_subsample": {"shared_seq": 95, "shared_observations": 39, "own_seq": 5, "own_observations": 3}} ; + var newick = "((03_subsample,(01_subsample,02_subsample):0.370):0.470);" ; /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/10-clustersStat.log --- a/test-data/references/10-clustersStat.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/clusters_stat.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/clusters_stat.py --input-biom res_3.2.2/09-normalisation.biom --output-file res_3.2.2/10-clustersStat.html --log-file res_3.2.2/10-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_3.2.2/09-normalisation.biom --output-file res_3.2.2/1617285771.5673287_17417_HClassif.newick > res_3.2.2/1617285771.5673287_17417_HClassif_log.txt - -Execution: - start: 01 Apr 2021 16:02:51 - end: 01 Apr 2021 16:02:53 - -######################################################################################################## -# Writes by abundance the number of clusters. (biomTools.py version : 0.10.1) -Command: - biomTools.py obsdepth --input-file res_3.2.2/09-normalisation.biom --output-file res_3.2.2/1617285771.5673287_17417_depths.tsv - -Execution: - start: 01 Apr 2021 16:02:53 - end: 01 Apr 2021 16:02:53 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/11-affiliationsStat.html --- a/test-data/references/11-affiliationsStat.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/11-affiliationsStat.html Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -19,7 +19,7 @@\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="3.2.2">\n+\t\t<meta name="version" content="3.2.3">\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@@ -1016,9 +1016,9 @@\n \t\t\t/* Example:\n \t\t\t\t["Surface-01", "Surface-02", "Surface-03", "Middle-01", "Middle-02", "Middle-03"]\n \t\t\t*/\n-\t\t\tvar tree_distribution = "(((((((\\"s__Coprinopsis_candidolanata\\":{\\"0\\": 3, \\"1\\": 3},\\"s__Coprinopsis_pachyderma\\":{\\"0\\": 4, \\"1\\": 3, \\"2\\": 3})\\"g__Coprinopsis\\",(\\"s__Psathyrella_multipedata\\":{\\"0\\": 2, \\"1\\": 1, \\"2\\": 3},\\"s__Psathyrella_sublatispora\\":{\\"1\\": 3, \\"2\\": 5})\\"g__Psathyrella\\")\\"f__Psathyrellaceae\\",((\\"s__Megacollybia_subfurfuracea\\":{\\"0\\": 5, \\"1\\": 1, \\"2\\": 3})\\"g__Megacollybia\\")\\"f__Marasmiaceae\\",((\\"s__Amanita_franchetii\\":{\\"0\\": 3, \\"1\\": 2, \\"2\\": 3})\\"g__Amanita\\")\\"f__Amanitaceae\\",((\\"s__Cortinarius_caesiocolor\\":{\\"0\\": 3, \\"1\\": 3, \\"2\\": 4},\\"s__Cortinarius_gentianeus\\":{\\"0\\": 2, \\"1\\": 2},\\"s__Cortinarius_aurantiobasis\\":{\\"0\\": 2, \\"2\\": 3},\\"s__Cortinarius_parkeri\\":{\\"0\\": 1},\\"s__Cortinarius_limonius\\":{\\"0\\": 1, \\"1\\": 8, \\"2\\": 4},\\"s__Cortinarius_sinapivelus\\":{\\"0\\": 3, \\"1\\": 3},\\"s__Cortinarius_calojanthinus\\":{\\"1\\": 2, \\"2\\": 2},\\"s__Cortinarius_amnicola\\":{\\"1\\": 2, \\"2\\": 3})\\"g__Cortinarius\\",(\\"s__Phaeocollybia_kauffmanii\\":{\\"0\\": 4, \\"2\\": 1})\\"g__Phaeocollybia\\")\\"f__Cortinariaceae\\",((\\"s__Entoloma_sp\\":{\\"0\\": 2, \\"1\\": 5, \\"2\\": 1})\\"g__Entoloma\\")\\"f__Entolomataceae\\",((\\"s__Tricholoma_portentosum\\":{\\"0\\": 5, \\"1\\": 1, \\"2\\": 1})\\"g__Tricholoma\\",(\\"s__Gamundia_leucophylla\\":{\\"0\\": 2, \\"1\\": 2, \\"2\\": 2})\\"g__Gamundia\\")\\"f__Tricholomataceae\\",((\\"s__Lepiota_geogenia\\":{\\"0\\": 3, \\"1\\": 3})\\"g__Lepiota\\")\\"f__Agaricaceae\\",((\\"s__Pholiota_highlandensis\\":{\\"0\\": 3, \\"1\\": 1, \\"2\\": 2})\\"g__Pholiota\\",(\\"s__Hypholoma_capnoides\\":{\\"1\\": 1, \\"2\\": 3})\\"g__Hypholoma\\")\\"f__Strophariaceae\\",((\\"s__Gymnopus_hybridus\\":{\\"0\\": 3, \\"1\\": 2, \\"2\\": 1})\\"g__Gymnopus\\")\\"f__Omphalotaceae\\",((\\"s__Inocybe_sindonia\\":{\\"0\\": 2, \\"1\\": 4, \\"2\\": 1})\\"g__Inocybe\\")\\"f__Inocybaceae\\")\\"o__Agaricales\\",(((\\"s__Lactarius_semisanguifluus\\":{\\"0\\": 3, \\"1\\": 2, \\"2\\": 3},\\"s__Lactarius_sp\\":{\\"0\\": 1, \\"1\\": 2, \\"2\\": 1},\\"s__Lactarius_cyathuliformis\\":{\\"0\\": 1, \\"1\\": 3, \\"2\\": 3})\\"g__Lactarius\\")\\"f__Russulaceae\\")\\"o__Russulales\\",(((\\"s__Hydnellum_suaveolens\\":{\\"0\\": 2, \\"1\\": 2, \\"2\\": 3},\\"s__Hydnellum_peckii\\":{\\"0\\": 2, \\"2\\": 1})\\"g__Hydnellum\\",(\\"s__Sarcodon_quercophilus\\":{\\"1\\": 1, \\"2\\": 5})\\"g__Sarcodon\\")\\"f__Bankeraceae\\")\\"o__Thelephorales\\",(((\\"s__Truncocolumella_rubra\\":{\\"0\\": 2, \\"1\\": 2, \\"2\\": 4})\\"g__Truncocolumella\\")\\"f__Suillaceae\\",((\\"s__Alpova_corsicus\\":{\\"0\\": 3, \\"1\\": 3, \\"2\\": 2},\\"s__Alpova_alpestris\\":{\\"0\\": 2, \\"1\\": 1})\\"g__Alpova\\")\\"f__Paxillaceae\\",((\\"s__Xerocomus_porophyllus\\":{\\"0\\": 2, \\"1\\": 4, \\"2\\": 1})\\"g__Xerocomus\\")\\"f__Boletaceae\\")\\"o__Boletales\\",(((\\"s__Hymenochaete_longispora\\":{\\"0\\": 2, \\"2\\": 4})\\"g__Hymenochaete\\",(\\"s__Pseudochaete_subrigidula\\":{\\"0\\": 1, \\"1\\": 1, \\"2\\": 2})\\"g__Pseudochaete\\")\\"f__Hymenochaetaceae\\")\\"o__Hymenochaetales\\")\\"c__Agaricomycetes\\")\\"p__Basidiomycota\\",(((((\\"s__Trichoderma_rodmanii\\":{\\"0\\": 1, \\"1\\": 3, \\"2\\": 2},\\"s__Trichoderma_aggressivum\\":{\\"0\\": 4, \\"1\\": 1, \\"2\\": 3},\\"s__Trichoderma_mienum\\":{\\"0\\": 1, \\"2\\": 4},\\"s__Trichoderma_cremeum\\":{\\"1\\": 2, \\"2\\": 1})\\"g__Trichoderma\\")\\"f__Hypocreaceae\\")\\"o__Hypocreales\\",(((\\"s__Hypoxylon_fragiforme\\":{\\"0\\": 4, \\"1\\": 6, \\"2\\": 2})\\"g__Hypoxylon\\")\\"f__Xylariaceae\\",((\\"s__Adisciso_tricellulare\\":{\\"0\\": 2, \\"1\\": 2, \\"2\\": 2})\\"g__Adisciso\\",(\\"s__Pestalotiopsis_diversiseta\\":{\\"1\\": 2, \\"2\\": 2})\\"g__Pestalotiopsis\\")\\"f__Amphisphaeriaceae\\")\\"o__Xylariales\\",(((\\"s__Pha'..b'28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29], "Species": [2, 4, 6, 8, 9, 10, 12, 14, 15, 16, 17, 18, 20, 21, 21, 23, 23, 25, 25, 25, 26, 26, 27, 29, 30, 30, 31, 31, 32, 33, 34, 34, 34, 35, 36, 37, 37, 37, 38, 38, 38, 39, 40, 40, 40, 40, 40, 40, 41, 41]}, "02_subsample": {"nb_seq": 100, "Family": [2, 4, 5, 7, 8, 10, 12, 13, 14, 15, 15, 15, 15, 15, 16, 17, 17, 17, 17, 17, 18, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 22, 22, 22, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24], "Genus": [2, 4, 6, 8, 9, 11, 13, 14, 15, 16, 16, 17, 17, 17, 18, 19, 19, 20, 20, 20, 21, 22, 22, 22, 23, 24, 24, 25, 25, 25, 25, 27, 27, 27, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30], "Species": [2, 4, 6, 8, 10, 12, 14, 15, 17, 18, 19, 20, 20, 22, 23, 24, 24, 26, 27, 28, 29, 30, 30, 30, 31, 32, 32, 34, 34, 34, 34, 36, 37, 38, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 41, 41, 42, 42, 42]}, "03_subsample": {"nb_seq": 100, "Family": [2, 3, 5, 7, 9, 10, 11, 11, 11, 11, 12, 13, 14, 15, 15, 15, 15, 15, 15, 15, 16, 16, 16, 17, 18, 18, 18, 18, 18, 18, 18, 19, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 22, 22, 24, 24, 24, 24], "Genus": [2, 4, 6, 8, 10, 11, 12, 12, 12, 12, 13, 14, 15, 17, 17, 17, 17, 17, 17, 17, 18, 19, 19, 20, 21, 22, 23, 23, 24, 24, 24, 25, 26, 26, 26, 26, 26, 26, 27, 27, 28, 28, 28, 28, 29, 29, 31, 31, 31, 31], "Species": [2, 4, 6, 8, 10, 11, 13, 15, 17, 18, 19, 20, 21, 23, 23, 24, 24, 24, 25, 26, 27, 28, 28, 30, 31, 32, 33, 33, 34, 34, 34, 35, 37, 37, 37, 37, 37, 37, 38, 38, 39, 39, 39, 39, 40, 40, 42, 42, 42, 42]}} ;\n+\t\t\tvar rarefaction = {"01_subsample": {"nb_seq": 100, "Family": [2, 4, 6, 7, 9, 10, 11, 12, 12, 12, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 20, 20, 20, 21, 21, 21, 21, 21, 22, 22, 22, 22, 23], "Genus": [2, 4, 6, 8, 10, 11, 12, 14, 15, 15, 16, 16, 16, 16, 17, 18, 18, 19, 19, 19, 20, 20, 20, 20, 20, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 25, 25, 25, 26, 26, 27, 27, 27, 28, 28, 28, 28, 29], "Species": [2, 4, 6, 8, 10, 12, 14, 16, 17, 18, 19, 19, 19, 19, 20, 21, 22, 24, 24, 24, 25, 26, 27, 27, 27, 29, 30, 30, 31, 31, 31, 32, 32, 32, 32, 33, 33, 35, 36, 36, 37, 37, 39, 40, 40, 41, 41, 41, 41, 42]}, "02_subsample": {"nb_seq": 100, "Family": [2, 3, 4, 6, 8, 8, 10, 11, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 17, 17, 18, 18, 18, 18, 19, 19, 19, 19, 21, 22, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24], "Genus": [2, 3, 5, 7, 9, 10, 12, 14, 16, 16, 18, 19, 19, 19, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 22, 22, 23, 23, 23, 23, 24, 24, 24, 24, 26, 27, 28, 29, 29, 30, 30, 30, 30, 30, 30, 30, 31], "Species": [2, 4, 6, 8, 10, 11, 13, 15, 17, 19, 21, 22, 22, 23, 24, 24, 25, 25, 25, 26, 27, 28, 28, 29, 29, 29, 30, 32, 32, 33, 33, 33, 33, 34, 34, 34, 34, 36, 37, 38, 39, 40, 42, 42, 42, 42, 42, 42, 42, 43]}, "03_subsample": {"nb_seq": 100, "Family": [2, 3, 5, 7, 9, 10, 12, 13, 13, 15, 16, 16, 16, 16, 16, 17, 18, 18, 18, 19, 19, 19, 19, 20, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24], "Genus": [2, 3, 5, 7, 9, 10, 12, 14, 14, 16, 17, 17, 17, 17, 18, 20, 21, 21, 22, 23, 25, 25, 25, 26, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30], "Species": [2, 3, 5, 7, 9, 10, 12, 14, 15, 17, 18, 19, 19, 19, 21, 23, 24, 24, 25, 27, 29, 29, 30, 32, 33, 33, 34, 34, 35, 36, 36, 36, 38, 38, 39, 39, 39, 41, 41, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42]}} ;\n \t\t\t/* Example:\n \t\t\t\t{\n \t\t\t\t\t"Surface-01": {\n@@ -1039,7 +1039,7 @@\n \t\t\t/* Example:\n \t\t\t\t["Family", "Genus", "Species"]\n \t\t\t*/\n-\t\t\tvar alignment_scores = [[100.0, 100.0, {"clstr": 49, "seq": 294}], [99.627, 100.0, {"clstr": 1, "seq": 6}]] ;\n+\t\t\tvar alignment_scores = [[100.0, 100.0, {"clstr": 51, "seq": 290}], [99.627, 100.0, {"clstr": 1, "seq": 10}]] ;\n \t\t\t/* Example:\n \t\t\t\t[\n \t\t\t\t\t[100, 100, { "clstr": 53, "seq": 20500 }],\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/11-affiliationsStat.log --- a/test-data/references/11-affiliationsStat.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ -## Application -Software: affiliations_stat.py (version: 3.2.2) -Command: /home/maria/miniconda3/envs/frogs@3.2.2/bin/affiliations_stat.py --input-biom res_3.2.2/09-normalisation.biom --output-file res_3.2.2/11-affiliationsStat.html --log-file res_3.2.2/11-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 --taxonomic-ranks Domain Phylum Class Order 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_3.2.2/09-normalisation.biom --output-file-pattern res_3.2.2/1617285773.930201_17428_rarefaction_rank_##RANK##.tsv --taxonomy-key "blast_taxonomy" --step-size 2 --ranks 4 5 6 - -Execution: - start: 01 Apr 2021 16:02:53 - end: 01 Apr 2021 16:02:54 - -######################################################################################################## -# Produces a taxonomy tree with counts by sample. (biomTools.py version : 0.10.1) -Command: - biomTools.py treeCount --input-file res_3.2.2/09-normalisation.biom --taxonomy-key "blast_taxonomy" --output-enewick res_3.2.2/1617285773.930201_17428_taxCount.enewick --output-samples res_3.2.2/1617285773.930201_17428_taxCount_ids.tsv - -Execution: - start: 01 Apr 2021 16:02:54 - end: 01 Apr 2021 16:02:54 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/12-biom2tsv.log --- a/test-data/references/12-biom2tsv.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/biom_to_tsv.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/biom_to_tsv.py --input-biom res_3.2.2/09-normalisation.biom --input-fasta res_3.2.2/09-normalisation.fasta --output-tsv res_3.2.2/12-biom2tsv.tsv --output-multi-affi res_3.2.2/12-biom2tsv-affiliation_multihit.tsv --log-file res_3.2.2/12-biom2tsv.log - -######################################################################################################## -# Converts a BIOM file in TSV file. (biom2tsv.py version : 1.5.0) -Command: - biom2tsv.py --input-file res_3.2.2/09-normalisation.biom --input-fasta res_3.2.2/09-normalisation.fasta --output-file res_3.2.2/12-biom2tsv.tsv --fields 'comment' '@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' '@sample_count' - -Execution: - start: 01 Apr 2021 16:02:54 - end: 01 Apr 2021 16:02:54 - -######################################################################################################## -# Extracts multi-affiliations data from a FROGS BIOM file. (multiAffiFromBiom.py version : 1.3.0) -Command: - multiAffiFromBiom.py --input-file res_3.2.2/09-normalisation.biom --output-file res_3.2.2/12-biom2tsv-affiliation_multihit.tsv - -Execution: - start: 01 Apr 2021 16:02:54 - end: 01 Apr 2021 16:02:54 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/12-biom2tsv.tsv --- a/test-data/references/12-biom2tsv.tsv Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/12-biom2tsv.tsv Fri Jun 04 14:56:24 2021 +0000 |
| b |
| b'@@ -1,51 +1,53 @@\n #comment\trdp_tax_and_bootstrap\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_subsample\t02_subsample\t03_subsample\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Chaetothyriales;(1.0);f__Herpotrichiellaceae;(1.0);g__Exophiala;(1.0);s__Exophiala_equina;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Chaetothyriales;f__Herpotrichiellaceae;g__Exophiala;s__Exophiala_equina\tJF747094_SH197643.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_54\tATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_1\t3\t0\t2\t1\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Pezizomycetes;(1.0);o__Pezizales;(1.0);f__Tuberaceae;(1.0);g__Tuber;(1.0);s__Tuber_latisporum;(1.0);\tk__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_92546\tCCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\tCluster_2\t7\t4\t2\t1\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Elaphomycetaceae;(1.0);g__Elaphomyces;(1.0);s__Elaphomyces_compleximurus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Elaphomycetaceae;g__Elaphomyces;s__Elaphomyces_compleximurus\tJN711441_SH022548.07FU_refs_singleton\t100.0\t100.0\t8.06e-132\t248\t01_59\tAGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_3\t6\t1\t3\t2\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Hypocreales;(1.0);f__Hypocreaceae;(1.0);g__Trichoderma;(1.0);s__Trichoderma_aggressivum;(1.0);\tk__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\tCCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_4\t8\t4\t1\t3\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Xylariales;(1.0);f__Amphisphaeriaceae;(1.0);g__Pestalotiopsis;(1.0);s__Pestalotiopsis_diversiseta;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta\tJX399009_SH268556.07FU_refs\t100.0\t100.0\t2.25e-132\t249\t01_25\tCATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_5\t4\t0\t2\t2\n-no data\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Bankeraceae;(1.0);g__Sarcodon;(1.0);s__Sarcodon_quercophilus;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Sarcodon;s__Sarcodon_quercophilus\tKM668101_SH491630.07FU_refs_singleton\t100.0\t100.0\t3.94e-140\t263\t01_74803\tAGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\tCluster_6\t6\t0\t1\t5\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycete'..b';g__Megacollybia;s__Megacollybia_subfurfuracea\tEU623745_SH215851.07FU_refs\t100.0\t100.0\t0.0\t390\t01_410\tGCGGAAGGATCATTACTGAATTGAAATGCGTTAGTTAGTTGAGCTGACCTTCTCCCTTTAATGGGGGGGGGAGTAGTATGTGCTCGCTATATCGCTTTTTCTAACTCCCCACTGTGCACCTCTATTGTAGGCTACGAGTGACTCTCAAGTAGACACACTCCCATAACACACCCTTTGTGCGCAGAAGGGGGGGGAAAAGGGTCTATTTGGGTTTAAGAAGGCTTATCGGGCATCCATTTTGCTTGCTTTCGACTTTGTAGCCTATGATCTTACAACAAACTACTTTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_47\t11\t4\t2\t5\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Trichocomaceae;(1.0);g__Aspergillus;(1.0);s__Aspergillus_caninus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_caninus\tGQ169315_SH195598.07FU_refs\t100.0\t100.0\t3.70e-130\t245\t01_86\tTGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t4\t0\t1\t3\n+no data\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Cortinariaceae;(1.0);g__Cortinarius;(1.0);s__Cortinarius_parkeri;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_parkeri\tGQ159830_SH222371.07FU_refs\t100.0\t100.0\t1.33e-129\t244\t01_88865\tTGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_49\t1\t0\t1\t0\n+FROGS_combined\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Lindgomycetaceae;(1.0);g__Lindgomyces;(1.0);s__Lindgomyces_breviappendiculatus;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Lindgomycetaceae;g__Lindgomyces;s__Lindgomyces_breviappendiculatus\tJF419897_SH181470.07FU_refs\t100.0\t100.0\t-1\t1017\t01_71070_FROGS_combined\tGATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_50_FROGS_combined\t11\t2\t6\t3\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Leptosphaeriaceae;(1.0);g__Leptosphaeria;(1.0);s__Leptosphaeria_polylepidis;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Leptosphaeriaceae;g__Leptosphaeria;s__Leptosphaeria_polylepidis\tAJ786644_SH470265.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_210\tCATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_51\t2\t0\t1\t1\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Trichocomaceae;(1.0);g__Aspergillus;(1.0);s__Aspergillus_microcysticus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_microcysticus\tEF669607_SH109271.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_1953\tCGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_52\t1\t0\t0\t1\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/13-affiliation_multihit.tsv --- a/test-data/references/13-affiliation_multihit.tsv Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/13-affiliation_multihit.tsv Fri Jun 04 14:56:24 2021 +0000 |
| b |
| b'@@ -1,51 +1,53 @@\n #OTUID\ttaxonomy\tsubject\tevalue\tperc_identity\tperc_query_coverage\taln_length\n-Cluster_19\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_candidolanata\tJX118682_SH219010.07FU_refs\t5.05e-139\t100.0\t100.0\t261\n+Cluster_23\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Phaeocollybia;s__Phaeocollybia_kauffmanii\tKF219570_SH182201.07FU_refs\t2.46e-147\t100.0\t100.0\t276\n+Cluster_50_FROGS_combined\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Lindgomycetaceae;g__Lindgomyces;s__Lindgomyces_breviappendiculatus\tJF419897_SH181470.07FU_refs\t-1\t100.0\t100.0\t1017\n+Cluster_1\tk__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_14\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Diaporthales;f__Togniniaceae;g__Phaeoacremonium;s__Phaeoacremonium_rubrigenum\tAF118139_SH214931.07FU_refs\t3.94e-140\t100.0\t100.0\t263\n+Cluster_15\tk__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_47\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea\tEU623745_SH215851.07FU_refs\t0.0\t100.0\t100.0\t390\n+Cluster_11\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Adisciso;s__Adisciso_tricellulare\tAB594796_SH278638.07FU_refs\t8.06e-132\t100.0\t100.0\t248\n+Cluster_10\tk__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_24\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Hydnellum;s__Hydnellum_peckii\tUDB003291_SH182302.07FU_refs\t7.05e-153\t100.0\t100.0\t286\n+Cluster_5\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta\tJX399009_SH268556.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n+Cluster_22\tk__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_35\tk__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_29\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_caesiocolor\tKF732603_SH223051.07FU_refs\t5.49e-154\t100.0\t100.0\t288\n+Cluster_34\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Hydnellum;s__Hydnellum_suaveolens\tUDB016091_SH210668.07FU_refs\t1.97e-153\t100.0\t100.0\t287\n Cluster_12\tk__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_22\tk__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_47\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea\tEU623745_SH215851.07FU_refs\t0.0\t100.0\t100.0\t390\n+Cluster_13\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Gamundia;s__Gamundia_leucophylla\tGU234142_SH201120.07FU_refs\t8.63e-142\t99.627\t100.0\t268\n+Cluster_6\tk__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_30\tk__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_26\tk__Fungi;p__Basidiomycota;c__Agar'..b'ypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t4.90e-134\t100.0\t100.0\t252\n-Cluster_42\tk__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_10\tk__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_45\tk__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_30\tk__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_46\tk__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_40\tk__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_38\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_sinapivelus\tGQ890305_SH122869.07FU_refs_singleton\t1.57e-159\t100.0\t100.0\t298\n-Cluster_13\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Gamundia;s__Gamundia_leucophylla\tGU234142_SH201120.07FU_refs\t8.63e-142\t99.627\t100.0\t268\n-Cluster_3\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Elaphomycetaceae;g__Elaphomyces;s__Elaphomyces_compleximurus\tJN711441_SH022548.07FU_refs_singleton\t8.06e-132\t100.0\t100.0\t248\n-Cluster_9\tk__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_50_FROGS_combined\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Lindgomycetaceae;g__Lindgomyces;s__Lindgomyces_breviappendiculatus\tJF419897_SH181470.07FU_refs\t-1\t100.0\t100.0\t1017\n-Cluster_21\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_cremeum\tAY737760_SH296378.07FU_refs\t1.45e-144\t100.0\t100.0\t271\n-Cluster_25\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Psathyrella;s__Psathyrella_sublatispora\tKC992854_SH220410.07FU_refs\t2.53e-152\t100.0\t100.0\t285\n-Cluster_31\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_calojanthinus\tKF732272_SH222375.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n-Cluster_1\tk__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_6\tk__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_5\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Pestalotiopsis;s__Pestalotiopsis_diversiseta\tJX399009_SH268556.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n-Cluster_7\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Rasamsonia;s__Rasamsonia_emersonii\tJF417478_SH216679.07FU_refs\t1.75e-133\t100.0\t100.0\t251\n-Cluster_28\tk__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_32\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_amnicola\tKF732249_SH136099.07FU_refs_singleton\t1.19e-155\t100.0\t100.0\t291\n+Cluster_52\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_microcysticus\tEF669607_SH109271.07FU_refs_singleton\t4.75e-129\t100.0\t100.0\t243\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/13-affiliation_std.biom --- a/test-data/references/13-affiliation_std.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/13-affiliation_std.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "Sampling 100 elements by sample from res_3.2.2/08-affiliation_postprocessed.biom", "date": "2021-04-01T16:02:51", "rows": [{"id": "Cluster_19", "metadata": {"comment": "", "seed_id": "01_66", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_candidolanata", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_candidolanata", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_candidolanata"]}}, {"id": "Cluster_12", "metadata": {"comment": "", "seed_id": "01_22", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_pachyderma", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_pachyderma", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Coprinopsis", "s__Coprinopsis_pachyderma"]}}, {"id": "Cluster_22", "metadata": {"comment": "", "seed_id": "01_155", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_semisanguifluus", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_semisanguifluus", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_semisanguifluus"]}}, {"id": "Cluster_47", "metadata": {"comment": "", "seed_id": "01_410", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"]}}, {"id": "Cluster_36", "metadata": {"comment": "", "seed_id": "01_222", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"]}}, {"id": "Cluster_18", "metadata": {"comment": "", "seed_id": "01_40", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rodmanii", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rodmanii", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rodmanii"]}}, {"id": "Cluster_34", "metadata": {"comment": "", "seed_id": "01_67", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Hydnellum;s__Hydnellum_suaveolens", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Hydnellum;s__Hydnellum_suaveolens", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Ban'..b';1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"]}}, {"id": "Cluster_7", "metadata": {"comment": "", "seed_id": "01_38", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Rasamsonia;s__Rasamsonia_emersonii", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Rasamsonia;s__Rasamsonia_emersonii", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"]}}, {"id": "Cluster_37", "metadata": {"comment": "", "seed_id": "01_19", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Entolomataceae;g__Entoloma;s__Entoloma_sp", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Entolomataceae;g__Entoloma;s__Entoloma_sp", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Entolomataceae", "g__Entoloma", "s__Entoloma_sp"]}}, {"id": "Cluster_44", "metadata": {"comment": "", "seed_id": "01_85242", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Paxillaceae;g__Alpova;s__Alpova_corsicus", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Paxillaceae;g__Alpova;s__Alpova_corsicus", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Paxillaceae", "g__Alpova", "s__Alpova_corsicus"]}}, {"id": "Cluster_52", "metadata": {"comment": "", "seed_id": "01_1953", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_microcysticus", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_microcysticus", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 4], [0, 2, 1], [1, 0, 2], [1, 1, 6], [1, 2, 3], [2, 0, 2], [2, 1, 2], [2, 2, 3], [3, 0, 3], [3, 1, 1], [3, 2, 1], [4, 0, 2], [4, 1, 2], [4, 2, 2], [5, 0, 4], [5, 1, 2], [5, 2, 5], [6, 0, 3], [6, 1, 2], [7, 0, 5], [7, 1, 2], [7, 2, 2], [8, 0, 3], [8, 1, 1], [9, 0, 3], [9, 1, 3], [10, 0, 6], [11, 0, 2], [11, 1, 2], [11, 2, 2], [12, 0, 2], [12, 1, 1], [12, 2, 3], [13, 0, 2], [13, 1, 3], [13, 2, 3], [14, 0, 2], [14, 1, 3], [15, 0, 3], [15, 1, 2], [15, 2, 5], [16, 0, 4], [16, 1, 4], [16, 2, 2], [17, 0, 4], [17, 1, 2], [18, 0, 2], [18, 1, 3], [18, 2, 1], [19, 0, 5], [19, 1, 3], [19, 2, 1], [20, 0, 3], [20, 1, 3], [21, 0, 5], [21, 1, 2], [21, 2, 3], [22, 0, 2], [22, 1, 3], [22, 2, 2], [23, 0, 1], [23, 1, 3], [23, 2, 2], [24, 0, 2], [24, 1, 1], [24, 2, 5], [25, 0, 1], [25, 1, 4], [25, 2, 1], [26, 0, 2], [26, 1, 7], [26, 2, 1], [27, 0, 3], [27, 1, 3], [27, 2, 1], [28, 0, 2], [28, 1, 1], [28, 2, 3], [29, 0, 1], [29, 1, 1], [29, 2, 3], [30, 0, 3], [30, 1, 2], [30, 2, 1], [31, 0, 1], [31, 1, 1], [32, 0, 1], [32, 1, 2], [32, 2, 1], [33, 0, 1], [33, 1, 3], [33, 2, 3], [34, 0, 1], [34, 1, 3], [35, 0, 1], [35, 1, 2], [35, 2, 3], [36, 0, 1], [36, 2, 2], [37, 0, 2], [37, 2, 3], [38, 0, 1], [38, 2, 1], [39, 0, 1], [39, 2, 1], [40, 0, 1], [40, 1, 1], [40, 2, 5], [41, 0, 1], [41, 1, 2], [41, 2, 1], [42, 1, 1], [42, 2, 3], [43, 1, 2], [43, 2, 4], [44, 1, 1], [44, 2, 1], [45, 1, 5], [45, 2, 3], [46, 1, 1], [46, 2, 4], [47, 1, 1], [48, 1, 1], [48, 2, 4], [49, 2, 2], [50, 2, 2], [51, 2, 1]], "shape": [52, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/13-biom2stdbiom.log --- a/test-data/references/13-biom2stdbiom.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/biom_to_stdBiom.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/biom_to_stdBiom.py --input-biom res_3.2.2/09-normalisation.biom --output-biom res_3.2.2/13-affiliation_std.biom --output-metadata res_3.2.2/13-affiliation_multihit.tsv --log-file res_3.2.2/13-biom2stdbiom.log - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/14-tsv2biom.biom --- a/test-data/references/14-tsv2biom.biom Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/14-tsv2biom.biom Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "FROGS_tsv2_biom", "date": "2021-04-01T16:02:54", "rows": [{"id": "Cluster_1", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "seed_id": "01_54", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "subject": "JF747094_SH197643.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "2.25e-132", "aln_length": "249"}]}}, {"id": "Cluster_2", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "seed_id": "01_92546", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "subject": "DQ898183_SH216206.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "2.25e-132", "aln_length": "249"}]}}, {"id": "Cluster_3", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "seed_id": "01_59", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "subject": "JN711441_SH022548.07FU_refs_singleton", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "8.06e-132", "aln_length": "248"}]}}, {"id": "Cluster_4", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "seed_id": "01_81", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "subject": "AF456924_SH097201.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "4.90e-134", "aln_length": "252"}]}}, {"id": "Cluster_5", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "seed_id": "01_25", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "subject": "JX399009_SH268556.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "2.25e'..b'Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "seed_id": "01_71070_FROGS_combined", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "subject": "JF419897_SH181470.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "-1", "aln_length": "1017"}]}}, {"id": "Cluster_51", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Leptosphaeriaceae", "g__Leptosphaeria", "s__Leptosphaeria_polylepidis"], "seed_id": "01_210", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Leptosphaeriaceae", "g__Leptosphaeria", "s__Leptosphaeria_polylepidis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Leptosphaeriaceae", "g__Leptosphaeria", "s__Leptosphaeria_polylepidis"], "subject": "AJ786644_SH470265.07FU_refs_singleton", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "4.75e-129", "aln_length": "243"}]}}, {"id": "Cluster_52", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "seed_id": "01_1953", "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "subject": "EF669607_SH109271.07FU_refs_singleton", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "4.75e-129", "aln_length": "243"}]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 2], [0, 1, 2], [0, 2, 3], [1, 0, 1], [1, 1, 1], [1, 2, 5], [2, 0, 2], [2, 1, 1], [2, 2, 5], [3, 0, 1], [3, 2, 1], [4, 0, 3], [4, 1, 3], [5, 0, 4], [5, 1, 4], [5, 2, 2], [6, 1, 1], [6, 2, 4], [7, 0, 2], [7, 1, 7], [7, 2, 1], [8, 0, 3], [8, 1, 3], [8, 2, 1], [9, 0, 5], [9, 1, 2], [9, 2, 2], [10, 0, 3], [10, 1, 2], [11, 0, 2], [11, 1, 3], [12, 0, 3], [12, 1, 2], [12, 2, 5], [13, 0, 3], [13, 1, 1], [13, 2, 1], [14, 0, 2], [14, 1, 2], [14, 2, 2], [15, 0, 1], [15, 2, 2], [16, 0, 1], [16, 1, 4], [16, 2, 1], [17, 1, 5], [17, 2, 3], [18, 0, 1], [18, 1, 2], [18, 2, 1], [19, 0, 2], [19, 2, 3], [20, 0, 1], [20, 1, 3], [20, 2, 2], [21, 0, 6], [22, 0, 4], [22, 2, 1], [23, 0, 1], [23, 1, 2], [23, 2, 3], [24, 0, 3], [24, 1, 1], [25, 0, 2], [25, 1, 3], [25, 2, 1], [26, 1, 1], [26, 2, 4], [27, 0, 5], [27, 1, 3], [27, 2, 1], [28, 0, 2], [28, 1, 1], [28, 2, 3], [29, 0, 4], [29, 1, 2], [30, 0, 1], [30, 2, 1], [31, 0, 1], [31, 1, 1], [31, 2, 3], [32, 0, 1], [32, 1, 3], [32, 2, 3], [33, 0, 2], [33, 1, 3], [33, 2, 3], [34, 0, 2], [34, 1, 2], [34, 2, 2], [35, 0, 1], [35, 1, 3], [36, 2, 2], [37, 0, 2], [37, 1, 3], [37, 2, 2], [38, 1, 2], [38, 2, 4], [39, 0, 2], [39, 1, 1], [39, 2, 3], [40, 0, 5], [40, 1, 2], [40, 2, 3], [41, 0, 1], [41, 1, 1], [42, 0, 1], [42, 1, 2], [42, 2, 1], [43, 2, 2], [44, 0, 3], [44, 1, 2], [44, 2, 1], [45, 0, 3], [45, 1, 3], [46, 0, 4], [46, 1, 2], [46, 2, 5], [47, 1, 1], [47, 2, 3], [48, 1, 1], [49, 0, 2], [49, 1, 6], [49, 2, 3], [50, 1, 1], [50, 2, 1], [51, 2, 1]], "shape": [52, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/14-tsv2biom.fasta --- a/test-data/references/14-tsv2biom.fasta Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/14-tsv2biom.fasta Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -98,3 +98,7 @@ TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC >Cluster_50_FROGS_combined GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC +>Cluster_51 +CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC +>Cluster_52 +CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/14-tsv2biom.log --- a/test-data/references/14-tsv2biom.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/tsv_to_biom.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/tsv_to_biom.py --input-tsv res_3.2.2/12-biom2tsv.tsv --input-multi-affi res_3.2.2/12-biom2tsv-affiliation_multihit.tsv --output-biom res_3.2.2/14-tsv2biom.biom --output-fasta res_3.2.2/14-tsv2biom.fasta --log-file res_3.2.2/14-tsv2biom.log - -######################################################################################################## -# Converts a TSV file in Biom. (tsv2biom.py version : 1.2.0) -Command: - tsv2biom.py --input-file res_3.2.2/12-biom2tsv.tsv --input-multihits res_3.2.2/12-biom2tsv-affiliation_multihit.tsv --output-file res_3.2.2/14-tsv2biom.biom --output-fasta res_3.2.2/14-tsv2biom.fasta --fields comment 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 --samples-names 01_subsample 02_subsample 03_subsample - -Execution: - start: 01 Apr 2021 16:02:54 - end: 01 Apr 2021 16:02:54 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/15-tree-mafft.html --- a/test-data/references/15-tree-mafft.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/15-tree-mafft.html Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -19,7 +19,7 @@\n \t<head>\n \t\t<title>FROGS Tree</title>\n \t\t<meta charset="UTF-8">\n-\t\t<meta name="version" content="3.2.2">\n+\t\t<meta name="version" content="3.2.3">\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@@ -182,7 +182,7 @@\n }\n #phylocanvas {\n width: 1150px;\n- height: 716px;\n+ height: 738px;\n }\n .onoffswitch {\n position: relative; width: 90px;\n@@ -410,7 +410,7 @@\n \t\t\t\t\n \t\t\t$(function() {\n \t\t\t\t// var summary = {"otu_removed": 4, "abundance_removed": 22025, "abundance_kept": 233756, "otu_kept": 48} ;\t\n-\t\t\t\tvar summary = {"otu_kept": 50, "otu_removed": 0, "abundance_kept": 300, "abundance_removed": 0} ;\n+\t\t\t\tvar summary = {"otu_kept": 52, "otu_removed": 0, "abundance_kept": 300, "abundance_removed": 0} ;\n \t\t\t\t// var removed_details_categories = ["Taxonomic Information", "Abundance Number", "% with abundance total", "Sequence length"] ;\n \t\t\t\tvar removed_details_categories = ["Taxonomic Information", "Abundance Number", "% with abundance total", "Sequence length"] ;\n \t\t\t\t// var removed_details_data = [\n@@ -488,7 +488,7 @@\n });\n tree.branchColour = "#8EADAC";\n tree.selectedColour = "#DE9F73";\n- tree.load(\'(((((((((Cluster_16 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Xylariaceae g__Hypoxylon s__Hypoxylon_fragiforme:0.294637021,(Cluster_5 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Amphisphaeriaceae g__Pestalotiopsis s__Pestalotiopsis_diversiseta:0.058546996,Cluster_11 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Amphisphaeriaceae g__Adisciso s__Adisciso_tricellulare:0.016025716)0.968:0.158266053)0.936:0.131162271,Cluster_14 k__Fungi p__Ascomycota c__Sordariomycetes o__Diaporthales f__Togniniaceae g__Phaeoacremonium s__Phaeoacremonium_rubrigenum:0.235307367)0.754:0.054791963,Cluster_2 k__Fungi p__Ascomycota c__Pezizomycetes o__Pezizales f__Tuberaceae g__Tuber s__Tuber_latisporum:0.474480884)0.691:0.049780986,(Cluster_1 k__Fungi p__Ascomycota c__Eurotiomycetes o__Chaetothyriales f__Herpotrichiellaceae g__Exophiala s__Exophiala_equina:0.213943848,(Cluster_3 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Elaphomycetaceae g__Elaphomyces s__Elaphomyces_compleximurus:0.187178327,(Cluster_7 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Trichocomaceae g__Rasamsonia s__Rasamsonia_emersonii:0.071227926,Cluster_48 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Trichocomaceae g__Aspergillus s__Aspergillus_caninus:0.177457902)0.791:0.044816189)0.990:0.149578112)0.571:0.060098474)0.878:0.1145429,(Cluster_18 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_rodmanii:0.018225688,(Cluster_9 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_mienum:0.041431417,(Cluster_4 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_aggressivum:0.037275191,Cluster_21 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_cremeum:0.077364146)0.139:0.011858572)0.788:0.03914001)0.998:0.237984437)0.615:0.089509622,Cluster_50_FROGS_combined k__Fungi p__Ascomycota c__Dothideomycetes o__Pleosporales f__Lindgomycetaceae g__Lindgomyces s__Lindgomyces_breviappendiculatus:0.447067258)0.631:0.098224826,Cluster_20 k__Fungi p__Ascomycota c__Pezizomycetes o__Pezizales f__Pezizaceae g__Terfezia s__Terfezia_claveryi:0.380823886)0.937:0.185254213,Cluster_6 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Sarcodon s__Sarcodon_quercophilus:0.433076597)0.582:0.0034002915,(((((Cluster_23 k__Fungi p__Ba'..b"3659122,(Cluster_10 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_cyathuliformis:5e-09,(Cluster_22 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_semisanguifluus:0.123022832,Cluster_17 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_sp:0.007911379)0.447:0.007942737)1.000:0.427330946)0.856:0.089374284)0.820:0.039578512)0.245:0.009874442,(((((Cluster_29 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_caesiocolor:0.042919164,(Cluster_31 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_calojanthinus:0.023205943,Cluster_32 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_amnicola:0.036383229)0.971:0.027390497)0.798:0.009167333,(Cluster_40 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_limonius:0.062565372,Cluster_49 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_parkeri:0.086069272)0.831:0.014848662)0.603:0.009776283,Cluster_27 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_gentianeus:0.065224781)0.759:0.006729621,Cluster_35 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_aurantiobasis:0.024764478)0.275:5e-09,Cluster_38 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_sinapivelus:0.073082327)0.999:0.108735239)0.880:0.042914049,(Cluster_26 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Agaricaceae g__Lepiota s__Lepiota_geogenia:0.211429154,Cluster_37 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Entolomataceae g__Entoloma s__Entoloma_sp:0.288997956)0.757:0.032549439)0.188:0.047155268,(Cluster_23 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Phaeocollybia s__Phaeocollybia_kauffmanii:0.156669249,Cluster_47 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Marasmiaceae g__Megacollybia s__Megacollybia_subfurfuracea:0.434570848)0.474:0.039850361)0.799:0.057651006,((Cluster_8 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Suillaceae g__Truncocolumella s__Truncocolumella_rubra:0.077924951,((Cluster_43 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Paxillaceae g__Alpova s__Alpova_alpestris:0.081751573,Cluster_44 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Paxillaceae g__Alpova s__Alpova_corsicus:0.010371184)1.000:0.243656453,Cluster_39 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Boletaceae g__Xerocomus s__Xerocomus_porophyllus:0.193593224)0.301:0.066026627)0.996:0.273843933,Cluster_15 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Omphalotaceae g__Gymnopus s__Gymnopus_hybridus:0.393067539)0.437:0.045071084)0.867:0.080669066,(Cluster_6 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Sarcodon s__Sarcodon_quercophilus:0.444965174,(Cluster_24 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Hydnellum s__Hydnellum_peckii:0.227921793,Cluster_34 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Hydnellum s__Hydnellum_suaveolens:0.294426018)0.195:0.072265706)0.832:0.134516905)0.742:0.057551817,(Cluster_45 k__Fungi p__Basidiomycota c__Agaricomycetes o__Hymenochaetales f__Hymenochaetaceae g__Hymenochaete s__Hymenochaete_longispora:0.366004501,Cluster_46 k__Fungi p__Basidiomycota c__Agaricomycetes o__Hymenochaetales f__Hymenochaetaceae g__Pseudochaete s__Pseudochaete_subrigidula:0.329813841)0.863:0.122725139)0.955:0.1075500335)NA;');\n tree.backColour = true;\n tree.draw();\n \t\t\t});\n" |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/15-tree-mafft.log --- a/test-data/references/15-tree-mafft.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,33 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/tree.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/tree.py --nb-cpus 2 --input-sequences res_3.2.2/09-normalisation.fasta --biom-file res_3.2.2/09-normalisation.biom --out-tree res_3.2.2/15-tree-mafft.nwk --html res_3.2.2/15-tree-mafft.html --log-file res_3.2.2/15-tree-mafft.log - -Number of input OTUs sequences: 50 - -######################################################################################################## -# Mafft multiple alignment. (mafft version : v7.407) -Command: - mafft --maxiterate 1000 --globalpair --thread 2 res_3.2.2/09-normalisation.fasta > res_3.2.2/1617285775.168374_17456_mafft_aligned.fasta 2> res_3.2.2/1617285775.168374_17456_mafft.stderr - -Execution: - start: 01 Apr 2021 16:02:55 - end: 01 Apr 2021 16:02:59 - -######################################################################################################## -# reconstruction a phylogenetic tree (FastTree version : 2.1.9) -Command: - FastTree -nt -gtr res_3.2.2/1617285775.168374_17456_mafft_aligned.fasta > res_3.2.2/1617285775.168374_17456_fasttree.nwk 2> res_3.2.2/1617285775.168374_17456_fasttree.stderr - -Execution: - start: 01 Apr 2021 16:02:59 - end: 01 Apr 2021 16:03:01 - -######################################################################################################## -# root newick tree with phangorn R package midpoint function. (root_tree.R version : 1.1.0 [R : 3.6.3; phangorn : 2.5.5]) -Command: - root_tree.R res_3.2.2/1617285775.168374_17456_fasttree.nwk res_3.2.2/15-tree-mafft.nwk - -Execution: - start: 01 Apr 2021 16:03:04 - end: 01 Apr 2021 16:03:06 - |
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| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/15-tree-mafft.nwk --- a/test-data/references/15-tree-mafft.nwk Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/15-tree-mafft.nwk Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -1,1 +1,1 @@ -(((((((((Cluster_16:0.294637021,(Cluster_5:0.058546996,Cluster_11:0.016025716)0.968:0.158266053)0.936:0.131162271,Cluster_14:0.235307367)0.754:0.054791963,Cluster_2:0.474480884)0.691:0.049780986,(Cluster_1:0.213943848,(Cluster_3:0.187178327,(Cluster_7:0.071227926,Cluster_48:0.177457902)0.791:0.044816189)0.990:0.149578112)0.571:0.060098474)0.878:0.1145429,(Cluster_18:0.018225688,(Cluster_9:0.041431417,(Cluster_4:0.037275191,Cluster_21:0.077364146)0.139:0.011858572)0.788:0.03914001)0.998:0.237984437)0.615:0.089509622,Cluster_50_FROGS_combined:0.447067258)0.631:0.098224826,Cluster_20:0.380823886)0.937:0.185254213,Cluster_6:0.433076597)0.582:0.0034002915,(((((Cluster_23:0.156578999,Cluster_47:0.389321876)0.726:0.045755266,(((((((((Cluster_29:0.046482454,(Cluster_49:0.088673283,(Cluster_40:0.06738745,(Cluster_31:0.023816152,Cluster_32:0.033996038)0.959:0.025473747)0.183:0.005896439)0.731:0.004204585)0.719:0.010771056,Cluster_27:0.062029078)0.778:0.006259972,Cluster_35:0.025392868)0.646:8e-09,Cluster_38:0.071799589)1.000:0.100797162,(Cluster_13:0.142777829,Cluster_36:0.261025139)0.732:0.042606501)0.692:0.018870899,((Cluster_26:0.222535801,((Cluster_25:0.033254493,Cluster_30:0.052359157)0.995:0.115222977,(Cluster_12:0.044056603,Cluster_19:0.103806741)0.870:0.044198623)0.973:0.105117908)0.540:0.022692709,(((Cluster_28:0.110526618,Cluster_33:0.092885557)0.814:0.049985863,(Cluster_10:0.006440785,(Cluster_22:0.131339581,Cluster_17:0.007841356)0.558:0.00137664)1.000:0.407651791)0.576:0.050558999,Cluster_41:0.109176272)0.923:0.055454674)0.500:0.029841001)0.272:0.021549163,Cluster_37:0.290557943)0.267:0.027757147,Cluster_42:0.38494924)0.656:0.010910853,Cluster_15:0.337166819)0.426:0.012687292)0.772:0.054937667,Cluster_45:0.442699665)0.013:0.053773292,((Cluster_43:0.075270238,Cluster_44:0.015753579)0.999:0.235752147,(Cluster_8:0.103502103,Cluster_39:0.171013076)0.456:0.049114709)0.996:0.222741056)0.842:0.085484652,(Cluster_46:0.448203133,(Cluster_24:0.119517963,Cluster_34:0.261732512)0.883:0.120552873)0.704:0.070724767)0.582:0.0779813415)NA; +(((((((Cluster_2:0.565519338,Cluster_14:0.253962007)0.357:0.040290393,(((Cluster_3:0.200678506,(Cluster_7:0.088418991,Cluster_48:0.201990305)0.456:0.029314029)0.854:0.057502839,Cluster_52:0.120741039)0.986:0.134618404,Cluster_1:0.184887592)0.934:0.103483495)0.844:0.052459882,(Cluster_16:0.233332685,(Cluster_5:0.065546609,Cluster_11:0.012977181)0.963:0.127628626)0.899:0.107338889)0.816:0.096326427,(Cluster_21:0.041074616,(Cluster_4:0.036800201,(Cluster_18:0.055473459,Cluster_9:0.027480818)0.612:0.015843866)0.884:0.047971353)0.991:0.253438548)0.755:0.103445723,(Cluster_50_FROGS_combined:0.35348703,Cluster_51:0.516823569)0.753:0.109855488)0.860:0.128744182,Cluster_20:0.435536194)0.955:0.1038290475,((((((((((Cluster_25:0.025860741,Cluster_30:0.060603985)0.998:0.118073548,(Cluster_12:0.053586934,Cluster_19:0.095397054)0.894:0.046532803)0.995:0.129201791,((Cluster_42:0.305111153,(Cluster_28:0.098783542,Cluster_33:0.108823979)0.925:0.057583371)0.765:0.024171338,Cluster_41:0.105304639)0.848:0.041702758)0.890:0.05608918,(Cluster_13:0.149263335,(Cluster_36:0.223659122,(Cluster_10:5e-09,(Cluster_22:0.123022832,Cluster_17:0.007911379)0.447:0.007942737)1.000:0.427330946)0.856:0.089374284)0.820:0.039578512)0.245:0.009874442,(((((Cluster_29:0.042919164,(Cluster_31:0.023205943,Cluster_32:0.036383229)0.971:0.027390497)0.798:0.009167333,(Cluster_40:0.062565372,Cluster_49:0.086069272)0.831:0.014848662)0.603:0.009776283,Cluster_27:0.065224781)0.759:0.006729621,Cluster_35:0.024764478)0.275:5e-09,Cluster_38:0.073082327)0.999:0.108735239)0.880:0.042914049,(Cluster_26:0.211429154,Cluster_37:0.288997956)0.757:0.032549439)0.188:0.047155268,(Cluster_23:0.156669249,Cluster_47:0.434570848)0.474:0.039850361)0.799:0.057651006,((Cluster_8:0.077924951,((Cluster_43:0.081751573,Cluster_44:0.010371184)1.000:0.243656453,Cluster_39:0.193593224)0.301:0.066026627)0.996:0.273843933,Cluster_15:0.393067539)0.437:0.045071084)0.867:0.080669066,(Cluster_6:0.444965174,(Cluster_24:0.227921793,Cluster_34:0.294426018)0.195:0.072265706)0.832:0.134516905)0.742:0.057551817,(Cluster_45:0.366004501,Cluster_46:0.329813841)0.863:0.122725139)0.955:0.1075500335)NA; |
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| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/16-phylo_import.Rdata |
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| Binary file test-data/references/16-phylo_import.Rdata has changed |
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| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/16-phylo_import.log --- a/test-data/references/16-phylo_import.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_import_data.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_import_data.py --biomfile data/chaillou.biom --samplefile data/sample_metadata.tsv --treefile data/tree.nwk --rdata res_3.2.2/16-phylo_import.Rdata --html res_3.2.2/16-phylo_import.nb.html --log-file res_3.2.2/16-phylo_import.log - -######################################################################################################## -# Run r_import_data.Rmd (Rscript version : [1] "R version 3.6.3 (2020-02-29)" -[1] "Rmarkdown version: 2.7" -[1] "Phyloseq version: 1.30.0") -Command: - Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_import_data.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.nb.html', params=list(biomfile='/home/maria/workspace/FROGS_dev/test/data/chaillou.biom', samplefile='/home/maria/workspace/FROGS_dev/test/data/sample_metadata.tsv', treefile='/home/maria/workspace/FROGS_dev/test/data/tree.nwk', normalisation=FALSE, outputRdata='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', ranks='Kingdom Phylum Class Order Family Genus Species', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285786.8105457_17665_rmarkdown.stderr - -Execution: - start: 01 Apr 2021 16:03:17 - end: 01 Apr 2021 16:04:10 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/16-phylo_import.nb.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/16-phylo_import.nb.html Fri Jun 04 14:56:24 2021 +0000 |
| [ |
| b'@@ -0,0 +1,479 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\n+<head>\n+\n+<meta charset="utf-8" />\n+<meta name="generator" content="pandoc" />\n+<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />\n+\n+\n+\n+\n+<title>FROGS Phyloseq: Import Data (version 3.2.3)</title>\n+\n+<script 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src="data:application/javascript;base64,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'..b'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add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+ $(\'tr.odd\').parent(\'tbody\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+ bootstrapStylePandocTables();\n+});\n+\n+$(document).ready(function () {\n+ $(\'.knitsql-table\').addClass(\'kable-table\');\n+ var container = $(\'.kable-table\');\n+ container.each(function() {\n+\n+ // move the caption out of the table\n+ var table = $(this).children(\'table\');\n+ var caption = table.children(\'caption\').detach();\n+ caption.insertBefore($(this)).css(\'display\', \'inherit\');\n+ });\n+});\n+\n+</script>\n+\n+<!-- tabsets -->\n+\n+<script>\n+$(document).ready(function () {\n+ window.buildTabsets("TOC");\n+});\n+\n+$(document).ready(function () {\n+ $(\'.tabset-dropdown > .nav-tabs > li\').click(function () {\n+ $(this).parent().toggleClass(\'nav-tabs-open\');\n+ });\n+});\n+</script>\n+\n+<!-- code folding -->\n+<script>\n+$(document).ready(function () {\n+ window.initializeSourceEmbed("phyloseq_import_data.Rmd");\n+ window.initializeCodeFolding("hide" === "show");\n+});\n+</script>\n+\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\n+<script>\n+ (function () {\n+ var script = document.createElement("script");\n+ script.type = "text/javascript";\n+ script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";\n+ document.getElementsByTagName("head")[0].appendChild(script);\n+ })();\n+</script>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/17-phylo_composition.log --- a/test-data/references/17-phylo_composition.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_composition.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_composition.py --varExp EnvType --taxaRank1 Kingdom --taxaSet1 Bacteria --taxaRank2 Phylum --numberOfTaxa 9 --rdata res_3.2.2/16-phylo_import.Rdata --html res_3.2.2/17-phylo_composition.nb.html --log-file res_3.2.2/17-phylo_composition.log - -######################################################################################################## -# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)" -[1] "Rmarkdown version: 2.7" -[1] "Phyloseq version: 1.30.0") -Command: - Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_composition.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/17-phylo_composition.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType',taxaRank1='Kingdom',taxaSet1='Bacteria',taxaRank2='Phylum',numberOfTaxa=9, libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285850.7980647_17725_rmarkdown.stderr - -Execution: - start: 01 Apr 2021 16:04:18 - end: 01 Apr 2021 16:05:08 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/18-phylo_alpha_div.log --- a/test-data/references/18-phylo_alpha_div.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_alpha_diversity.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_alpha_diversity.py --varExp EnvType --rdata res_3.2.2/16-phylo_import.Rdata --alpha-measures Observed Chao1 Shannon --alpha-out res_3.2.2/18-phylo_alpha_div.tsv --html res_3.2.2/18-phylo_alpha_div.nb.html --log-file res_3.2.2/18-phylo_alpha_div.log - -######################################################################################################## -# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)" -[1] "Rmarkdown version: 2.7" -[1] "Phyloseq version: 1.30.0") -Command: - Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_alpha_diversity.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/18-phylo_alpha_div.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', measures='Observed,Chao1,Shannon', varExp='EnvType',fileAlpha='/home/maria/workspace/FROGS_dev/test/res_3.2.2/18-phylo_alpha_div.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285909.0499587_17788_rmarkdown.stderr - -Execution: - start: 01 Apr 2021 16:05:16 - end: 01 Apr 2021 16:05:48 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/18-phylo_alpha_div.nb.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/18-phylo_alpha_div.nb.html Fri Jun 04 14:56:24 2021 +0000 |
| [ |
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| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/19-phylo_beta_div.log --- a/test-data/references/19-phylo_beta_div.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_beta_diversity.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_beta_diversity.py --varExp EnvType --distance-methods cc,unifrac --rdata res_3.2.2/16-phylo_import.Rdata --matrix-outdir res_3.2.2 --html res_3.2.2/19-phylo_beta_div.nb.html --log-file res_3.2.2/19-phylo_beta_div.log - -######################################################################################################## -# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)" -[1] "Rmarkdown version: 2.7" -[1] "Phyloseq version: 1.30.0") -Command: - Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_beta_diversity.Rmd',knit_root_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/19-phylo_beta_div.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType', methods='cc,unifrac', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285948.7069905_17848_rmarkdown.stderr - -Execution: - start: 01 Apr 2021 16:05:56 - end: 01 Apr 2021 16:06:07 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/19-phylo_beta_div.nb.html --- a/test-data/references/19-phylo_beta_div.nb.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/19-phylo_beta_div.nb.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGS Phyloseq: Beta Diversity Visualisation (version 3.2.2)</title>\n+<title>FROGS Phyloseq: Beta Diversity Visualisation (version 3.2.3)</title>\n \n <script src="data:application/javascript;base64,Ly8gUGFuZG9jIDIuOSBhZGRzIGF0dHJpYnV0ZXMgb24gYm90aCBoZWFkZXIgYW5kIGRpdi4gV2UgcmVtb3ZlIHRoZSBmb3JtZXIgKHRvCi8vIGJlIGNvbXBhdGlibGUgd2l0aCB0aGUgYmVoYXZpb3Igb2YgUGFuZG9jIDwgMi44KS4KZG9jdW1lbnQuYWRkRXZlbnRMaXN0ZW5lcignRE9NQ29udGVudExvYWRlZCcsIGZ1bmN0aW9uKGUpIHsKICB2YXIgaHMgPSBkb2N1bWVudC5xdWVyeVNlbGVjdG9yQWxsKCJkaXYuc2VjdGlvbltjbGFzcyo9J2xldmVsJ10gPiA6Zmlyc3QtY2hpbGQiKTsKICB2YXIgaSwgaCwgYTsKICBmb3IgKGkgPSAwOyBpIDwgaHMubGVuZ3RoOyBpKyspIHsKICAgIGggPSBoc1tpXTsKICAgIGlmICghL15oWzEtNl0kL2kudGVzdChoLnRhZ05hbWUpKSBjb250aW51ZTsgIC8vIGl0IHNob3VsZCBiZSBhIGhlYWRlciBoMS1oNgogICAgYSA9IGguYXR0cmlidXRlczsKICAgIHdoaWxlIChhLmxlbmd0aCA+IDApIGgucmVtb3ZlQXR0cmlidXRlKGFbMF0ubmFtZSk7CiAgfQp9KTsK"></script>\n <script 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\n \n \n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/20-phylo_structure.log --- a/test-data/references/20-phylo_structure.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_structure.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_structure.py --varExp EnvType --ordination-method MDS --rdata res_3.2.2/16-phylo_import.Rdata --distance-matrix res_3.2.2/unifrac.tsv --html res_3.2.2/20-phylo_structure.nb.html --log-file res_3.2.2/20-phylo_structure.log - -######################################################################################################## -# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)" -[1] "Rmarkdown version: 2.7" -[1] "Phyloseq version: 1.30.0") -Command: - Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_structure.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/20-phylo_structure.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.2/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617285967.7486155_17907_rmarkdown.stderr - -Execution: - start: 01 Apr 2021 16:06:15 - end: 01 Apr 2021 16:07:04 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/21-phylo_clustering.log --- a/test-data/references/21-phylo_clustering.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_clustering.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_clustering.py --varExp EnvType --rdata res_3.2.2/16-phylo_import.Rdata --distance-matrix res_3.2.2/unifrac.tsv --html res_3.2.2/21-phylo_clutering.nb.html --log-file res_3.2.2/21-phylo_clustering.log - -######################################################################################################## -# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)" -[1] "Rmarkdown version: 2.7" -[1] "Phyloseq version: 1.30.0") -Command: - Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_clustering.Rmd',output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/21-phylo_clutering.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.2/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617286024.6000283_17972_rmarkdown.stderr - -Execution: - start: 01 Apr 2021 16:07:11 - end: 01 Apr 2021 16:07:22 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/21-phylo_clustering.nb.html --- a/test-data/references/21-phylo_clustering.nb.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/21-phylo_clustering.nb.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGS Phyloseq: Sample clustering using different linkage method (version 3.2.2)</title>\n+<title>FROGS Phyloseq: Sample clustering using different linkage method (version 3.2.3)</title>\n \n <script src="data:application/javascript;base64,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"></script>\n <script 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\n \n \n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/22-phylo_manova.log --- a/test-data/references/22-phylo_manova.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,15 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_manova.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_manova.py --varExp "EnvType" --rdata res_3.2.2/16-phylo_import.Rdata --distance-matrix res_3.2.2/unifrac.tsv --html res_3.2.2/22-phylo_manova.nb.html --log-file res_3.2.2/22-phylo_manova.log - -######################################################################################################## -# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.6.3 (2020-02-29)" -[1] "Rmarkdown version: 2.7" -[1] "Phyloseq version: 1.30.0") -Command: - Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/phyloseq_manova.Rmd', output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/22-phylo_manova.nb.html', params=list(phyloseq='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', varExp='EnvType',distance='/home/maria/workspace/FROGS_dev/test/res_3.2.2/unifrac.tsv', libdir ='/home/maria/miniconda3/envs/frogs@3.2.2/lib/external-lib'), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617286042.4697833_18033_rmarkdown.stderr - -Execution: - start: 01 Apr 2021 16:07:29 - end: 01 Apr 2021 16:07:39 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/22-phylo_manova.nb.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/22-phylo_manova.nb.html Fri Jun 04 14:56:24 2021 +0000 |
| [ |
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add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+ $(\'tr.odd\').parent(\'tbody\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+ bootstrapStylePandocTables();\n+});\n+\n+$(document).ready(function () {\n+ $(\'.knitsql-table\').addClass(\'kable-table\');\n+ var container = $(\'.kable-table\');\n+ container.each(function() {\n+\n+ // move the caption out of the table\n+ var table = $(this).children(\'table\');\n+ var caption = table.children(\'caption\').detach();\n+ caption.insertBefore($(this)).css(\'display\', \'inherit\');\n+ });\n+});\n+\n+</script>\n+\n+<!-- tabsets -->\n+\n+<script>\n+$(document).ready(function () {\n+ window.buildTabsets("TOC");\n+});\n+\n+$(document).ready(function () {\n+ $(\'.tabset-dropdown > .nav-tabs > li\').click(function () {\n+ $(this).parent().toggleClass(\'nav-tabs-open\');\n+ });\n+});\n+</script>\n+\n+<!-- code folding -->\n+<script>\n+$(document).ready(function () {\n+ window.initializeSourceEmbed("phyloseq_manova.Rmd");\n+ window.initializeCodeFolding("hide" === "show");\n+});\n+</script>\n+\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\n+<script>\n+ (function () {\n+ var script = document.createElement("script");\n+ script.type = "text/javascript";\n+ script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";\n+ document.getElementsByTagName("head")[0].appendChild(script);\n+ })();\n+</script>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/23-deseq2_preprocess.Rdata |
| b |
| Binary file test-data/references/23-deseq2_preprocess.Rdata has changed |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/23-deseq2_preprocess.log --- a/test-data/references/23-deseq2_preprocess.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,13 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_preprocess.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_preprocess.py --data res_3.2.2/16-phylo_import.Rdata --log-file res_3.2.2/23-deseq2_preprocess.log --out-Rdata res_3.2.2/23-deseq2_preprocess.Rdata --var EnvType - -######################################################################################################## -# Construc DESeq2 object from a Phyloseq one. (deseq2_preprocess.R version : 1.1.0 [R : 3.6.3; DESeq2 : 1.26.0; Phyloseq : 1.30.0]) -Command: - deseq2_preprocess.R --inRdata /home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata --var EnvType --outRdata /home/maria/workspace/FROGS_dev/test/res_3.2.2/23-deseq2_preprocess.Rdata 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617286059.6610422_18092_R.stderr - -Execution: - start: 01 Apr 2021 16:07:54 - end: 01 Apr 2021 16:08:17 - |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/24-deseq2_visualisation.log --- a/test-data/references/24-deseq2_visualisation.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,14 +0,0 @@ -## Application -Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_visualisation.py (version : 3.2.2) -Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_visualisation.py --phyloseqData res_3.2.2/16-phylo_import.Rdata --dds res_3.2.2/23-deseq2_preprocess.Rdata --log-file res_3.2.2/24-deseq2_visualisation.log --html res_3.2.2/24-deseq2_visualisation.nb.html --var EnvType --mod1 BoeufHache --mod2 SaumonFume - -######################################################################################################## -# Run deseq2_visualisation.Rmd (Rscript version : [1] "R version 3.6.3 (2020-02-29)" -[1] "DESeq2 version: 1.26.0") -Command: - Rscript -e "rmarkdown::render('/home/maria/miniconda3/envs/frogs@3.2.2/bin/deseq2_visualisation.Rmd', output_file='/home/maria/workspace/FROGS_dev/test/res_3.2.2/24-deseq2_visualisation.nb.html', params=list(phyloseq_data='/home/maria/workspace/FROGS_dev/test/res_3.2.2/16-phylo_import.Rdata', dds='/home/maria/workspace/FROGS_dev/test/res_3.2.2/23-deseq2_preprocess.Rdata', var='EnvType', mod1='BoeufHache', mod2='SaumonFume', padj=0.05), intermediates_dir='/home/maria/workspace/FROGS_dev/test/res_3.2.2')" 2> /home/maria/workspace/FROGS_dev/test/res_3.2.2/1617286097.1064806_18132_R.stderr - -Execution: - start: 01 Apr 2021 16:08:27 - end: 01 Apr 2021 16:09:29 - |
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| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/24-deseq2_visualisation.nb.html --- a/test-data/references/24-deseq2_visualisation.nb.html Thu Apr 08 14:30:48 2021 +0000 +++ b/test-data/references/24-deseq2_visualisation.nb.html Fri Jun 04 14:56:24 2021 +0000 |
| b |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGSSTAT DESeq2: Visualisation (version 3.2.2)</title>\n+<title>FROGSSTAT DESeq2: Visualisation (version 3.2.3)</title>\n \n <script src="data:application/javascript;base64,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"></script>\n <script src="data:application/javascript;base64,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'..b'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\n \n \n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 test-data/references/demultiplex.log --- a/test-data/references/demultiplex.log Thu Apr 08 14:30:48 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,473 +0,0 @@\n-## Application\n-Software :/home/maria/miniconda3/envs/frogs@3.2.2/bin/demultiplex.py (version : 3.2.2)\n-Command : /home/maria/miniconda3/envs/frogs@3.2.2/bin/demultiplex.py --input-R1 data/demultiplex.fastq.gz --input-barcode data/demultiplex.barcode.txt --mismatches 1 --end both --output-demultiplexed res_3.2.2//demultiplexed.tar.gz --output-excluded res_3.2.2//undemultiplexed.tar.gz --log-file res_3.2.2//demultiplex.log --summary res_3.2.2//demultiplex_summary.txt\n-\n-\n-#Demultiplexing demultiplex.fastq.gz with forward_bc in bol strand\n-########################################################################################################\n-# Demultiplex reads. (splitbc.pl version : unknown)\n-Command:\n-\tsplitbc.pl data/demultiplex.fastq.gz --bol --bcfile res_3.2.2/forward_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Demult.log\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:55:53\n-\tend: 01 Apr 2021 15:55:54\n-\n-Results :\n-\tnb seq before demultiplexing : 4513.0\n-\tnb seq after process matched : 4271.0\n-\tnb seq after process non-ambiguous : 4271.0\n-\n-#Demultiplexing ACAGCGT_R1.fastq with ACAGCGT_reverse_bc in eol strand\n-########################################################################################################\n-# Demultiplex reads. (splitbc.pl version : unknown)\n-Command:\n-\tsplitbc.pl res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/ACAGCGT_R1.fastq --eol --bcfile res_3.2.2/ACAGCGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285354.2635067_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Demult.log\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:55:54\n-\tend: 01 Apr 2021 15:55:54\n-\n-Results :\n-\tnb seq before demultiplexing : 119.0\n-\tnb seq after process matched : 85.0\n-\tnb seq after process non-ambiguous : 85.0\n-\n-#Demultiplexing ACAGTAG_R1.fastq with ACAGTAG_reverse_bc in eol strand\n-########################################################################################################\n-# Demultiplex reads. (splitbc.pl version : unknown)\n-Command:\n-\tsplitbc.pl res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/ACAGTAG_R1.fastq --eol --bcfile res_3.2.2/ACAGTAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285354.3785884_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Demult.log\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:55:54\n-\tend: 01 Apr 2021 15:55:54\n-\n-Results :\n-\tnb seq before demultiplexing : 91.0\n-\tnb seq after process matched : 65.0\n-\tnb seq after process non-ambiguous : 65.0\n-\n-#Demultiplexing ACGTCAG_R1.fastq with ACGTCAG_reverse_bc in eol strand\n-########################################################################################################\n-# Demultiplex reads. (splitbc.pl version : unknown)\n-Command:\n-\tsplitbc.pl res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/ACGTCAG_R1.fastq --eol --bcfile res_3.2.2/ACGTCAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285354.483847_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Demult.log\n-\n-Execution:\n-\tstart: 01 Apr 2021 15:55:54\n-\tend: 01 Apr 2021 15:55:54\n-\n-Results :\n-\tnb seq before demultiplexing : 166.0\n-\tnb seq after process matched : 152.0\n-\tnb seq after process non-ambiguous : 152.0\n-\n-#Demultiplexing ACTCAGT_R1.fastq with ACTCAGT_reverse_bc in eol strand\n-########################################################################################################\n-# Demultiplex reads. (splitbc.pl version : unknown)\n-Command:\n-\tsplitbc.pl res_3.2.2/1617285353.3248255_15591_tmp/1617285353.339855_15591/ACTCAGT_R1.fastq --eol --bcfile res_3.2.2/ACTCAGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617285353.3248255_15591_tmp/1617285354.5917869_15591/%_R1.fastq >> res_3.2.2/1617285353.3248255_15591_Dem'..b'ary.txt\n-\n-\n-#Demultiplexing demultiplex_test2_R1.fq.gz and demultiplex_test2_R2.fq.gz with forward_bc in bol strand\n-########################################################################################################\n-# Demultiplex reads. (splitbc.pl version : unknown)\n-Command:\n-\tsplitbc.pl data/demultiplex_test2_R1.fq.gz data/demultiplex_test2_R2.fq.gz --bol --bcfile res_3.2.2/forward_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/%_R1.fastq --prefix-r2 res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/%_R2.fastq >> res_3.2.2/1617717494.3218324_20409_Demult.log\n-\n-Execution:\n-\tstart: 06 Apr 2021 15:58:14\n-\tend: 06 Apr 2021 15:58:15\n-\n-Results :\n-\tnb seq before demultiplexing : 10.0\n-\tnb seq after process matched : 9.0\n-\tnb seq after process non-ambiguous : 8.0\n-\n-#Demultiplexing ACAGCGT_R1.fastq and ACAGCGT_R2.fastq with ACAGCGT_reverse_bc in eol strand\n-########################################################################################################\n-# Demultiplex reads. (splitbc.pl version : unknown)\n-Command:\n-\tsplitbc.pl res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/ACAGCGT_R1.fastq res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/ACAGCGT_R2.fastq --eol --bcfile res_3.2.2/ACAGCGT_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617717494.3218324_20409_tmp/1617717495.3003461_20409/%_R1.fastq --prefix-r2 res_3.2.2/1617717494.3218324_20409_tmp/1617717495.3003461_20409/%_R2.fastq >> res_3.2.2/1617717494.3218324_20409_Demult.log\n-\n-Execution:\n-\tstart: 06 Apr 2021 15:58:15\n-\tend: 06 Apr 2021 15:58:15\n-\n-Results :\n-\tnb seq before demultiplexing : 4.0\n-\tnb seq after process matched : 0.0\n-\tnb seq after process non-ambiguous : 0.0\n-\n-#Demultiplexing ACAGTAG_R1.fastq and ACAGTAG_R2.fastq with ACAGTAG_reverse_bc in eol strand\n-########################################################################################################\n-# Demultiplex reads. (splitbc.pl version : unknown)\n-Command:\n-\tsplitbc.pl res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/ACAGTAG_R1.fastq res_3.2.2/1617717494.3218324_20409_tmp/1617717494.3568892_20409/ACAGTAG_R2.fastq --eol --bcfile res_3.2.2/ACAGTAG_reverse_bc --mismatches 1 --trim --no_adapt --prefix-r1 res_3.2.2/1617717494.3218324_20409_tmp/1617717495.4231894_20409/%_R1.fastq --prefix-r2 res_3.2.2/1617717494.3218324_20409_tmp/1617717495.4231894_20409/%_R2.fastq >> res_3.2.2/1617717494.3218324_20409_Demult.log\n-\n-Execution:\n-\tstart: 06 Apr 2021 15:58:15\n-\tend: 06 Apr 2021 15:58:15\n-\n-Results :\n-\tnb seq before demultiplexing : 4.0\n-\tnb seq after process matched : 0.0\n-\tnb seq after process non-ambiguous : 0.0\n-\n-#Summarising result\n-\n-#Concatenation of undemultiplexed files 1\n-\n-#Concatenation of undemultiplexed files 2\n-\n-#Archive demultiplexed R1 and R2 files\n-########################################################################################################\n-# Archives files. (tar version : unknown)\n-Command:\n-\ttar -zcf res_3.2.2/demultiplexed.tar.gz -C res_3.2.2/1617717495.5449557_20409 MgArd0001_A_R1.fastq MgArd0002_R1.fastq MgArd0003_R1.fastq MgArd0004_R1.fastq MgArd0009_R1.fastq MgArd0010_R1.fastq MgArd0011_R1.fastq MgArd0012_R1.fastq MgArd0001_A_R2.fastq MgArd0002_R2.fastq MgArd0003_R2.fastq MgArd0004_R2.fastq MgArd0009_R2.fastq MgArd0010_R2.fastq MgArd0011_R2.fastq MgArd0012_R2.fastq\n-\n-Execution:\n-\tstart: 06 Apr 2021 15:58:15\n-\tend: 06 Apr 2021 15:58:15\n-\n-\n-#Archive undemultiplexed R1 and R2 files\n-########################################################################################################\n-# Archives files. (tar version : unknown)\n-Command:\n-\ttar -zcf res_3.2.2/undemultiplexed.tar.gz -C res_3.2.2/1617717495.557461_20409 demultiplex_test2_R1.fq.gz_excluded_demult demultiplex_test2_R2.fq.gz_excluded_demult\n-\n-Execution:\n-\tstart: 06 Apr 2021 15:58:15\n-\tend: 06 Apr 2021 15:58:15\n-\n-\n-#Removing temporary files\n' |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 tool-data/frogs_contaminant_db.loc.sample --- a/tool-data/frogs_contaminant_db.loc.sample Thu Apr 08 14:30:48 2021 +0000 +++ b/tool-data/frogs_contaminant_db.loc.sample Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -43,4 +43,4 @@ #-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq # #phiX phiX tool-data/contaminant_db/phi.fa -#Arabido_TAIR10_Chl_Mito Arabidopsis TAIR10 Chloroplast and mitochondrie tool-data/contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa +#Arabido_TAIR10_Chl_Mito Arabidopsis TAIR10 Chloroplast and mitochondria tool-data/contaminant_db/Araport11-TAIR10Col0_Chl_MT.fa |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 tree.xml --- a/tree.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/tree.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,14 +15,15 @@ # 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="3.2.2"> +<tool id="FROGS_Tree" name="FROGS Tree" version="3.2.3"> <description>Reconstruction of phylogenetic tree </description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> <requirement type="package" version="7.407">mafft</requirement> <requirement type="package" version="2.1.09">fasttree</requirement> - <requirement type="package" version="3.6.3">r-base</requirement> - <requirement type="package" version="2.5.5">r-phangorn</requirement> + <requirement type="package" version="4.0.5">r-base</requirement> + <requirement type="package" version="4.0">r-essentials</requirement> + <requirement type="package" version="2.7.0">r-phangorn</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -62,7 +63,7 @@ <has_text_matching expression="abundance_removed.*:\s0" /> <has_text_matching expression="abundance_kept.*:\s300" /> <has_text_matching expression="otu_removed.*:\s0" /> - <has_text_matching expression="otu_kept.*:\s50" /> + <has_text_matching expression="otu_kept.*:\s52" /> </assert_contents> </output> </test> |
| b |
| diff -r 834843ebe569 -r 2ed857799fd5 tsv_to_biom.xml --- a/tsv_to_biom.xml Thu Apr 08 14:30:48 2021 +0000 +++ b/tsv_to_biom.xml Fri Jun 04 14:56:24 2021 +0000 |
| b |
| @@ -15,10 +15,10 @@ # 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="3.2.2"> +<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="3.2.3"> <description>Converts a TSV file in a BIOM file.</description> <requirements> - <requirement type="package" version="3.2.2">frogs</requirement> + <requirement type="package" version="3.2.3">frogs</requirement> </requirements> <stdio> <exit_code range="1:" /> |
