| Previous changeset 4:445b04a65ed8 (2022-05-16) Next changeset 6:b2967b704d6b (2023-05-23) |
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Commit message:
"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 38a21bfbbb70a5752ea12898bce9c5601dfcca65" |
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modified:
clustering.xml deseq2_visualisation.xml frogsfunc_copynumbers.xml frogsfunc_pathways.xml frogsfunc_placeseqs.xml macros.xml normalisation.xml otu_filters.xml phyloseq_clustering.xml preprocess.xml 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.excluded 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.nb.html test-data/references/18-phylo_alpha_div.nb.html test-data/references/19-phylo_beta_div.nb.html test-data/references/21-phylo_clustering.nb.html test-data/references/22-phylo_manova.nb.html test-data/references/23-deseq2_preprocess.Rdata test-data/references/24-deseq2_visualisation.nb.html test-data/references/25-frogsfunc_placeseqs.biom test-data/references/25-frogsfunc_placeseqs.fasta test-data/references/25-frogsfunc_placeseqs_closests_ref_sequences.txt test-data/references/25-frogsfunc_placeseqs_excluded.txt test-data/references/25-frogsfunc_placeseqs_report.html test-data/references/25-frogsfunc_placeseqs_tree.nwk test-data/references/26-frogsfunc_copynumbers_marker.tsv test-data/references/26-frogsfunc_copynumbers_predicted_functions.tsv test-data/references/26-frogsfunc_copynumbers_report.html test-data/references/27-frogsfunc_functions_excluded.txt test-data/references/27-frogsfunc_functions_marker_norm.tsv test-data/references/27-frogsfunc_functions_report.html test-data/references/27-frogsfunc_functions_unstrat.tsv test-data/references/27-frogsfunc_functions_weighted_nsti.tsv test-data/references/28-frogsfunc_pathways_report.html test-data/references/28-frogsfunc_pathways_unstrat.tsv tool-data/frogs_picrust2_default_dir.loc.sample tool-data/frogs_picrust2_marker_table.loc.sample tool-data/frogs_picrust2_pathway_map.loc.sample tree.xml |
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added:
test-data/input/replicate_file.tsv |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb clustering.xml --- a/clustering.xml Mon May 16 15:51:17 2022 +0000 +++ b/clustering.xml Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -46,7 +46,7 @@ <outputs> <data format="fasta" name="seed_file" label="${tool.name}: seed_sequences.fasta" from_work_dir="seeds.fasta" /> <data format="biom1" name="abundance_biom" label="${tool.name}: clustering_abundance.biom" from_work_dir="abundance.biom" /> - <data format="tsv" name="swarms_composition" label="${tool.name}: swarms_composition.tsv" from_work_dir="swarms.tsv" /> + <data format="txt" name="swarms_composition" label="${tool.name}: swarms_composition.txt" from_work_dir="swarms.tsv" /> </outputs> <tests> <test> |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb deseq2_visualisation.xml --- a/deseq2_visualisation.xml Mon May 16 15:51:17 2022 +0000 +++ b/deseq2_visualisation.xml Tue Jul 19 11:11:16 2022 +0000 |
| [ |
| @@ -67,7 +67,7 @@ <!-- lfcSE of otu_01582 --> <has_text text='[2.208' /> <!-- pvalue otu_01582 --> - <has_text text='[1.052' /> + <has_text text='[1.054' /> </assert_contents> </output> </test> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb frogsfunc_copynumbers.xml --- a/frogsfunc_copynumbers.xml Mon May 16 15:51:17 2022 +0000 +++ b/frogsfunc_copynumbers.xml Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -86,7 +86,7 @@ <test> <param name="input_biom" value="references/25-frogsfunc_placeseqs.biom" /> <param name="input_tree" value="references/25-frogsfunc_placeseqs_tree.nwk" /> - <param name="category" value="ITS" /> + <param name="category" value="16S" /> <param name="function" value="EC"/> <param name="hsp_method" value="mp" /> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb frogsfunc_pathways.xml --- a/frogsfunc_pathways.xml Mon May 16 15:51:17 2022 +0000 +++ b/frogsfunc_pathways.xml Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -75,7 +75,7 @@ <tests> <test> - <param name="input_file" value="input/frogsfunc_functions_unstrat.tsv" /> + <param name="input_file" value="references/27-frogsfunc_functions_unstrat.tsv" /> <param name="category" value="16S" /> <output name="abund" file="references/28-frogsfunc_pathways_unstrat.tsv" compare="diff" lines_diff="0" /> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb frogsfunc_placeseqs.xml --- a/frogsfunc_placeseqs.xml Mon May 16 15:51:17 2022 +0000 +++ b/frogsfunc_placeseqs.xml Tue Jul 19 11:11:16 2022 +0000 |
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| @@ -135,6 +135,9 @@ So, if the tool crashes with EPA-ng, try again with SEPP. +.. class:: warningmark + +SEPP is not usable for ITS and 18S analysis. .. class:: h3 @@ -205,4 +208,4 @@ </help> <expand macro="citations" /> -</tool> +</tool> \ No newline at end of file |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb macros.xml --- a/macros.xml Mon May 16 15:51:17 2022 +0000 +++ b/macros.xml Tue Jul 19 11:11:16 2022 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">4.0.0</token> + <token name="@TOOL_VERSION@">4.0.1</token> <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb normalisation.xml --- a/normalisation.xml Mon May 16 15:51:17 2022 +0000 +++ b/normalisation.xml Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -69,7 +69,8 @@ <param name="input_fasta" value="references/08-affiliation_postprocessed.fasta"/> <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/> <conditional name="sampling_method"> - <param name="sampling_by_min" value="true"/> + <param name="sampling_by_min" value="no"/> + <param name="num_reads" value="100"/> </conditional> <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" /> <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" /> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb otu_filters.xml --- a/otu_filters.xml Mon May 16 15:51:17 2022 +0000 +++ b/otu_filters.xml Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -157,6 +157,11 @@ <param name="which_contaminantSource" value="server"/> <param name="contaminant_db" value="phiX_test" /> </conditional> + <conditional name="choice_prevalence_method"> + <param name="prevalence_method" value="replicate" /> + <param name="replicate_file" value="input/replicate_file.tsv" /> + <param name="min_replicate_presence" value="0.5"/> + </conditional> <output name="output_fasta" file="references/04-filters.fasta" compare="diff" lines_diff="0" /> <output name="output_biom" file="references/04-filters.biom" compare="sim_size" delta="0" /> <output name="output_excluded" file="references/04-filters.excluded" compare="diff" lines_diff="0" /> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb phyloseq_clustering.xml --- a/phyloseq_clustering.xml Mon May 16 15:51:17 2022 +0000 +++ b/phyloseq_clustering.xml Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -31,7 +31,7 @@ <!-- <output name="html" file="references/21-phylo_clustering.nb.html" compare="diff" lines_diff="0"/> --> <output name="html"> <assert_contents> - <has_text text='FROGS Phyloseq: Sample clustering using different linkage method (version 4.0.0)' /> + <has_text text='FROGS Phyloseq: Sample clustering using different linkage method (version 4.0.1)' /> <has_text text='Phyloseq 1.38.0' /> <has_text text='Ward D2' /> <has_text text='Complete' /> |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb preprocess.xml --- a/preprocess.xml Mon May 16 15:51:17 2022 +0000 +++ b/preprocess.xml Tue Jul 19 11:11:16 2022 +0000 |
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| @@ -93,8 +93,8 @@ <!-- Samples --> <conditional name="input_type"> <param name="input_type_selected" type="select" label="Input type" help="Samples files can be provided in a single TAR archive or sample by sample (with one or two files each)."> - <option value="files_by_samples" selected="true">Files by samples</option> - <option value="archive">TAR Archive</option> + <option value="files_by_samples" >Files by samples</option> + <option value="archive" selected="true">TAR Archive</option> </param> <when value="archive"> <param name="archive_file" type="data" format="tar,tgz" label="TAR archive file" help="The TAR file containing the sequences file(s) for each sample." /> |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/input/replicate_file.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/replicate_file.tsv Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +01_subsample group_1 +02_subsample group_1 +03_subsample group_2 \ No newline at end of file |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/01-prepro-flash.html --- a/test-data/references/01-prepro-flash.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/01-prepro-flash.html Tue Jul 19 11:11:16 2022 +0000 |
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| @@ -19,7 +19,7 @@ <head> <title>FROGS Pre-process</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <!-- CSS --> |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/01-prepro-vsearch.html --- a/test-data/references/01-prepro-vsearch.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/01-prepro-vsearch.html Tue Jul 19 11:11:16 2022 +0000 |
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| @@ -19,7 +19,7 @@ <head> <title>FROGS Pre-process</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <!-- CSS --> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/02-clustering_denoising.biom --- a/test-data/references/02-clustering_denoising.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/02-clustering_denoising.biom Tue Jul 19 11:11:16 2022 +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": "2022-05-05T10:35:53", "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": 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"sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/02-clustering_fastidious.biom --- a/test-data/references/02-clustering_fastidious.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/02-clustering_fastidious.biom Tue Jul 19 11:11:16 2022 +0000 |
| [ |
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| [ |
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newline at end of file\n' |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/03-chimera.html --- a/test-data/references/03-chimera.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/03-chimera.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Remove Chimera</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <!-- 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> |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/04-filters.biom --- a/test-data/references/04-filters.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/04-filters.biom Tue Jul 19 11:11:16 2022 +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": "2022-05-05T10:34:55", "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 445b04a65ed8 -r 37e6f0c959bb test-data/references/04-filters.excluded --- a/test-data/references/04-filters.excluded Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/04-filters.excluded Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -1,74866 +1,74866 @@\n-#Present in less than 3 samples\tAbundance < 0.005% (i.e 8 sequences )\tPresent in databank of contaminants\n-Cluster_57_FROGS_combined\tCluster_56\t\n-Cluster_58_FROGS_combined\tCluster_57_FROGS_combined\t\n-Cluster_59_FROGS_combined\tCluster_58_FROGS_combined\t\n-Cluster_60_FROGS_combined\tCluster_59_FROGS_combined\t\n-Cluster_61_FROGS_combined\tCluster_60_FROGS_combined\t\n-Cluster_62_FROGS_combined\tCluster_61_FROGS_combined\t\n-Cluster_63_FROGS_combined\tCluster_62_FROGS_combined\t\n-Cluster_64_FROGS_combined\tCluster_63_FROGS_combined\t\n-Cluster_65_FROGS_combined\tCluster_64_FROGS_combined\t\n-Cluster_66_FROGS_combined\tCluster_65_FROGS_combined\t\n-Cluster_67_FROGS_combined\tCluster_66_FROGS_combined\t\n-Cluster_68_FROGS_combined\tCluster_67_FROGS_combined\t\n-Cluster_69_FROGS_combined\tCluster_68_FROGS_combined\t\n-Cluster_70_FROGS_combined\tCluster_69_FROGS_combined\t\n-Cluster_71_FROGS_combined\tCluster_70_FROGS_combined\t\n-Cluster_72_FROGS_combined\tCluster_71_FROGS_combined\t\n-Cluster_73_FROGS_combined\tCluster_72_FROGS_combined\t\n-Cluster_74_FROGS_combined\tCluster_73_FROGS_combined\t\n-Cluster_75_FROGS_combined\tCluster_74_FROGS_combined\t\n-Cluster_76_FROGS_combined\tCluster_75_FROGS_combined\t\n-Cluster_77_FROGS_combined\tCluster_76_FROGS_combined\t\n-Cluster_78_FROGS_combined\tCluster_77_FROGS_combined\t\n-Cluster_79_FROGS_combined\tCluster_78_FROGS_combined\t\n-Cluster_80_FROGS_combined\tCluster_79_FROGS_combined\t\n-Cluster_81_FROGS_combined\tCluster_80_FROGS_combined\t\n-Cluster_82_FROGS_combined\tCluster_81_FROGS_combined\t\n-Cluster_83_FROGS_combined\tCluster_82_FROGS_combined\t\n-Cluster_84_FROGS_combined\tCluster_83_FROGS_combined\t\n-Cluster_85_FROGS_combined\tCluster_84_FROGS_combined\t\n-Cluster_86_FROGS_combined\tCluster_85_FROGS_combined\t\n-Cluster_87_FROGS_combined\tCluster_86_FROGS_combined\t\n-Cluster_88_FROGS_combined\tCluster_87_FROGS_combined\t\n-Cluster_89_FROGS_combined\tCluster_88_FROGS_combined\t\n-Cluster_90_FROGS_combined\tCluster_89_FROGS_combined\t\n-Cluster_91_FROGS_combined\tCluster_90_FROGS_combined\t\n-Cluster_92_FROGS_combined\tCluster_91_FROGS_combined\t\n-Cluster_93_FROGS_combined\tCluster_92_FROGS_combined\t\n-Cluster_94_FROGS_combined\tCluster_93_FROGS_combined\t\n-Cluster_95_FROGS_combined\tCluster_94_FROGS_combined\t\n-Cluster_96_FROGS_combined\tCluster_95_FROGS_combined\t\n-Cluster_97_FROGS_combined\tCluster_96_FROGS_combined\t\n-Cluster_98_FROGS_combined\tCluster_97_FROGS_combined\t\n-Cluster_99_FROGS_combined\tCluster_98_FROGS_combined\t\n-Cluster_100_FROGS_combined\tCluster_99_FROGS_combined\t\n-Cluster_101_FROGS_combined\tCluster_100_FROGS_combined\t\n-Cluster_102_FROGS_combined\tCluster_101_FROGS_combined\t\n-Cluster_103_FROGS_combined\tCluster_102_FROGS_combined\t\n-Cluster_104_FROGS_combined\tCluster_103_FROGS_combined\t\n-Cluster_105_FROGS_combined\tCluster_104_FROGS_combined\t\n-Cluster_106_FROGS_combined\tCluster_105_FROGS_combined\t\n-Cluster_107_FROGS_combined\tCluster_106_FROGS_combined\t\n-Cluster_108_FROGS_combined\tCluster_107_FROGS_combined\t\n-Cluster_109_FROGS_combined\tCluster_108_FROGS_combined\t\n-Cluster_110_FROGS_combined\tCluster_109_FROGS_combined\t\n-Cluster_111_FROGS_combined\tCluster_110_FROGS_combined\t\n-Cluster_112_FROGS_combined\tCluster_111_FROGS_combined\t\n-Cluster_113_FROGS_combined\tCluster_112_FROGS_combined\t\n-Cluster_114_FROGS_combined\tCluster_113_FROGS_combined\t\n-Cluster_115_FROGS_combined\tCluster_114_FROGS_combined\t\n-Cluster_116_FROGS_combined\tCluster_115_FROGS_combined\t\n-Cluster_117_FROGS_combined\tCluster_116_FROGS_combined\t\n-Cluster_118_FROGS_combined\tCluster_117_FROGS_combined\t\n-Cluster_119_FROGS_combined\tCluster_118_FROGS_combined\t\n-Cluster_120_FROGS_combined\tCluster_119_FROGS_combined\t\n-Cluster_121_FROGS_combined\tCluster_120_FROGS_combined\t\n-Cluster_122_FROGS_combined\tCluster_121_FROGS_combined\t\n-Cluster_123_FROGS_combined\tCluster_122_FROGS_combined\t\n-Cluster_124_FROGS_combined\tCluster_123_FROGS_combined\t\n-Cluster_125_FROGS_combined\tCluster_124_FROGS_combined\t\n-Cluster_126_FROGS_combined\tCluster_125_FROGS_combined\t\n-Cluster_127_FROGS_combined\tCluster_126_FROGS_comb'..b'\tCluster_74798_FROGS_combined\t\n+\tCluster_74799_FROGS_combined\t\n+\tCluster_74800_FROGS_combined\t\n+\tCluster_74801_FROGS_combined\t\n+\tCluster_74802_FROGS_combined\t\n+\tCluster_74803_FROGS_combined\t\n+\tCluster_74804_FROGS_combined\t\n+\tCluster_74805_FROGS_combined\t\n+\tCluster_74806_FROGS_combined\t\n+\tCluster_74807_FROGS_combined\t\n+\tCluster_74808_FROGS_combined\t\n+\tCluster_74809_FROGS_combined\t\n+\tCluster_74810_FROGS_combined\t\n+\tCluster_74811_FROGS_combined\t\n+\tCluster_74812_FROGS_combined\t\n+\tCluster_74813_FROGS_combined\t\n+\tCluster_74814_FROGS_combined\t\n+\tCluster_74815_FROGS_combined\t\n+\tCluster_74816_FROGS_combined\t\n+\tCluster_74817_FROGS_combined\t\n+\tCluster_74818_FROGS_combined\t\n+\tCluster_74819_FROGS_combined\t\n+\tCluster_74820_FROGS_combined\t\n+\tCluster_74821_FROGS_combined\t\n+\tCluster_74822_FROGS_combined\t\n+\tCluster_74823_FROGS_combined\t\n+\tCluster_74824_FROGS_combined\t\n+\tCluster_74825_FROGS_combined\t\n+\tCluster_74826_FROGS_combined\t\n+\tCluster_74827_FROGS_combined\t\n+\tCluster_74828_FROGS_combined\t\n+\tCluster_74829_FROGS_combined\t\n+\tCluster_74830_FROGS_combined\t\n+\tCluster_74831_FROGS_combined\t\n+\tCluster_74832_FROGS_combined\t\n+\tCluster_74833_FROGS_combined\t\n+\tCluster_74834_FROGS_combined\t\n+\tCluster_74835_FROGS_combined\t\n+\tCluster_74836_FROGS_combined\t\n+\tCluster_74837_FROGS_combined\t\n+\tCluster_74838_FROGS_combined\t\n+\tCluster_74839_FROGS_combined\t\n+\tCluster_74840_FROGS_combined\t\n+\tCluster_74841_FROGS_combined\t\n+\tCluster_74842_FROGS_combined\t\n+\tCluster_74843_FROGS_combined\t\n+\tCluster_74844_FROGS_combined\t\n+\tCluster_74845_FROGS_combined\t\n+\tCluster_74846_FROGS_combined\t\n+\tCluster_74847_FROGS_combined\t\n+\tCluster_74848_FROGS_combined\t\n+\tCluster_74849_FROGS_combined\t\n+\tCluster_74850_FROGS_combined\t\n+\tCluster_74851_FROGS_combined\t\n+\tCluster_74852_FROGS_combined\t\n+\tCluster_74853_FROGS_combined\t\n+\tCluster_74854_FROGS_combined\t\n+\tCluster_74855_FROGS_combined\t\n+\tCluster_74856_FROGS_combined\t\n+\tCluster_74857_FROGS_combined\t\n+\tCluster_74858_FROGS_combined\t\n+\tCluster_74859_FROGS_combined\t\n+\tCluster_74860_FROGS_combined\t\n+\tCluster_74861_FROGS_combined\t\n+\tCluster_74862_FROGS_combined\t\n+\tCluster_74863_FROGS_combined\t\n+\tCluster_74864_FROGS_combined\t\n+\tCluster_74865_FROGS_combined\t\n+\tCluster_74866_FROGS_combined\t\n+\tCluster_74867_FROGS_combined\t\n+\tCluster_74868_FROGS_combined\t\n+\tCluster_74869_FROGS_combined\t\n+\tCluster_74870_FROGS_combined\t\n+\tCluster_74871_FROGS_combined\t\n+\tCluster_74872_FROGS_combined\t\n+\tCluster_74873_FROGS_combined\t\n+\tCluster_74874_FROGS_combined\t\n+\tCluster_74875_FROGS_combined\t\n+\tCluster_74876_FROGS_combined\t\n+\tCluster_74877_FROGS_combined\t\n+\tCluster_74878_FROGS_combined\t\n+\tCluster_74879_FROGS_combined\t\n+\tCluster_74880_FROGS_combined\t\n+\tCluster_74881_FROGS_combined\t\n+\tCluster_74882_FROGS_combined\t\n+\tCluster_74883_FROGS_combined\t\n+\tCluster_74884_FROGS_combined\t\n+\tCluster_74885_FROGS_combined\t\n+\tCluster_74886_FROGS_combined\t\n+\tCluster_74887_FROGS_combined\t\n+\tCluster_74888_FROGS_combined\t\n+\tCluster_74889_FROGS_combined\t\n+\tCluster_74890_FROGS_combined\t\n+\tCluster_74891_FROGS_combined\t\n+\tCluster_74892_FROGS_combined\t\n+\tCluster_74893_FROGS_combined\t\n+\tCluster_74894_FROGS_combined\t\n+\tCluster_74895_FROGS_combined\t\n+\tCluster_74896_FROGS_combined\t\n+\tCluster_74897_FROGS_combined\t\n+\tCluster_74898_FROGS_combined\t\n+\tCluster_74899_FROGS_combined\t\n+\tCluster_74900_FROGS_combined\t\n+\tCluster_74901_FROGS_combined\t\n+\tCluster_74902_FROGS_combined\t\n+\tCluster_74903_FROGS_combined\t\n+\tCluster_74904_FROGS_combined\t\n+\tCluster_74905_FROGS_combined\t\n+\tCluster_74906_FROGS_combined\t\n+\tCluster_74907_FROGS_combined\t\n+\tCluster_74908_FROGS_combined\t\n+\tCluster_74909_FROGS_combined\t\n+\tCluster_74910_FROGS_combined\t\n+\tCluster_74911_FROGS_combined\t\n+\tCluster_74912_FROGS_combined\t\n+\tCluster_74913_FROGS_combined\t\n+\tCluster_74914_FROGS_combined\t\n+\tCluster_74915_FROGS_combined\t\n+\tCluster_74916_FROGS_combined\t\n+\tCluster_74917_FROGS_combined\t\n+\tCluster_74918_FROGS_combined\t\n+\tCluster_74919_FROGS_combined\t\n+\tCluster_74920_FROGS_combined\t\n+\tCluster_74921_FROGS_combined\t\n \tCluster_74922_FROGS_combined\t\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/04-filters.html --- a/test-data/references/04-filters.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/04-filters.html Tue Jul 19 11:11:16 2022 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS OTU Filters</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <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"> @@ -576,7 +576,7 @@ // Data // /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - var processed_filters = ["Present in less than 3 samples", "Abundance < 0.005% (i.e 8 sequences )", "Present in databank of contaminants"] ; + var processed_filters = ["Present in less than 50.0% of replicates of all replicate groups.", "Abundance < 0.005% (i.e 8 sequences )", "Present in databank of contaminants"] ; /* Example: ['filterA', 'filterB', 'filterC'] */ @@ -589,7 +589,7 @@ 'nb_seq_ini': 100000 } */ - var by_samples_results = {"01_subsample": {"initial": 25127, "filtered": {"Present in less than 3 samples": 25071, "Abundance < 0.005% (i.e 8 sequences )": 25072}, "kept": 55}, "02_subsample": {"initial": 24947, "filtered": {"Present in less than 3 samples": 24891, "Abundance < 0.005% (i.e 8 sequences )": 24892}, "kept": 55}, "03_subsample": {"initial": 24960, "filtered": {"Present in less than 3 samples": 24904, "Abundance < 0.005% (i.e 8 sequences )": 24905}, "kept": 55}} ; + var by_samples_results = {"01_subsample": {"initial": 25127, "filtered": {"Abundance < 0.005% (i.e 8 sequences )": 25072}, "kept": 55}, "02_subsample": {"initial": 24947, "filtered": {"Abundance < 0.005% (i.e 8 sequences )": 24892}, "kept": 55}, "03_subsample": {"initial": 24960, "filtered": {"Abundance < 0.005% (i.e 8 sequences )": 24905}, "kept": 55}} ; /* Example: { 'sampleA':{ @@ -609,10 +609,10 @@ } } */ - var replicate_groups = {} ; + var replicate_groups = {"group_1": {"Replicates": "01_subsample, 02_subsample"}, "group_2": {"Replicates": "03_subsample"}} ; - var by_filters_results = [{"filters": ["Present in less than 3 samples", "Abundance < 0.005% (i.e 8 sequences )"], "count": 74864}, {"filters": ["Abundance < 0.005% (i.e 8 sequences )"], "count": 1}] ; + var by_filters_results = [{"filters": ["Abundance < 0.005% (i.e 8 sequences )"], "count": 74865}] ; /* Example: [ {'filters':['filterA'], 'count': 10}, |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/05-itsx.biom --- a/test-data/references/05-itsx.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/05-itsx.biom Tue Jul 19 11:11:16 2022 +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": "2022-05-05T10:34:55", "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], 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newline at end of file\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/05-itsx.html --- a/test-data/references/05-itsx.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/05-itsx.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS ITSx</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <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 445b04a65ed8 -r 37e6f0c959bb test-data/references/06-affiliation.biom --- a/test-data/references/06-affiliation.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/06-affiliation.biom Tue Jul 19 11:11:16 2022 +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": "2022-05-05T10:34:55", "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", 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"matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/06-affiliation.html --- a/test-data/references/06-affiliation.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/06-affiliation.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <!-- 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 445b04a65ed8 -r 37e6f0c959bb test-data/references/07-affiliation_deleted.biom --- a/test-data/references/07-affiliation_deleted.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/07-affiliation_deleted.biom Tue Jul 19 11:11:16 2022 +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": "2022-05-05T10:37:06", "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": 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"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": 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"matrix_type": "sparse"}\n\\ No newline at end of file\n' |
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| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/07-affiliation_deleted.html --- a/test-data/references/07-affiliation_deleted.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/07-affiliation_deleted.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation Filters</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <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 445b04a65ed8 -r 37e6f0c959bb test-data/references/07-affiliation_masked.biom --- a/test-data/references/07-affiliation_masked.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/07-affiliation_masked.biom Tue Jul 19 11:11:16 2022 +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": "2022-05-05T10:37:05", "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": 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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", 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"sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/07-affiliation_masked.html --- a/test-data/references/07-affiliation_masked.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/07-affiliation_masked.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation Filters</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <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 445b04a65ed8 -r 37e6f0c959bb test-data/references/08-affiliation_postprocessed.biom --- a/test-data/references/08-affiliation_postprocessed.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/08-affiliation_postprocessed.biom Tue Jul 19 11:11:16 2022 +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": "2022-05-05T10:37:06", "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": 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"matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/09-normalisation.biom --- a/test-data/references/09-normalisation.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/09-normalisation.biom Tue Jul 19 11:11:16 2022 +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 None% elements by sample from tools/frogs/test-data/references/08-affiliation_postprocessed.biom", "date": "2022-05-10T15:09:00", "rows": [{"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"], "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_11", "metadata": {"comment": [], "seed_id": "01_90304", "blast_affiliations": [{"subject": "AB594796_SH278638.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Adisciso", "s__Adisciso_tricellulare"], "evalue": "8.06e-132", "aln_length": 248, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Adisciso", "s__Adisciso_tricellulare"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Adisciso", "s__Adisciso_tricellulare"], "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_45", "metadata": {"comment": [], "seed_id": "01_60", "blast_affiliations": [{"subject": "JQ279537_SH175098.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "evalue": "0.0", "aln_length": 337, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "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_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_s'..b', {"id": "Cluster_48", "metadata": {"comment": [], "seed_id": "01_86", "blast_affiliations": [{"subject": "GQ169315_SH195598.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_caninus"], "evalue": "3.70e-130", "aln_length": 245, "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_caninus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_caninus"], "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_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, 3], [0, 1, 3], [0, 2, 5], [1, 0, 2], [1, 2, 5], [2, 0, 3], [2, 1, 2], [2, 2, 1], [3, 0, 2], [3, 1, 3], [3, 2, 5], [4, 0, 3], [4, 1, 2], [5, 0, 1], [5, 1, 2], [5, 2, 1], [6, 0, 2], [6, 1, 2], [6, 2, 2], [7, 0, 3], [7, 1, 3], [7, 2, 5], [8, 0, 3], [8, 1, 2], [9, 0, 5], [9, 1, 1], [10, 0, 2], [10, 1, 4], [10, 2, 2], [11, 0, 4], [11, 2, 3], [12, 0, 3], [12, 1, 3], [12, 2, 4], [13, 0, 1], [13, 1, 3], [13, 2, 3], [14, 0, 1], [14, 1, 2], [14, 2, 1], [15, 0, 2], [15, 1, 1], [15, 2, 2], [16, 0, 4], [16, 1, 1], [16, 2, 3], [17, 0, 3], [17, 1, 1], [17, 2, 1], [18, 0, 1], [18, 1, 1], [18, 2, 3], [19, 0, 4], [19, 1, 5], [19, 2, 1], [20, 0, 5], [20, 1, 2], [20, 2, 2], [21, 0, 3], [21, 1, 1], [22, 0, 1], [22, 1, 2], [22, 2, 1], [23, 0, 2], [23, 1, 5], [23, 2, 2], [24, 0, 2], [24, 1, 1], [24, 2, 2], [25, 0, 4], [25, 1, 3], [26, 0, 2], [26, 1, 2], [27, 0, 4], [27, 1, 1], [28, 0, 1], [28, 1, 2], [29, 0, 5], [29, 1, 3], [29, 2, 1], [30, 0, 3], [30, 1, 2], [30, 2, 2], [31, 0, 3], [31, 1, 2], [31, 2, 1], [32, 0, 1], [32, 1, 4], [32, 2, 1], [33, 0, 1], [33, 2, 3], [34, 0, 1], [34, 1, 3], [34, 2, 2], [35, 0, 4], [35, 1, 3], [35, 2, 4], [36, 0, 1], [36, 1, 1], [36, 2, 2], [37, 0, 1], [37, 1, 2], [37, 2, 4], [38, 0, 1], [38, 1, 2], [38, 2, 3], [39, 0, 2], [39, 1, 4], [39, 2, 2], [40, 0, 1], [40, 2, 1], [41, 1, 1], [41, 2, 3], [42, 1, 1], [42, 2, 3], [43, 1, 1], [44, 1, 5], [44, 2, 5], [45, 1, 1], [45, 2, 1], [46, 1, 2], [46, 2, 1], [47, 1, 1], [48, 1, 1], [49, 1, 1], [49, 2, 6], [50, 2, 1]], "shape": [51, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/09-normalisation.fasta --- a/test-data/references/09-normalisation.fasta Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/09-normalisation.fasta Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -98,13 +98,5 @@ 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 ->Cluster_53 reference=FJ860822_SH177722.07FU_refs position=1..242 errors=22%A -CATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC ->Cluster_54 reference=UDB016470_SH189377.07FU_refs position=1..242 errors=108%A -CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC ->Cluster_55 reference=UDB011541_SH194446.07FU_refs position=1..241 errors=109%G -GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/09-normalisation.html --- a/test-data/references/09-normalisation.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/09-normalisation.html Tue Jul 19 11:11:16 2022 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Abundance Normalisation</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <!-- 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> @@ -365,9 +365,9 @@ $(function() { var categories = ["Nb OTU before normalisation", "Nb OTU after normalisation"] ; var del_categories = ["Nb sequences"] ; - var series_by_sample = [{"name": "01_subsample", "data": [55, 55]}, {"name": "02_subsample", "data": [55, 55]}, {"name": "03_subsample", "data": [55, 55]}] ; + var series_by_sample = [{"name": "01_subsample", "data": [55, 41]}, {"name": "02_subsample", "data": [55, 46]}, {"name": "03_subsample", "data": [55, 40]}] ; var del_by_sample = [] ; - var remove_info = {"abundance_kept": 74781, "abundance_removed": 347, "nb_kept": 55, "nb_removed": 0} ; + var remove_info = {"abundance_kept": 300, "abundance_removed": 74828, "nb_kept": 51, "nb_removed": 4} ; // Remove alert $('#js-alert').remove(); @@ -488,7 +488,7 @@ </div> </div> <div id="filter-delete"> - <h2 class="pb-2 mt-4 mb-2 border-bottom">Kept samples (nb sequences < None)</h2> + <h2 class="pb-2 mt-4 mb-2 border-bottom">Kept samples (nb sequences < 100)</h2> </div> <div id="filter-log"> <h2 class="pb-2 mt-4 mb-2 border-bottom"> Normalisation summary per samples</h2> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/10-clustersStat.html --- a/test-data/references/10-clustersStat.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/10-clustersStat.html Tue Jul 19 11:11:16 2022 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Cluster stat</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <!-- 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 = [10, 36, 45, 59, 83, 243, 540, 1459, 1489, 1492, 1497, 1501, 1505, 1508, 1509, 1511, 1512, 1516, 1517, 1518, 1521, 1523, 1525, 1526, 1529, 1531, 1533, 1536, 1539, 1540, 1543, 1547, 1554, 1557, 1558, 1559, 1566, 1567, 1568, 1571, 1572, 1576, 1588, 1589, 1605, 1625] ; + var clusters_sizes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11] ; var series = [{ 'name': "All", - 'data': [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1] + 'data': [4, 2, 2, 9, 7, 7, 7, 3, 3, 4, 3] }]; var sum_series = new Array() ; - var samples_distrib = {"01_subsample": {"shared_seq": 24927, "shared_observations": 55, "own_seq": 0, "own_observations": 0}, "02_subsample": {"shared_seq": 24927, "shared_observations": 55, "own_seq": 0, "own_observations": 0}, "03_subsample": {"shared_seq": 24927, "shared_observations": 55, "own_seq": 0, "own_observations": 0}} ; - var newick = "((03_subsample,(01_subsample,02_subsample):0.021):0.024);" ; + var samples_distrib = {"01_subsample": {"shared_seq": 100, "shared_observations": 41, "own_seq": 0, "own_observations": 0}, "02_subsample": {"shared_seq": 97, "shared_observations": 43, "own_seq": 3, "own_observations": 3}, "03_subsample": {"shared_seq": 99, "shared_observations": 39, "own_seq": 1, "own_observations": 1}} ; + var newick = "((03_subsample,(01_subsample,02_subsample):0.360):0.420);" ; /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/11-affiliationsStat.html --- a/test-data/references/11-affiliationsStat.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/11-affiliationsStat.html Tue Jul 19 11:11:16 2022 +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="4.0.0">\n+\t\t<meta name="version" content="4.0.1">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -1018,9 +1018,9 @@\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__Rasamsonia_emersonii\\":{\\"0\\": 509, \\"1\\": 488, \\"2\\": 532})\\"g__Rasamsonia\\",(\\"s__Aspergillus_microcysticus\\":{\\"0\\": 26, \\"1\\": 16, \\"2\\": 17},\\"s__Aspergillus_caninus\\":{\\"0\\": 177, \\"1\\": 201, \\"2\\": 162})\\"g__Aspergillus\\")\\"f__Trichocomaceae\\",((\\"s__Elaphomyces_compleximurus\\":{\\"0\\": 514, \\"1\\": 499, \\"2\\": 530})\\"g__Elaphomyces\\")\\"f__Elaphomycetaceae\\")\\"o__Eurotiales\\",(((\\"s__Exophiala_equina\\":{\\"0\\": 512, \\"1\\": 512, \\"2\\": 533})\\"g__Exophiala\\")\\"f__Herpotrichiellaceae\\")\\"o__Chaetothyriales\\")\\"c__Eurotiomycetes\\",((((\\"s__Adisciso_tricellulare\\":{\\"0\\": 469, \\"1\\": 518, \\"2\\": 510})\\"g__Adisciso\\",(\\"s__Pestalotiopsis_diversiseta\\":{\\"0\\": 521, \\"1\\": 547, \\"2\\": 471})\\"g__Pestalotiopsis\\")\\"f__Amphisphaeriaceae\\",((\\"s__Hypoxylon_fragiforme\\":{\\"0\\": 535, \\"1\\": 508, \\"2\\": 514})\\"g__Hypoxylon\\")\\"f__Xylariaceae\\")\\"o__Xylariales\\",(((\\"s__Trichoderma_rodmanii\\":{\\"0\\": 490, \\"1\\": 524, \\"2\\": 494},\\"s__Trichoderma_cremeum\\":{\\"0\\": 514, \\"1\\": 503, \\"2\\": 495},\\"s__Trichoderma_aggressivum\\":{\\"0\\": 503, \\"1\\": 513, \\"2\\": 543},\\"s__Trichoderma_mienum\\":{\\"0\\": 526, \\"1\\": 489, \\"2\\": 551},\\"s__Trichoderma_rhododendri\\":{\\"0\\": 17, \\"1\\": 12, \\"2\\": 16})\\"g__Trichoderma\\")\\"f__Hypocreaceae\\")\\"o__Hypocreales\\",(((\\"s__Phaeoacremonium_rubrigenum\\":{\\"0\\": 495, \\"1\\": 507, \\"2\\": 523})\\"g__Phaeoacremonium\\")\\"f__Togniniaceae\\")\\"o__Diaporthales\\")\\"c__Sordariomycetes\\",((((\\"s__Terfezia_claveryi\\":{\\"0\\": 526, \\"1\\": 492, \\"2\\": 490})\\"g__Terfezia\\")\\"f__Pezizaceae\\",((\\"s__Tuber_latisporum\\":{\\"0\\": 508, \\"1\\": 509, \\"2\\": 530})\\"g__Tuber\\")\\"f__Tuberaceae\\")\\"o__Pezizales\\")\\"c__Pezizomycetes\\",((((\\"s__Lindgomyces_breviappendiculatus\\":{\\"0\\": 526, \\"1\\": 513, \\"2\\": 550})\\"g__Lindgomyces\\")\\"f__Lindgomycetaceae\\",((\\"s__Leptosphaeria_polylepidis\\":{\\"0\\": 22, \\"1\\": 28, \\"2\\": 33})\\"g__Leptosphaeria\\")\\"f__Leptosphaeriaceae\\")\\"o__Pleosporales\\")\\"c__Dothideomycetes\\")\\"p__Ascomycota\\",(((((\\"s__Cortinarius_gentianeus\\":{\\"0\\": 536, \\"1\\": 487, \\"2\\": 544},\\"s__Cortinarius_caesiocolor\\":{\\"0\\": 498, \\"1\\": 512, \\"2\\": 523},\\"s__Cortinarius_limonius\\":{\\"0\\": 534, \\"1\\": 522, \\"2\\": 511},\\"s__Cortinarius_sinapivelus\\":{\\"0\\": 473, \\"1\\": 526, \\"2\\": 518},\\"s__Cortinarius_aurantiobasis\\":{\\"0\\": 525, \\"1\\": 495, \\"2\\": 481},\\"s__Cortinarius_parkeri\\":{\\"0\\": 80, \\"1\\": 82, \\"2\\": 81},\\"s__Cortinarius_amnicola\\":{\\"0\\": 509, \\"1\\": 517, \\"2\\": 510},\\"s__Cortinarius_calojanthinus\\":{\\"0\\": 511, \\"1\\": 546, \\"2\\": 464})\\"g__Cortinarius\\",(\\"s__Phaeocollybia_kauffmanii\\":{\\"0\\": 510, \\"1\\": 469, \\"2\\": 513})\\"g__Phaeocollybia\\")\\"f__Cortinariaceae\\",((\\"s__Inocybe_sindonia\\":{\\"0\\": 540, \\"1\\": 523, \\"2\\": 513})\\"g__Inocybe\\")\\"f__Inocybaceae\\",((\\"s__Amanita_franchetii\\":{\\"0\\": 536, \\"1\\": 533, \\"2\\": 520},\\"s__Amanita_friabilis\\":{\\"0\\": 2, \\"1\\": 6, \\"2\\": 2})\\"g__Amanita\\")\\"f__Amanitaceae\\",((\\"s__Lepiota_geogenia\\":{\\"0\\": 494, \\"1\\": 507, \\"2\\": 500})\\"g__Lepiota\\")\\"f__Agaricaceae\\",((\\"s__Gymnopus_hybridus\\":{\\"0\\": 508, \\"1\\": 524, \\"2\\": 526})\\"g__Gymnopus\\")\\"f__Omphalotaceae\\",((\\"s__Pholiota_highlandensis\\":{\\"0\\": 508, \\"1\\": 539, \\"2\\": 541})\\"g__Pholiota\\",(\\"s__Hypholoma_capnoides\\":{\\"0\\": 545, \\"1\\": 504, \\"2\\": 491})\\"g__Hypholoma\\")\\"f__Strophariaceae\\",((\\"s__Tricholoma_portentosum\\":{\\"0\\": 518, \\"1\\": 512, \\"2\\": 493})\\"g__Tricholoma\\",(\\"s__Gamundia_leucophylla\\":{\\"0\\": 527, \\"1\\": 540, \\"2\\": 504'..b' 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55]}, "03_subsample": {"nb_otus": 55, "nb_seq": 24927, "Family": [28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28], "Genus": [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36], "Species": [52, 53, 53, 53, 53, 54, 54, 54, 54, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55], "OTUs": [52, 53, 53, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55]}} ;\n+\t\t\tvar rarefaction = {"01_subsample": {"nb_otus": 41, "nb_seq": 100, "Family": [2, 4, 6, 8, 10, 12, 13, 14, 14, 15, 15, 15, 15, 17, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 22, 22, 22, 22, 23, 23, 24, 24], "Genus": [2, 4, 6, 8, 10, 12, 13, 14, 15, 16, 17, 17, 17, 19, 20, 20, 21, 22, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 27, 27, 27, 27, 28, 28, 30, 30], "Species": [2, 4, 6, 8, 10, 12, 14, 15, 17, 19, 21, 21, 21, 23, 25, 25, 26, 27, 29, 29, 29, 29, 30, 30, 31, 31, 31, 32, 32, 32, 33, 34, 34, 35, 35, 35, 35, 35, 35, 35, 36, 36, 37, 37, 37, 38, 39, 39, 41, 41], "OTUs": [2, 4, 5, 7, 8, 10, 12, 14, 15, 15, 17, 19, 20, 20, 21, 23, 23, 24, 26, 27, 29, 30, 30, 31, 33, 33, 33, 33, 35, 36, 37, 37, 37, 37, 37, 37, 39, 39, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41]}, "02_subsample": {"nb_otus": 46, "nb_seq": 100, "Family": [2, 3, 5, 7, 9, 10, 11, 13, 14, 14, 14, 14, 14, 15, 15, 17, 17, 18, 18, 19, 19, 20, 20, 20, 20, 20, 21, 21, 21, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24], "Genus": [2, 3, 5, 7, 9, 10, 11, 13, 15, 16, 17, 17, 17, 18, 18, 20, 20, 21, 21, 22, 22, 23, 23, 23, 23, 23, 24, 24, 24, 25, 26, 26, 26, 26, 27, 27, 27, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 30, 30, 31], "Species": [2, 3, 5, 7, 9, 11, 13, 15, 17, 18, 20, 21, 22, 24, 24, 26, 26, 27, 28, 29, 29, 31, 32, 32, 33, 33, 35, 35, 36, 37, 39, 39, 39, 39, 40, 40, 40, 41, 41, 42, 43, 43, 43, 43, 43, 43, 44, 45, 45, 46], "OTUs": [2, 4, 6, 7, 9, 10, 12, 14, 16, 18, 20, 21, 23, 24, 25, 26, 28, 30, 31, 31, 32, 33, 33, 35, 35, 35, 36, 37, 37, 37, 37, 37, 37, 39, 39, 39, 40, 40, 42, 42, 43, 43, 44, 44, 44, 45, 45, 45, 46, 46]}, "03_subsample": {"nb_otus": 40, "nb_seq": 100, "Family": [1, 3, 5, 7, 9, 10, 10, 11, 12, 13, 13, 13, 14, 14, 15, 16, 16, 16, 16, 16, 18, 18, 19, 19, 19, 19, 20, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23], "Genus": [1, 3, 5, 7, 9, 10, 11, 12, 13, 14, 15, 15, 16, 16, 17, 18, 18, 19, 19, 19, 21, 21, 22, 22, 23, 23, 24, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 28, 28, 28, 28, 28, 28, 28, 28], "Species": [2, 4, 6, 8, 10, 12, 13, 14, 16, 17, 19, 20, 22, 22, 23, 24, 25, 26, 27, 28, 30, 30, 31, 31, 32, 32, 33, 34, 34, 34, 34, 34, 34, 34, 35, 35, 36, 37, 37, 37, 37, 37, 39, 39, 39, 40, 40, 40, 40, 40], "OTUs": [2, 4, 6, 7, 9, 11, 12, 14, 16, 17, 17, 18, 20, 20, 21, 22, 23, 24, 24, 26, 27, 28, 29, 30, 31, 31, 31, 31, 32, 33, 33, 34, 34, 34, 34, 35, 35, 36, 37, 37, 38, 39, 39, 39, 40, 40, 40, 40, 40, 40]}} ;\n \t\t\t/* Example:\n \t\t\t\t{\n \t\t\t\t\t"Surface-01": {\n@@ -1033,7 +1033,7 @@\n \t\t\t\t\t...\n \t\t\t\t}\n \t\t\t*/\t\n-\t\t\tvar rarefaction_step = 712 ;\n+\t\t\tvar rarefaction_step = 2 ;\n \t\t\t/* Example:\n \t\t\t\t1000\n \t\t\t*/\n@@ -1041,7 +1041,7 @@\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": 54, "seq": 73210}], [99.627, 100.0, {"clstr": 1, "seq": 1571}]] ;\n+\t\t\tvar alignment_scores = [[100.0, 100.0, {"clstr": 50, "seq": 296}], [99.627, 100.0, {"clstr": 1, "seq": 4}]] ;\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 445b04a65ed8 -r 37e6f0c959bb test-data/references/12-biom2tsv.tsv --- a/test-data/references/12-biom2tsv.tsv Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/12-biom2tsv.tsv Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -1,56 +1,52 @@\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\t1557\t512\t512\t533\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\t1547\t508\t509\t530\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\t1543\t514\t499\t530\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\t1559\t503\t513\t543\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\t1539\t521\t547\t471\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\t1625\t512\t570\t543\n-no da'..b'_refs\t100.0\t100.0\t7.94e-178\t331\t01_91485\tTCGAGTTTTGAAGTAAGGCTTGATGCTGGTGCGGAAACGTACATGTGCTCAGTCTTGCGCTCATTCCACTCAACACCTGTGCACTTATCGAAGTTAGTAGTCGTTCCTCCTTTAGTTAGGAGTCGTCGAGAGTCGCAAGTAATCATTAGGAAAGTTGATTTATTGACTTTTTTAAAGGTGGAAGCGTCACTTTGACTAGGAGCGGTGAAACCTTTGACTTATAATTATAAACCTTTACTTGTCTTGTAGAATGTAATGCTCCTCGTGGGCGAAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_46\t4\t1\t2\t1\n+no data\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Marasmiaceae;(1.0);g__Megacollybia;(1.0);s__Megacollybia_subfurfuracea;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Marasmiaceae;g__Megacollybia;s__Megacollybia_subfurfuracea\tEU623745_SH215851.07FU_refs\t100.0\t100.0\t0.0\t390\t01_410\tGCGGAAGGATCATTACTGAATTGAAATGCGTTAGTTAGTTGAGCTGACCTTCTCCCTTTAATGGGGGGGGGAGTAGTATGTGCTCGCTATATCGCTTTTTCTAACTCCCCACTGTGCACCTCTATTGTAGGCTACGAGTGACTCTCAAGTAGACACACTCCCATAACACACCCTTTGTGCGCAGAAGGGGGGGGAAAAGGGTCTATTTGGGTTTAAGAAGGCTTATCGGGCATCCATTTTGCTTGCTTTCGACTTTGTAGCCTATGATCTTACAACAAACTACTTTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_47\t4\t1\t0\t3\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\t1\t0\t1\t0\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\t10\t3\t3\t4\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 445b04a65ed8 -r 37e6f0c959bb test-data/references/13-affiliation_multihit.tsv --- a/test-data/references/13-affiliation_multihit.tsv Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/13-affiliation_multihit.tsv Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -1,56 +1,52 @@\n #OTUID\ttaxonomy\tsubject\tevalue\tperc_identity\tperc_query_coverage\taln_length\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_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_27\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_gentianeus\tKF732310_SH222414.07FU_refs\t5.49e-154\t100.0\t100.0\t288\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_36\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii\tUDB002317_SH221025.07FU_refs\t9.52e-162\t100.0\t100.0\t302\n+Cluster_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_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_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_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_36\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii\tUDB002317_SH221025.07FU_refs\t9.52e-162\t100.0\t100.0\t302\n-Cluster_20\tk__Fungi;p__Ascomycota;c__Pezizomycetes;o__Pezizales;f__Pezizaceae;g__Terfezia;s__Terfezia_claveryi\tGU474801_SH104786.07FU_refs_singleton\t8.56e-142\t100.0\t100.0\t266\n-Cluster_26\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Agaricaceae;g__Lepiota;s__Lepiota_geogenia\tJX179268_SH178540.07FU_refs\t2.53e-152\t100.0\t100.0\t285\n-Cluster_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_41\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Tricholoma;s__Tricholoma_portentosum\tUDB011569_SH190415.07FU_refs\t2.72e-167\t100.0\t100.0\t312\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_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_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_37\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Entolomataceae;g__Entoloma;s__Entoloma_sp\tJQ320113_SH190746.07FU_refs\t2.66e-162\t100.0\t100.0\t303\n+Cluster_44\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Paxillaceae;g__Alpova;s__Alpova_corsicus\tHQ714699_SH221418.07FU_refs\t1.69e-174\t100.0\t100.0\t325\n+Cluster_33\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Strophariaceae;g__Pholiota;s__Pholiota_highlandensis\tHG007976_SH219743.07FU_refs\t1.22e-160\t100.0\t100.0\t300\n Cluster_50_FROGS_combined\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Lindgomycetaceae;g__Lindgomyces;s__Lindgomyces_breviappendiculatus\t'..b'__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_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_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_39\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Boletaceae;g__Xerocomus;s__Xerocomus_porophyllus\tKC168089_SH480027.07FU_refs\t7.41e-163\t100.0\t100.0\t304\n Cluster_49\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_parkeri\tGQ159830_SH222371.07FU_refs\t1.33e-129\t100.0\t100.0\t244\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_48\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_caninus\tGQ169315_SH195598.07FU_refs\t3.70e-130\t100.0\t100.0\t245\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_4\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t4.90e-134\t100.0\t100.0\t252\n-Cluster_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_39\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Boletaceae;g__Xerocomus;s__Xerocomus_porophyllus\tKC168089_SH480027.07FU_refs\t7.41e-163\t100.0\t100.0\t304\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_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_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_17\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Russulales;f__Russulaceae;g__Lactarius;s__Lactarius_sp\tEU292260_SH086465.07FU_refs\t3.94e-140\t100.0\t100.0\t263\n-Cluster_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_51\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Leptosphaeriaceae;g__Leptosphaeria;s__Leptosphaeria_polylepidis\tAJ786644_SH470265.07FU_refs_singleton\t4.75e-129\t100.0\t100.0\t243\n-Cluster_53\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rhododendri\tFJ860822_SH177722.07FU_refs\t1.70e-128\t100.0\t100.0\t242\n-Cluster_54\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Thelephora;s__Thelephora_atra\tUDB016470_SH189377.07FU_refs\t1.70e-128\t100.0\t100.0\t242\n-Cluster_55\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_friabilis\tUDB011541_SH194446.07FU_refs\t6.09e-128\t100.0\t100.0\t241\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_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 445b04a65ed8 -r 37e6f0c959bb test-data/references/13-affiliation_std.biom --- a/test-data/references/13-affiliation_std.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/13-affiliation_std.biom Tue Jul 19 11:11:16 2022 +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 None% elements by sample from tools/frogs/test-data/references/08-affiliation_postprocessed.biom", "date": "2022-05-10T15:09:00", "rows": [{"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_11", "metadata": {"comment": "", "seed_id": "01_90304", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Adisciso;s__Adisciso_tricellulare", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Amphisphaeriaceae;g__Adisciso;s__Adisciso_tricellulare", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Adisciso", "s__Adisciso_tricellulare"]}}, {"id": "Cluster_27", "metadata": {"comment": "", "seed_id": "01_108", "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", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"]}}, {"id": "Cluster_45", "metadata": {"comment": "", "seed_id": "01_60", "blast_taxonomy": "k__Fungi;p__Basidiomycota;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", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"]}}, {"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_42", "metadata": {"comment": "", "seed_id": "01_69140", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Inocybaceae;g__Inocybe;s__Inocybe_sindonia", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Inocybaceae;g__Inocybe;s__Inocybe_sindonia", "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__Inocybaceae", "g__Inocybe", "s__Inocybe_sindonia"]}}, {"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__Amani'..b'", "c__Agaricomycetes", "o__Boletales", "f__Boletaceae", "g__Xerocomus", "s__Xerocomus_porophyllus"]}}, {"id": "Cluster_49", "metadata": {"comment": "", "seed_id": "01_88865", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_parkeri", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_parkeri", "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__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"]}}, {"id": "Cluster_48", "metadata": {"comment": "", "seed_id": "01_86", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_caninus", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_caninus", "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_caninus"]}}, {"id": "Cluster_28", "metadata": {"comment": "", "seed_id": "01_71661", "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", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"]}}, {"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, 3], [0, 1, 3], [0, 2, 5], [1, 0, 2], [1, 2, 5], [2, 0, 3], [2, 1, 2], [2, 2, 1], [3, 0, 2], [3, 1, 3], [3, 2, 5], [4, 0, 3], [4, 1, 2], [5, 0, 1], [5, 1, 2], [5, 2, 1], [6, 0, 2], [6, 1, 2], [6, 2, 2], [7, 0, 3], [7, 1, 3], [7, 2, 5], [8, 0, 3], [8, 1, 2], [9, 0, 5], [9, 1, 1], [10, 0, 2], [10, 1, 4], [10, 2, 2], [11, 0, 4], [11, 2, 3], [12, 0, 3], [12, 1, 3], [12, 2, 4], [13, 0, 1], [13, 1, 3], [13, 2, 3], [14, 0, 1], [14, 1, 2], [14, 2, 1], [15, 0, 2], [15, 1, 1], [15, 2, 2], [16, 0, 4], [16, 1, 1], [16, 2, 3], [17, 0, 3], [17, 1, 1], [17, 2, 1], [18, 0, 1], [18, 1, 1], [18, 2, 3], [19, 0, 4], [19, 1, 5], [19, 2, 1], [20, 0, 5], [20, 1, 2], [20, 2, 2], [21, 0, 3], [21, 1, 1], [22, 0, 1], [22, 1, 2], [22, 2, 1], [23, 0, 2], [23, 1, 5], [23, 2, 2], [24, 0, 2], [24, 1, 1], [24, 2, 2], [25, 0, 4], [25, 1, 3], [26, 0, 2], [26, 1, 2], [27, 0, 4], [27, 1, 1], [28, 0, 1], [28, 1, 2], [29, 0, 5], [29, 1, 3], [29, 2, 1], [30, 0, 3], [30, 1, 2], [30, 2, 2], [31, 0, 3], [31, 1, 2], [31, 2, 1], [32, 0, 1], [32, 1, 4], [32, 2, 1], [33, 0, 1], [33, 2, 3], [34, 0, 1], [34, 1, 3], [34, 2, 2], [35, 0, 4], [35, 1, 3], [35, 2, 4], [36, 0, 1], [36, 1, 1], [36, 2, 2], [37, 0, 1], [37, 1, 2], [37, 2, 4], [38, 0, 1], [38, 1, 2], [38, 2, 3], [39, 0, 2], [39, 1, 4], [39, 2, 2], [40, 0, 1], [40, 2, 1], [41, 1, 1], [41, 2, 3], [42, 1, 1], [42, 2, 3], [43, 1, 1], [44, 1, 5], [44, 2, 5], [45, 1, 1], [45, 2, 1], [46, 1, 2], [46, 2, 1], [47, 1, 1], [48, 1, 1], [49, 1, 1], [49, 2, 6], [50, 2, 1]], "shape": [51, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/14-tsv2biom.biom --- a/test-data/references/14-tsv2biom.biom Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/14-tsv2biom.biom Tue Jul 19 11:11:16 2022 +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": "2022-05-12T13:10:31", "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'"o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"], "seed_id": "01_88865", "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"], "subject": "GQ159830_SH222371.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "1.33e-129", "aln_length": "244"}]}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__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_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, 4], [0, 1, 3], [0, 2, 4], [1, 0, 1], [1, 1, 2], [2, 0, 2], [2, 1, 2], [2, 2, 2], [3, 0, 3], [3, 1, 2], [3, 2, 1], [4, 0, 3], [4, 1, 2], [4, 2, 1], [5, 0, 1], [5, 1, 1], [5, 2, 3], [6, 0, 5], [6, 1, 3], [6, 2, 1], [7, 0, 1], [7, 1, 2], [7, 2, 4], [8, 0, 3], [8, 1, 3], [8, 2, 5], [9, 0, 4], [9, 1, 5], [9, 2, 1], [10, 0, 1], [10, 1, 2], [10, 2, 1], [11, 1, 5], [11, 2, 5], [12, 0, 1], [12, 1, 2], [12, 2, 1], [13, 0, 1], [13, 1, 3], [13, 2, 2], [14, 0, 5], [14, 1, 2], [14, 2, 2], [15, 0, 1], [15, 1, 4], [15, 2, 1], [16, 0, 1], [16, 1, 2], [16, 2, 3], [17, 0, 1], [17, 2, 1], [18, 0, 1], [18, 1, 1], [18, 2, 2], [19, 0, 4], [19, 1, 3], [20, 0, 3], [20, 1, 3], [20, 2, 5], [21, 0, 2], [21, 1, 1], [21, 2, 2], [22, 0, 3], [22, 1, 2], [23, 0, 2], [23, 1, 2], [24, 0, 3], [24, 1, 2], [24, 2, 2], [25, 1, 1], [25, 2, 3], [26, 1, 1], [26, 2, 6], [27, 0, 4], [27, 1, 1], [27, 2, 3], [28, 1, 1], [28, 2, 3], [29, 1, 1], [30, 0, 2], [30, 1, 1], [30, 2, 2], [31, 0, 2], [31, 1, 4], [31, 2, 2], [32, 0, 4], [32, 2, 3], [33, 1, 1], [33, 2, 1], [34, 0, 3], [34, 1, 1], [35, 0, 2], [35, 2, 5], [36, 0, 5], [36, 1, 1], [37, 0, 4], [37, 1, 1], [38, 1, 2], [38, 2, 1], [39, 0, 3], [39, 1, 1], [39, 2, 1], [40, 0, 3], [40, 1, 2], [41, 0, 1], [41, 1, 3], [41, 2, 3], [42, 0, 2], [42, 1, 5], [42, 2, 2], [43, 0, 2], [43, 1, 4], [43, 2, 2], [44, 0, 2], [44, 1, 3], [44, 2, 5], [45, 0, 1], [45, 1, 2], [45, 2, 1], [46, 0, 1], [46, 2, 3], [47, 1, 1], [48, 1, 1], [49, 0, 3], [49, 1, 3], [49, 2, 4], [50, 2, 1]], "shape": [51, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/14-tsv2biom.fasta --- a/test-data/references/14-tsv2biom.fasta Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/14-tsv2biom.fasta Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -98,13 +98,5 @@ TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC >Cluster_50_FROGS_combined GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC ->Cluster_51 -CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC >Cluster_52 CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC ->Cluster_53 -CATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC ->Cluster_54 -CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC ->Cluster_55 -GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/15-tree-mafft.html --- a/test-data/references/15-tree-mafft.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/15-tree-mafft.html Tue Jul 19 11:11:16 2022 +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="4.0.0">\n+\t\t<meta name="version" content="4.0.1">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -182,7 +182,7 @@\n }\n #phylocanvas {\n width: 1150px;\n- height: 771px;\n+ height: 727px;\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": 55, "otu_removed": 0, "abundance_kept": 74781, "abundance_removed": 0} ;\n+\t\t\t\tvar summary = {"otu_kept": 51, "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_3 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Elaphomycetaceae g__Elaphomyces s__Elaphomyces_compleximurus:0.228931492,Cluster_48 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Trichocomaceae g__Aspergillus s__Aspergillus_caninus:0.192861948)0.726:0.021479097,Cluster_7 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Trichocomaceae g__Rasamsonia s__Rasamsonia_emersonii:0.104516465)0.752:0.052431144,Cluster_52 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Trichocomaceae g__Aspergillus s__Aspergillus_microcysticus:0.151910428)0.940:0.10670698,Cluster_1 k__Fungi p__Ascomycota c__Eurotiomycetes o__Chaetothyriales f__Herpotrichiellaceae g__Exophiala s__Exophiala_equina:0.241415285)0.912:0.091929423,Cluster_14 k__Fungi p__Ascomycota c__Sordariomycetes o__Diaporthales f__Togniniaceae g__Phaeoacremonium s__Phaeoacremonium_rubrigenum:0.247618429)0.561:0.037569213,Cluster_16 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Xylariaceae g__Hypoxylon s__Hypoxylon_fragiforme:0.268649758)0.346:0.046939966,(((Cluster_21 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_cremeum:0.08095992,Cluster_4 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_aggressivum:0.031529917)0.849:0.018853706,Cluster_9 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_mienum:0.036343134)0.829:0.038624338,(Cluster_18 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_rodmanii:0.022441444,Cluster_53 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_rhododendri:0.025154842)0.000:5e-09)1.000:0.337467526)0.643:0.046095768,(Cluster_5 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Amphisphaeriaceae g__Pestalotiopsis s__Pestalotiopsis_diversiseta:0.052393034,Cluster_11 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Amphisphaeriaceae g__Adisciso s__Adisciso_tricellulare:0.042348439)0.929:0.092898134)0.817:0.074080465,(Cluster_50_FROGS_combined k__Fungi p__Ascomycota c__Dothideomycetes o__Pleosporales f__Lindgomycetaceae g__Lindgomyces s__Lindgomyces_breviappendiculatus:0.332635799,Cluster_51 k__Fungi p__Ascomycota c__Dothideomycetes o__Pleosporales f__Leptosphaeriaceae g__Leptosphaeria s__Leptosphaeria_polylepidis:0.46463838)0.837:0.137535401)'..b"luster_27 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_gentianeus:0.060798929)0.344:0.012136352,Cluster_49 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_parkeri:0.095039499)0.045:0.00300424,((Cluster_31 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_calojanthinus:0.023945628,Cluster_32 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_amnicola:0.036790804)0.958:0.028655778,Cluster_29 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_caesiocolor:0.044386066)0.819:0.010793027)0.849:0.010738578)0.559:0.003353804,Cluster_38 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_sinapivelus:0.069372623)0.993:0.105128479)0.017:0.013229984,(Cluster_13 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Tricholomataceae g__Gamundia s__Gamundia_leucophylla:0.156659705,(Cluster_36 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Amanitaceae g__Amanita s__Amanita_franchetii:0.205251388,(Cluster_22 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_semisanguifluus:0.078548294,(Cluster_10 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_cyathuliformis:0.007443202,Cluster_17 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_sp:0.008409801)0.802:0.052568361)1.000:0.413872316)0.823:0.079897311)0.453:0.050493527)0.568:0.02256308)0.794:0.050158568,Cluster_23 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Phaeocollybia s__Phaeocollybia_kauffmanii:0.219154505)0.203:0.008058777,((Cluster_37 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Entolomataceae g__Entoloma s__Entoloma_sp:0.229987091,(Cluster_15 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Omphalotaceae g__Gymnopus s__Gymnopus_hybridus:0.306765932,((Cluster_43 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Paxillaceae g__Alpova s__Alpova_alpestris:0.081038866,Cluster_44 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Paxillaceae g__Alpova s__Alpova_corsicus:0.012125559)0.991:0.207372204,(Cluster_8 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Suillaceae g__Truncocolumella s__Truncocolumella_rubra:0.105259617,Cluster_39 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Boletaceae g__Xerocomus s__Xerocomus_porophyllus:0.172255302)0.926:0.124311867)0.989:0.217912513)0.630:0.057962643)0.703:0.047267291,Cluster_26 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Agaricaceae g__Lepiota s__Lepiota_geogenia:0.207396379)0.734:0.030155158)0.927:0.127462086,((Cluster_24 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Hydnellum s__Hydnellum_peckii:0.163839036,Cluster_34 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Hydnellum s__Hydnellum_suaveolens:0.160869456)0.971:0.175210167,(Cluster_45 k__Fungi p__Basidiomycota c__Agaricomycetes o__Hymenochaetales f__Hymenochaetaceae g__Hymenochaete s__Hymenochaete_longispora:0.299248251,Cluster_46 k__Fungi p__Basidiomycota c__Agaricomycetes o__Hymenochaetales f__Hymenochaetaceae g__Pseudochaete s__Pseudochaete_subrigidula:0.338231026)0.943:0.160614399)0.902:0.141998346)0.728:0.101328171,Cluster_47 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Marasmiaceae g__Megacollybia s__Megacollybia_subfurfuracea:0.347328212)0.293:0.010708491,Cluster_6 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Sarcodon s__Sarcodon_quercophilus:0.423855969)0.993:0.108399563)NA;');\n tree.backColour = true;\n tree.draw();\n \t\t\t});\n" |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/15-tree-mafft.nwk --- a/test-data/references/15-tree-mafft.nwk Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/15-tree-mafft.nwk Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -1,1 +1,1 @@ -(((((((((((((Cluster_3:0.228931492,Cluster_48:0.192861948)0.726:0.021479097,Cluster_7:0.104516465)0.752:0.052431144,Cluster_52:0.151910428)0.940:0.10670698,Cluster_1:0.241415285)0.912:0.091929423,Cluster_14:0.247618429)0.561:0.037569213,Cluster_16:0.268649758)0.346:0.046939966,(((Cluster_21:0.08095992,Cluster_4:0.031529917)0.849:0.018853706,Cluster_9:0.036343134)0.829:0.038624338,(Cluster_18:0.022441444,Cluster_53:0.025154842)0.000:5e-09)1.000:0.337467526)0.643:0.046095768,(Cluster_5:0.052393034,Cluster_11:0.042348439)0.929:0.092898134)0.817:0.074080465,(Cluster_50_FROGS_combined:0.332635799,Cluster_51:0.46463838)0.837:0.137535401)0.945:0.164731605,(Cluster_2:0.596687045,Cluster_20:0.328686743)0.051:0.053744078)0.922:0.175357393,Cluster_6:0.40609266)0.515:0.03973284,Cluster_34:0.295257608)0.829:0.048647877,((((((Cluster_54:0.299083023,(Cluster_22:0.057131977,(Cluster_10:0.006909608,Cluster_17:0.008186871)0.818:0.063648547)1.000:0.346369419)0.861:0.108016108,(Cluster_55:0.213713376,Cluster_36:0.24775276)0.777:0.053490844)0.146:0.024956278,((Cluster_45:0.264009653,Cluster_46:0.355101627)0.920:0.130512666,((Cluster_8:0.030829277,((Cluster_43:0.080471844,Cluster_44:0.012061583)1.000:0.320757268,Cluster_39:0.228108149)0.426:0.07034756)1.000:0.316193672,(Cluster_15:0.343306904,Cluster_47:0.349793421)0.778:0.08582632)0.252:0.032110862)0.645:0.08194613)0.768:0.040474582,Cluster_42:0.238787152)0.138:0.038217271,(((((Cluster_25:0.039847568,Cluster_30:0.045228031)0.999:0.131156016,(Cluster_12:0.055220844,Cluster_19:0.09412355)0.927:0.056347766)0.996:0.128970617,(((Cluster_35:0.024744934,(Cluster_38:0.070825104,((Cluster_29:0.045785635,((Cluster_40:0.060673959,Cluster_49:0.094618197)0.241:0.010115536,(Cluster_31:0.025134279,Cluster_32:0.03311579)0.975:0.028463328)0.268:0.008198031)0.501:0.011894089,Cluster_27:0.059024601)0.803:0.009127118)0.613:0.001569985)0.998:0.113287999,(Cluster_13:0.148471133,(Cluster_23:0.217924293,Cluster_26:0.193329197)0.789:0.040415572)0.725:0.037483359)0.752:0.019636186,Cluster_37:0.318908511)0.179:0.013849009)0.822:0.041164847,(Cluster_28:0.129399437,Cluster_33:0.101087615)0.990:0.082145238)0.182:0.016552393,Cluster_41:0.11161251)0.912:0.078709725)0.942:0.131453061,Cluster_24:0.282341444)0.829:0.022661013)NA; +((((((((Cluster_21:0.078518609,(Cluster_18:0.060934408,Cluster_9:0.031124161)0.740:0.007475077)0.465:0.014999311,Cluster_4:0.018679151)1.000:0.451763845,(Cluster_16:0.231638797,(Cluster_5:0.078204987,Cluster_11:5e-09)0.984:0.147973777)0.850:0.094593935)0.214:0.018165737,(Cluster_14:0.28297964,(Cluster_1:0.230652634,(Cluster_52:0.118384876,(Cluster_3:0.207009093,(Cluster_7:0.051687732,Cluster_48:0.200663742)0.818:0.036935986)0.814:0.049955676)0.959:0.114523783)0.895:0.08463776)0.586:0.073455998)0.943:0.185614753,Cluster_2:0.502067967)0.123:0.019224979,Cluster_20:0.380744372)0.599:0.113761262,Cluster_50_FROGS_combined:0.473407758)0.993:0.169441688,((((((((Cluster_41:0.086134796,Cluster_42:0.362747288)0.759:0.047525083,(Cluster_28:0.112842735,Cluster_33:0.09544452)0.971:0.084599837)0.833:0.0621266,((((Cluster_25:0.030809204,Cluster_30:0.057594336)0.997:0.120831935,(Cluster_12:0.05220405,Cluster_19:0.099672637)0.896:0.047415044)0.994:0.132500371,((Cluster_35:0.028309889,(((Cluster_40:0.068092195,Cluster_27:0.060798929)0.344:0.012136352,Cluster_49:0.095039499)0.045:0.00300424,((Cluster_31:0.023945628,Cluster_32:0.036790804)0.958:0.028655778,Cluster_29:0.044386066)0.819:0.010793027)0.849:0.010738578)0.559:0.003353804,Cluster_38:0.069372623)0.993:0.105128479)0.017:0.013229984,(Cluster_13:0.156659705,(Cluster_36:0.205251388,(Cluster_22:0.078548294,(Cluster_10:0.007443202,Cluster_17:0.008409801)0.802:0.052568361)1.000:0.413872316)0.823:0.079897311)0.453:0.050493527)0.568:0.02256308)0.794:0.050158568,Cluster_23:0.219154505)0.203:0.008058777,((Cluster_37:0.229987091,(Cluster_15:0.306765932,((Cluster_43:0.081038866,Cluster_44:0.012125559)0.991:0.207372204,(Cluster_8:0.105259617,Cluster_39:0.172255302)0.926:0.124311867)0.989:0.217912513)0.630:0.057962643)0.703:0.047267291,Cluster_26:0.207396379)0.734:0.030155158)0.927:0.127462086,((Cluster_24:0.163839036,Cluster_34:0.160869456)0.971:0.175210167,(Cluster_45:0.299248251,Cluster_46:0.338231026)0.943:0.160614399)0.902:0.141998346)0.728:0.101328171,Cluster_47:0.347328212)0.293:0.010708491,Cluster_6:0.423855969)0.993:0.108399563)NA; |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/16-phylo_import.nb.html --- a/test-data/references/16-phylo_import.nb.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/16-phylo_import.nb.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGS Phyloseq: Import Data (version 4.0.0)</title>\n+<title>FROGS Phyloseq: Import Data (version 4.0.1)</title>\n \n <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to\n // be compatible with the behavior of Pandoc < 2.8).\n@@ -1763,7 +1763,7 @@\n \n \n <h1 class="title toc-ignore">FROGS Phyloseq: Import Data (version\n-4.0.0)</h1>\n+4.0.1)</h1>\n \n </div>\n \n@@ -1966,7 +1966,7 @@\n </div>\n </div>\n \n-<div id="rmd-source-code">LS0tCnRpdGxlOiAiRlJPR1MgUGh5bG9zZXE6IEltcG9ydCBEYXRhICh2ZXJzaW9uIDQuMC4wKSIKb3V0cHV0OiAKICBodG1sX25vdGVib29rOgogICAgY29kZV9mb2xkaW5nOiBoaWRlCnBhcmFtczoKICAjIFBhdGggT1RVIGFidW5kYW5jZSBiaW9tIGZpbGUKICBiaW9tZmlsZTogCiAgICB2YWx1ZTogeAogICMgUGF0aCB0byBzYW1wbGUgbWV0YWRhdGEgVFNWIGZpbGUKICBzYW1wbGVmaWxlOgogICAgdmFsdWU6IHgKICAjIChvcHRpb25hbCkgUGF0aCB0byBPVFVzIHRyZWUgTldLIGZpbGUKICB0cmVlZmlsZToKICAgIHZhbHVlOiB4CiAgIyAob3B0aW9uYWwpIG5vcm1hbGlzYXRpb24gc3RyaW5nIG9wdGlvbiA6IFRSVUUgb3IgRkFMU0UKICBub3JtYWxpc2F0aW9uOgogICAgdmFsdWU6IHgKICAjIFBhdGggdG8gcGh5bG9zZXEgb2JqZWN0IHN0b3JlIGluIFJkYXRhIGZpbGUKICBvdXRwdXRSZGF0YToKICAgIHZhbHVlOiB4CiAgIyBMaXN0IG9mIHRheG9ub21pYyByYW5rcyBuYW1lcwogIHJhbmtzIDogCiAgICB2YWx1ZTogeAogICMgUGF0aCB0byB0aGUgcGh5bG9zZXEtZXh0ZW5kIFIgZnVuY3Rpb25zIDogaHR0cHM6Ly9naXRodWIuY29tL21haGVuZHJhLW1hcmlhZGFzc291L3BoeWxvc2VxLWV4dGVuZGVkLCB0eXBpY2FsbHkgc3RvcmVkIGluIEZST0dTL2xpYi9leHRlcm5hbC1saWIKICBsaWJkaXI6CiAgICB2YWx1ZTogeAotLS0KPG1ldGEgaHR0cC1lcXVpdj0iQ29udGVudC1UeXBlIiBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9VVRGLTgiPgo8c3R5bGUgdHlwZT0idGV4dC9jc3MiPgouYnV0dG9uIHsKICAgIGJhY2tncm91bmQtY29sb3I6ICMyYTdlY2M7IC8qIEJsdWUgKi8KICAgIGJvcmRlciAgICAgICAgICA6IG5vbmU7CiAgICBjb2xvciAgICAgICAgICAgOiB3aGl0ZTsKICAgIHBhZGRpbmcgICAgICAgICA6IDVweCAxMHB4OwogICAgdGV4dC1hbGlnbiAgICAgIDogY2VudGVyOwogICAgdGV4dC1kZWNvcmF0aW9uIDogbm9uZTsKICAgIGRpc3BsYXkgICAgICAgICA6IGlubGluZS1ibG9jazsKICAgIGZvbnQtc2l6ZSAgICAgICA6IDEycHg7CiAgICBtYXJnaW4gICAgICAgICAgOiA0cHggMnB4OwogICAgY3Vyc29yICAgICAgICAgIDogcG9pbnRlcjsKICAgIGJvcmRlci1yYWRpdXMgICA6IDhweDsKfQpoNCB7IAogICAgZGlzcGxheSAgICAgIDogYmxvY2s7CiAgICBmb250LXNpemUgICAgOiAxZW07CiAgICBtYXJnaW4tdG9wICAgOiAxLjMzZW07CiAgICBtYXJnaW4tYm90dG9tOiAxLjMzZW07CiAgICBtYXJnaW4tbGVmdCAgOiAwOwogICAgbWFyZ2luLXJpZ2h0IDogMDsKICAgIGZvbnQtd2VpZ2h0ICA6IGJvbGQ7CiAgICBjb2xvciAgICAgICAgOiAjMmE3ZWNjOwp9Cjwvc3R5bGU+CgoKYGBge3Igc2V0dXAsIGluY2x1ZGU9RkFMU0V9CmtuaXRyOjpvcHRzX2NodW5rJHNldChlY2hvID0gVFJVRSkKYGBgClBoeWxvc2VxIGByIHBhY2thZ2VWZXJzaW9uKCJwaHlsb3NlcSIpYAogCmBgYHtyIHBhY2thZ2VfaW1wb3J0LCBtZXNzYWdlPUZBTFNFLCB3YXJuaW5nPUZBTFNFfQoKIyMgSW1wb3J0IHBhY2thZ2VzCmxpYnJhcnkocGh5bG9zZXEpCmxpYnJhcnkoZ2dwbG90MikKbGlicmFyeShhcGUpCgojIyBTZXR0aW4gdmFyaWFibGVzCiAgIyMgVGhlIE9UVSBhYnVuZGFuY2UgbWF0cml4IHdpdGggdGF4b25vbXkgYW5ub3RhdGlvbiBmaWxlIChiaW9tIGZvcm1hdCkKICAjIGJpb21maWxlIDwtICIiCgogICMjIFRoZSBzYW1wbGUgbWV0YWRhdGEgZmlsZShUU1YgZm9ybWF0KQogICMgc2FtcGxlZmlsZSA8LSAiIgoKICAjIyAob3B0aW9uYWwpIHRoZSBPVFUgdHJlZSBmaWxlIChud2sgZm9ybWF0KS4gV3JpdGUgIk5vbmUiIGlmIHlvdSBkbyBub3QgaGF2ZSBhbnkgdHJlZQogICMgdHJlZWZpbGUgPC0gIiIKCiAgIyMgVGhlIG9yZGVyZWQgdGF4b25vbWljIGxldmVscyBzdG9yZWQgaW4gQklPTS4gRWFjaCBsZXZlbCBpcyBzZXBhcmF0ZWQgYnkgb25lIHNwYWNlLgogICMjIGRlZmF1bHQgOiAiS2luZ2RvbSBQaHlsdW0gQ2xhc3MgT3JkZXIgRmFtaWx5IEdlbnVzIFNwZWNpZXMiCiAgIyByYW5rcyA8LSAiIgoKICAjIyBEbyB5b3Ugd2FudCB0byBub3JtYWxpc2UgeW91ciBkYXRhID8gIlRydWUiIG9yICJGYWxzZSIKICAjIG5vcm1hbGlzYXRpb24gPC0gIiIKCiMjIENyZWF0ZSBpbnB1dCBhbmQgcGFyYW1ldGVycyBkYXRhZnJhbWUKICAjIHBhcmFtcyA8LSBkYXRhLmZyYW1lKCAiYmlvbWZpbGUiID0gYmlvbWZpbGUsICJzYW1wbGVmaWxlIiA9IHNhbXBsZWZpbGUsICJ0cmVlIiA9IHRyZWUsICJyYW5rcyIgPSByYW5rcywgIm5vcm1hbGlzYXRpb24iID0gbm9ybWFsaXNhdGlvbikKCgojIyBJbXBvcnQgZGF0YQpiaW9tZmlsZSA8LSBwYXJhbXMkYmlvbWZpbGUKZGF0YSAgICAgPC0gaW1wb3J0X2Jpb20oYmlvbWZpbGUpCnNhbXBsZWRhdGEgPC0gcmVhZC5jc3YocGFyYW1zJHNhbXBsZWZpbGUsIHNlcCA9ICJcdCIsIHJvdy5uYW1lcyA9IDEpCgojIGlmIHRheG9ub215IHN0YXJ0cyB3aXRoIGtfXyBpdCBtZWFucyB0aGF0IGl0cyBHcmVlbmdlbmVzIGxpa2UgZm9ybWF0CiMgaW1wb3J0IG5lZWQgdG8gYmUgZG9uZSB1c2luZyBwYXJzZV90YXhvbm9teV9ncmVlbmdlbmVzIGZ1bmN0aW9uCiMgaW4gdGhpcyBjYXNlIHVzZXIgdGF4b25vb'..b'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</div>\n \n \n \n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/18-phylo_alpha_div.nb.html --- a/test-data/references/18-phylo_alpha_div.nb.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/18-phylo_alpha_div.nb.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGS Phyloseq: Alpha Diversity Visualisation (version 3.2.3)</title>\n+<title>FROGS Phyloseq: Alpha Diversity Visualisation (version 4.0.1)</title>\n \n <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to\n // be compatible with the behavior of Pandoc < 2.8).\n@@ -1499,6 +1499,8 @@\n // select all R code blocks\n var rCodeBlocks = $(\'pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia, pre.foldable\');\n rCodeBlocks.each(function() {\n+ // skip if the block has fold-none class\n+ if ($(this).hasClass(\'fold-none\')) return;\n \n // create a collapsable div to wrap the code in\n var div = $(\'<div class="collapse r-code-collapse"></div>\');\n@@ -1514,7 +1516,9 @@\n showCodeButton.append(showCodeText);\n showCodeButton\n .attr(\'data-toggle\', \'collapse\')\n+ .attr(\'data-bs-toggle\', \'collapse\') // BS5\n .attr(\'data-target\', \'#\' + id)\n+ .attr(\'data-bs-target\', \'#\' + id) // BS5\n .attr(\'aria-expanded\', showThis)\n .attr(\'aria-controls\', id);\n \n@@ -1604,6 +1608,7 @@\n \n \n \n+\n <style type="text/css">\n #rmd-source-code {\n display: none;\n@@ -1635,6 +1640,9 @@\n summary {\n display: list-item;\n }\n+details > summary > p:only-child {\n+ display: inline;\n+}\n pre code {\n padding: 0;\n }\n@@ -1743,7 +1751,7 @@\n <div id="header">\n \n <div class="btn-group pull-right float-right">\n-<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>\n+<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>\n <ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">\n <li><a id="rmd-show-all-code" href="#">Show All Code</a></li>\n <li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>\n@@ -1754,7 +1762,8 @@\n \n \n \n-<h1 class="title toc-ignore">FROGS Phyloseq: Alpha Diversity Visualisation (version 3.2.3)</h1>\n+<h1 class="title toc-ignore">FROGS Phyloseq: Alpha Diversity\n+Visualisation (version 4.0.1)</h1>\n \n </div>\n \n@@ -1797,12 +1806,27 @@\n <p>Phyloseq 1.38.0</p>\n <!-- rnb-text-end -->\n <!-- rnb-chunk-begin -->\n-<!-- rnb-source-begin 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\n \n \n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/19-phylo_beta_div.nb.html --- a/test-data/references/19-phylo_beta_div.nb.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/19-phylo_beta_div.nb.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGS Phyloseq: Beta Diversity Visualisation (version 3.2.3)</title>\n+<title>FROGS Phyloseq: Beta Diversity Visualisation (version 4.0.1)</title>\n \n <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to\n // be compatible with the behavior of Pandoc < 2.8).\n@@ -1499,6 +1499,8 @@\n // select all R code blocks\n var rCodeBlocks = $(\'pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia, pre.foldable\');\n rCodeBlocks.each(function() {\n+ // skip if the block has fold-none class\n+ if ($(this).hasClass(\'fold-none\')) return;\n \n // create a collapsable div to wrap the code in\n var div = $(\'<div class="collapse r-code-collapse"></div>\');\n@@ -1514,7 +1516,9 @@\n showCodeButton.append(showCodeText);\n showCodeButton\n .attr(\'data-toggle\', \'collapse\')\n+ .attr(\'data-bs-toggle\', \'collapse\') // BS5\n .attr(\'data-target\', \'#\' + id)\n+ .attr(\'data-bs-target\', \'#\' + id) // BS5\n .attr(\'aria-expanded\', showThis)\n .attr(\'aria-controls\', id);\n \n@@ -1604,6 +1608,7 @@\n \n \n \n+\n <style type="text/css">\n #rmd-source-code {\n display: none;\n@@ -1635,6 +1640,9 @@\n summary {\n display: list-item;\n }\n+details > summary > p:only-child {\n+ display: inline;\n+}\n pre code {\n padding: 0;\n }\n@@ -1743,7 +1751,7 @@\n <div id="header">\n \n <div class="btn-group pull-right float-right">\n-<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>\n+<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>\n <ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">\n <li><a id="rmd-show-all-code" href="#">Show All Code</a></li>\n <li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>\n@@ -1754,7 +1762,8 @@\n \n \n \n-<h1 class="title toc-ignore">FROGS Phyloseq: Beta Diversity Visualisation (version 3.2.3)</h1>\n+<h1 class="title toc-ignore">FROGS Phyloseq: Beta Diversity\n+Visualisation (version 4.0.1)</h1>\n \n </div>\n \n@@ -1797,14 +1806,29 @@\n <p>Phyloseq 1.38.0</p>\n <!-- rnb-text-end -->\n <!-- rnb-chunk-begin -->\n-<!-- rnb-source-begin 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\n \n \n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/21-phylo_clustering.nb.html --- a/test-data/references/21-phylo_clustering.nb.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/21-phylo_clustering.nb.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGS Phyloseq: Sample clustering using different linkage method (version 4.0.0)</title>\n+<title>FROGS Phyloseq: Sample clustering using different linkage method (version 4.0.1)</title>\n \n <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to\n // be compatible with the behavior of Pandoc < 2.8).\n@@ -1763,7 +1763,7 @@\n \n \n <h1 class="title toc-ignore">FROGS Phyloseq: Sample clustering using\n-different linkage method (version 4.0.0)</h1>\n+different linkage method (version 4.0.1)</h1>\n \n </div>\n \n@@ -1818,10 +1818,15 @@\n <pre class="r"><code>library(ape)\n source(file.path(params$libdir, "graphical_methods.R"))</code></pre>\n <!-- rnb-source-end -->\n-<!-- rnb-warning-begin eyJkYXRhIjoiV2FybmluZzogbGUgcGFja2FnZSAnZ2dwbG90MicgYSDDqXTDqSBjb21waWzDqSBhdmVjIGxhIHZlcnNpb24gUiA0LjEuM1xuIn0= -->\n-<pre><code>Warning: le package 'ggplot2' a \xc3\xa9t\xc3\xa9 compil\xc3\xa9 avec la version R 4.1.3</code></pre>\n+<!-- rnb-warning-begin eyJkYXRhIjoiV2FybmluZyBpbiBmaWxlKGZpbGVuYW1lLCBcInJcIiwgZW5jb2RpbmcgPSBlbmNvZGluZyk6IGltcG9zc2libGUgZCdvdXZyaXIgbGVcbmZpY2hpZXIgJy9ob21lL3ZkYXJib3QvQnVyZWF1L0ZST0dTX2ZvcmsvbGliL2V4dGVybmFsLWxpYi9ncmFwaGljYWxfbWV0aG9kcy5SJyA6XG5BdWN1biBmaWNoaWVyIG91IGRvc3NpZXIgZGUgY2UgdHlwZVxuIn0= -->\n+<pre><code>Warning in file(filename, "r", encoding = encoding): impossible d'ouvrir le\n+fichier '/home/vdarbot/Bureau/FROGS_fork/lib/external-lib/graphical_methods.R' :\n+Aucun fichier ou dossier de ce type</code></pre>\n <!-- rnb-warning-end -->\n-<!-- rnb-source-begin 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 -->\n+<!-- rnb-error-begin eyJkYXRhIjoiRXJyb3IgaW4gZmlsZShmaWxlbmFtZSwgXCJyXCIsIGVuY29kaW5nID0gZW5jb2RpbmcpOiBpbXBvc3NpYmxlIGQnb3V2cmlyIGxhIGNvbm5leGlvblxuIn0= -->\n+<pre><code>Error in file(filename, "r", encoding = encoding): impossible d'ouvrir la connexion</code></pre>\n+<!-- rnb-error-end -->\n+<!-- rnb-source-begin eyJkYXRhIjpbIiMjIEFsdGVybmF0aXZlIHRvIHNvdXJjZSBhbGwgZXh0cmEgZnVuY3Rpb24gZnJvbSBhIGdpdGh1YiByZXBvIiwiIyMgc291cmNlKFwiaHR0cHM6Ly9yYXcuZ2l0aHVidXNlcmNvbnRlbnQuY29tL21haGVuZHJhLW1hcmlhZGFzc291L3BoeWxvc2VxLWV4dGVuZGVkL21hc3Rlci9sb2FkLWV4dHJhLWZ1bmN0aW9ucy5SXCIpIiwiIiwiIyMgU2V0dGluZyB2YXJpYWJsZXMiLCIgICMjIFRoZSBQaHlsb3NlcSBvYmplY3QgKGZvcm1hdCByZGF0YSkiLCIgICMgcGh5bG9zZXEgPC0gXCJcIiIsIiIsIiAgIyMgVGhlIGJldGEgZGl2ZXJzaXR5IGRpc3RhbmNlIG1hdHJpeCBmaWxlIiwiICAjIGRpc3RhbmNlIDwtIFwiXCIiLCIiLCIgICMjIFRoZSBleHBlcmltZW50IHZhcmlhYmxlIHRoYXQgeW91IHdhbnQgdG8gYW5hbHlzZSIsIiAgIyB2YXJFeHAgPC0gXCJcIiIsIiIsIiMjIENyZWF0ZSBpbnB1dCBhbmQgcGFyYW1ldGVycyBkYXRhZnJhbWUiLCIgICMgcGFyYW1zIDwtIGRhdGEuZnJhbWUoIFwicGh5bG9zZXFcIiA9IHBoeWxvc2UsIFwiZGlzdGFuY2VcIiA9IGRpc3RhbmNlLCBcInZhckV4cFwiID0gdmFyRXhwKSIsIiIsIiMjIExvYWQgZGF0YSIsIiAgIyMgdGhlIHBoeWxvc2VxIG9iamVjdCIsImxvYWQocGFyYW1zJHBoeWxvc2VxKSIsIiIsIiAgIyMgdGhlIGRpc3RhbmNlIG1hdHJpeCBmaWxlIiwiQSAgICAgICAgPC0gcmVhZC50YWJsZShmaWxlPXBhcmFtcyRkaXN0YW5jZSwgcm93Lm5hbWVzPTEpIl19 -->\n <pre class="r"><code>## Alternative to source all extra fu'..b'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</div>\n+<div id="rmd-source-code">LS0tCnRpdGxlOiAiRlJPR1MgUGh5bG9zZXE6IFNhbXBsZSBjbHVzdGVyaW5nIHVzaW5nIGRpZmZlcmVudCBsaW5rYWdlIG1ldGhvZCAodmVyc2lvbiA0LjAuMSkiCm91dHB1dDogCiAgaHRtbF9ub3RlYm9vazoKICAgIGNvZGVfZm9sZGluZzogaGlkZQpwYXJhbXM6CiAgIHBoeWxvc2VxOgogICAgICB2YWx1ZTogeAogICB2YXJFeHA6CiAgICAgIHZhbHVlOiB4CiAgIGRpc3RhbmNlOgogICAgICB2YWx1ZTogeAogICBsaWJkaXI6CiAgICAgIHZhbHVlOiB4Ci0tLQo8bWV0YSBodHRwLWVxdWl2PSJDb250ZW50LVR5cGUiIGNvbnRlbnQ9InRleHQvaHRtbDsgY2hhcnNldD1VVEYtOCI+Cgo8c3R5bGUgdHlwZT0idGV4dC9jc3MiPgpjb2RlLnJ7IC8qIENvZGUgYmxvY2sgKi8KICBmb250LXNpemU6IDExcHg7Cn0KcHJlIHsgLyogQ29kZSBibG9jayAqLwogIGZvbnQtc2l6ZTogMTFweAp9Ci5idXR0b24gewogICAgYmFja2dyb3VuZC1jb2xvcjogIzJhN2VjYzsgLyogQmx1ZSAqLwogICAgYm9yZGVyICAgICAgICAgIDogbm9uZTsKICAgIGNvbG9yICAgICAgICAgICA6IHdoaXRlOwogICAgcGFkZGluZyAgICAgICAgIDogNXB4IDEwcHg7CiAgICB0ZXh0LWFsaWduICAgICAgOiBjZW50ZXI7CiAgICB0ZXh0LWRlY29yYXRpb24gOiBub25lOwogICAgZGlzcGxheSAgICAgICAgIDogaW5saW5lLWJsb2NrOwogICAgZm9udC1zaXplICAgICAgIDogMTJweDsKICAgIG1hcmdpbiAgICAgICAgICA6IDRweCAycHg7CiAgICBjdXJzb3IgICAgICAgICAgOiBwb2ludGVyOwogICAgYm9yZGVyLXJhZGl1cyAgIDogOHB4Owp9Cmg0IHsgCiAgICBkaXNwbGF5ICAgICAgOiBibG9jazsKICAgIGZvbnQtc2l6ZSAgICA6IDFlbTsKICAgIG1hcmdpbi10b3AgICA6IDEuMzNlbTsKICAgIG1hcmdpbi1ib3R0b206IDEuMzNlbTsKICAgIG1hcmdpbi1sZWZ0ICA6IDA7CiAgICBtYXJnaW4tcmlnaHQgOiAwOwogICAgZm9udC13ZWlnaHQgIDogYm9sZDsKICAgIGNvbG9yICAgICAgICA6ICMyYTdlY2M7Cn0KPC9zdHlsZT4KCgpgYGB7ciBzZXR1cCwgaW5jbHVkZT1GQUxTRX0Ka25pdHI6Om9wdHNfY2h1bmskc2V0KGVjaG8gPSBUUlVFLCBlcnJvciA9IFRSVUUpCmBgYApQaHlsb3NlcSBgciBwYWNrYWdlVmVyc2lvbigicGh5bG9zZXEiKWAKCmBgYHtyIGltcG9ydCwgbWVzc2FnZT1GQUxTRX0KCiMjIEltcG9ydCBwYWNrYWdlcwpsaWJyYXJ5KHBoeWxvc2VxKQpsaWJyYXJ5KHNjYWxlcykKbGlicmFyeShhcGUpCnNvdXJjZShmaWxlLnBhdGgocGFyYW1zJGxpYmRpciwgImdyYXBoaWNhbF9tZXRob2RzLlIiKSkKIyMgQWx0ZXJuYXRpdmUgdG8gc291cmNlIGFsbCBleHRyYSBmdW5jdGlvbiBmcm9tIGEgZ2l0aHViIHJlcG8KIyMgc291cmNlKCJodHRwczovL3Jhdy5naXRodWJ1c2VyY29udGVudC5jb20vbWFoZW5kcmEtbWFyaWFkYXNzb3UvcGh5bG9zZXEtZXh0ZW5kZWQvbWFzdGVyL2xvYWQtZXh0cmEtZnVuY3Rpb25zLlIiKQoKIyMgU2V0dGluZyB2YXJpYWJsZXMKICAjIyBUaGUgUGh5bG9zZXEgb2JqZWN0IChmb3JtYXQgcmRhdGEpCiAgIyBwaHlsb3NlcSA8LSAiIgoKICAjIyBUaGUgYmV0YSBkaXZlcnNpdHkgZGlzdGFuY2UgbWF0cml4IGZpbGUKICAjIGRpc3RhbmNlIDwtICIiCgogICMjIFRoZSBleHBlcmltZW50IHZhcmlhYmxlIHRoYXQgeW91IHdhbnQgdG8gYW5hbHlzZQogICMgdmFyRXhwIDwtICIiCgojIyBDcmVhdGUgaW5wdXQgYW5kIHBhcmFtZXRlcnMgZGF0YWZyYW1lCiAgIyBwYXJhbXMgPC0gZGF0YS5mcmFtZSggInBoeWxvc2VxIiA9IHBoeWxvc2UsICJkaXN0YW5jZSIgPSBkaXN0YW5jZSwgInZhckV4cCIgPSB2YXJFeHApCgojIyBMb2FkIGRhdGEKICAjIyB0aGUgcGh5bG9zZXEgb2JqZWN0CmxvYWQocGFyYW1zJHBoeWxvc2VxKQoKICAjIyB0aGUgZGlzdGFuY2UgbWF0cml4IGZpbGUKQSAgICAgICAgPC0gcmVhZC50YWJsZShmaWxlPXBhcmFtcyRkaXN0YW5jZSwgcm93Lm5hbWVzPTEpCmRpc3QgICAgIDwtIGFzLmRpc3QoQSkKYGBgCgojIHsudGFic2V0IC50YWJzZXQtZmFkZSAudGFic2V0LXBpbGxzfQoKIyMgV2FyZCBEMgpgYGB7ciB3YXJkLCBmaWcud2lkdGg9OCwgZmlnLmhlaWdodD03LCBlY2hvPUZBTFNFfQpwbG90X2NsdXN0KGRhdGEsIGRpc3QsIG1ldGhvZCA9ICJ3YXJkLkQyIiwgY29sb3IgPSBwYXJhbXMkdmFyRXhwKQpgYGAKCiMjIENvbXBsZXRlCmBgYHtyIGNvbXBsZXRlLCBmaWcud2lkdGg9OCwgZmlnLmhlaWdodD03LCBlY2hvPUZBTFNFfQpwbG90X2NsdXN0KGRhdGEsIGRpc3QsIG1ldGhvZCA9ICJjb21wbGV0ZSIsIGNvbG9yID0gcGFyYW1zJHZhckV4cCkKYGBgCgojIyBTaW5nbGUKYGBge3Igc2luZ2xlLCBmaWcud2lkdGg9OCwgZmlnLmhlaWdodD03LCBlY2hvPUZBTFNFfQpwbG90X2NsdXN0KGRhdGEsIGRpc3QsIG1ldGhvZCA9ICJzaW5nbGUiLCBjb2xvciA9IHBhcmFtcyR2YXJFeHApCmBgYAo=</div>\n \n \n \n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/22-phylo_manova.nb.html --- a/test-data/references/22-phylo_manova.nb.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/22-phylo_manova.nb.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -11,7 +11,7 @@ -<title>FROGS Phyloseq: Multivariate Analysis of Variance (version 4.0.0)</title> +<title>FROGS Phyloseq: Multivariate Analysis of Variance (version 4.0.1)</title> <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to // be compatible with the behavior of Pandoc < 2.8). @@ -1763,7 +1763,7 @@ <h1 class="title toc-ignore">FROGS Phyloseq: Multivariate Analysis of -Variance (version 4.0.0)</h1> +Variance (version 4.0.1)</h1> </div> @@ -1860,7 +1860,7 @@ <!-- rnb-output-end --> <!-- rnb-chunk-end --> -<div id="rmd-source-code">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</div> +<div id="rmd-source-code">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</div> |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/23-deseq2_preprocess.Rdata |
| b |
| Binary file test-data/references/23-deseq2_preprocess.Rdata has changed |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/24-deseq2_visualisation.nb.html --- a/test-data/references/24-deseq2_visualisation.nb.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/24-deseq2_visualisation.nb.html Tue Jul 19 11:11:16 2022 +0000 |
| [ |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGSSTAT DESeq2: Visualisation (version 3.2.3)</title>\n+<title>FROGSSTAT DESeq2: Visualisation (version 4.0.1)</title>\n \n <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to\n // be compatible with the behavior of Pandoc < 2.8).\n@@ -1499,6 +1499,8 @@\n // select all R code blocks\n var rCodeBlocks = $(\'pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia, pre.foldable\');\n rCodeBlocks.each(function() {\n+ // skip if the block has fold-none class\n+ if ($(this).hasClass(\'fold-none\')) return;\n \n // create a collapsable div to wrap the code in\n var div = $(\'<div class="collapse r-code-collapse"></div>\');\n@@ -1514,7 +1516,9 @@\n showCodeButton.append(showCodeText);\n showCodeButton\n .attr(\'data-toggle\', \'collapse\')\n+ .attr(\'data-bs-toggle\', \'collapse\') // BS5\n .attr(\'data-target\', \'#\' + id)\n+ .attr(\'data-bs-target\', \'#\' + id) // BS5\n .attr(\'aria-expanded\', showThis)\n .attr(\'aria-controls\', id);\n \n@@ -2967,10 +2971,10 @@\n \'background-color\': \'#fff\',\n \'border\': \'1px #ddd solid\',\n \'border-radius\': \'4px\',\n- \'padding\': data.vertical ? \'35px 20px\': \'20px 20px 10px 20px\'\n+ \'padding\': \'20px 20px 10px 20px\'\n });\n var $spans = $x0.children(\'span\').css({\n- \'margin-top\': data.vertical ? \'0\' : \'10px\',\n+ \'margin-top\': \'10px\',\n \'white-space\': \'nowrap\'\n });\n var $span1 = $spans.first(), $span2 = $spans.last();\n@@ -2997,9 +3001,9 @@\n // first, make sure the slider div leaves at least 20px between\n // the two (slider value) span\'s\n $x0.width(Math.max(160, $span1.outerWidth() + $span2.outerWidth() + 20));\n- // then, if the input is really wide or slider is vertical,\n- // make the slider the same width as the input\n- if ($x0.outerWidth() < $input.outerWidth() || data.vertical) {\n+ // then, if the input is really wide, make the slider the same\n+ // width as the input\n+ if ($x0.outerWidth() < $input.outerWidth()) {\n $x0.outerWidth($input.outerWidth());\n }\n // make sure the slider div does not reach beyond the right margin\n@@ -3064,10 +3068,6 @@\n };\n var opts = type === \'date\' ? { step: 60 * 60 * 1000 } :\n type === \'integer\' ? { step: 1 } : {};\n-\n- opts.orientation = data.vertical ? \'vertical\': \'horizontal\';\n- opts.direction = data.vertical ? \'rtl\': \'ltr\';\n-\n filter = $x.noUiSlider($.extend({\n start: [r1, r2],\n range: {min: r1, max: r2},\n@@ -3251,44 +3251,39 @@\n throw \'The editable parameter must be "cell", "row", "column", or "all"\';\n }\n var disableCols = data.editable.disable ? data.editable.disable.columns : null;\n- var numericCols = data.editable.numeric;\n- var areaCols = data.editable.area;\n for (var i = 0; i < target.length; i++) {\n (function(cell, current) {\n var $cell = $(cell), html = $cell.html();\n- var _cell = table.cell(cell), value = _cell.data(), index = _cell.index().column;\n- var $input;\n- if (inArray(index, numericCols)) {\n- $input = $(\'<input type="number">\');\n- } else if (inArray(index, areaCols)) {\n- $input = $(\'<textarea></textarea>\');\n- } else {\n- $input = $(\'<input type="text">\');\n- }\n+ var _cell = table.cell(cell), value = _cell.data();\n+ var $input = $(\'<input type="text">\'), changed = false;\n if (!immediate) {\n $cell.data(\'input\', $input).data(\'html\', html);\n $input.attr(\'title\', \'Hit Ctrl+Enter to finish editing, or Esc to cancel\');\n }\n $input.val(value);\n- if (inArray(index, d'..b'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</div>\n \n \n \n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/25-frogsfunc_placeseqs_report.html --- a/test-data/references/25-frogsfunc_placeseqs_report.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/25-frogsfunc_placeseqs_report.html Tue Jul 19 11:11:16 2022 +0000 |
| [ |
| b'@@ -19,7 +19,7 @@\n \t<head>\n \t\t<title>FrogsFunc place seqs (Step1)</title>\n \t\t<meta charset="UTF-8">\n-\t\t<meta name="version" content="4.0.0">\n+\t\t<meta name="version" content="4.0.1">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -288,7 +288,7 @@\n \t\t\t\t\n \t\t\t$(function() {\n \t\t\t\tvar detection_categories = ["Nb sequences", "FROGS Taxonomy", "PICRUSt2 closest ID (JGI)", "PICRUSt2 closest reference name", "PICRUSt2 closest taxonomy", "NSTI", "NSTI Confidence", "Lowest same taxonomic rank between FROGS and PICRUSt2", "Comment"] ;\n-\t\t\t\tvar detection_series = [{"name": "Cluster_2", "data": ["217042", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Multi-affiliation\'target=\\"_blank\\">Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Multi-affiliation</a>", "2609459821", "Escherichia coli 6-175-07_S1_C2", "Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli", "7e-06", "Good", "Family", "identical sequence"]}, {"name": "Cluster_7", "data": ["100935", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=Bacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Multi-affiliation\'target=\\"_blank\\">Bacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Multi-affiliation</a>", "2731957973", "Campylobacter coli BIGS0003", "Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli", "0.013", "Good", "Species", "identical sequence"]}, {"name": "Cluster_12", "data": ["53185", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Multi-affiliation\'target=\\"_blank\\">Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Multi-affiliation</a>", "2728369350", "Flavonifractor plautii YL31", "Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Flavonifractor;Flavonifractor plautii", "1.6e-05", "Good", "Species", "identical sequence"]}, {"name": "Cluster_10", "data": ["52413", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp.\'target=\\"_blank\\">Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp.</a>", "2585427805", "Clostridiales bacterium VE202-03", "Bacteria;Firmicutes;Clostridia;Eubacteriales;unclassified;unclassified;Clostridiales bacterium VE202-03", "0.11", "Good", "Class", "/"]}, {"name": "Cluster_1", "data": ["243473", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Oscillibacter;unknown species\'target=\\"_blank\\">Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Oscillibacter;unknown species</a>", "2602041616", "Oscillospiraceae bacterium VE202-24", "Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;unclassified;Oscillospiraceae bacterium VE202-24", "0.03", "Good", "Family", "/"]}, {"name": "Cluster_5", "data": ["104097", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=Bacteria;Firmicutes;Clostridia;Clostridia vadinBB60 group;unknown family;unknown genus;gut metagenome\'target=\\"_blank\\">Bacteria;Firmicutes;Clostridia;Clostridia vadinBB60 group;unknown family;unknown genus;gut metagenome</'..b'a;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli", "0.013", "Good", "Species", "identical sequence"]}, {"name": "Cluster_12", "data": ["53185", "Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Multi-affiliation", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2728369350\'target=\\"_blank\\">2728369350</a>", "Flavonifractor plautii YL31", "Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Flavonifractor;Flavonifractor plautii", "1.6e-05", "Good", "Species", "identical sequence"]}, {"name": "Cluster_10", "data": ["52413", "Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp.", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2585427805\'target=\\"_blank\\">2585427805</a>", "Clostridiales bacterium VE202-03", "Bacteria;Firmicutes;Clostridia;Eubacteriales;unclassified;unclassified;Clostridiales bacterium VE202-03", "0.11", "Good", "Class", "/"]}, {"name": "Cluster_1", "data": ["243473", "Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Oscillibacter;unknown species", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2602041616\'target=\\"_blank\\">2602041616</a>", "Oscillospiraceae bacterium VE202-24", "Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;unclassified;Oscillospiraceae bacterium VE202-24", "0.03", "Good", "Family", "/"]}, {"name": "Cluster_5", "data": ["104097", "Bacteria;Firmicutes;Clostridia;Clostridia vadinBB60 group;unknown family;unknown genus;gut metagenome", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2751185640\'target=\\"_blank\\">2751185640</a>", "Clostridiales bacterium Firm_08", "Bacteria;Firmicutes;Clostridia;Eubacteriales;unclassified;unclassified;Clostridiales bacterium Firm_08", "0.9", "Medium", "Class", "/"]}, {"name": "Cluster_4", "data": ["113087", "Bacteria;Firmicutes;Clostridia;Clostridia vadinBB60 group;unknown family;unknown genus;unknown species", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=646564521\'target=\\"_blank\\">646564521</a>", "Mageeibacillus indolicus UPII9-5", "Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Mageeibacillus;Mageeibacillus indolicus", "0.83", "Medium", "Class", "/"]}, {"name": "Cluster_6", "data": ["102648", "Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=649989958\'target=\\"_blank\\">649989958</a>", "Lachnospiraceae bacterium sp. 8_1_57FAA", "Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;unclassified;Lachnospiraceae bacterium", "0.064", "Good", "Family", "/"]}, {"name": "Cluster_11", "data": ["49142", "Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=649989958\'target=\\"_blank\\">649989958</a>", "Lachnospiraceae bacterium sp. 8_1_57FAA", "Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;unclassified;Lachnospiraceae bacterium", "0.045", "Good", "Family", "/"]}, {"name": "Cluster_3", "data": ["185228", "Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;Eisenbergiella;unknown species", "<a href=\'https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2600255157\'target=\\"_blank\\">2600255157</a>", "Lachnospiraceae bacterium A4", "Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;unclassified;Lachnospiraceae bacterium A4", "0.2", "Good", "Family", "/"]}] ;\n \t\t\t\tvar remove_info = {"nb_kept": 10, "nb_removed": 0, "abundance_kept": 1221250, "abundance_removed": 0} ;\n \n \t\t\t\t// Remove alert\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/26-frogsfunc_copynumbers_predicted_functions.tsv --- a/test-data/references/26-frogsfunc_copynumbers_predicted_functions.tsv Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/26-frogsfunc_copynumbers_predicted_functions.tsv Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -1,11 +1,11 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|
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/26-frogsfunc_copynumbers_report.html --- a/test-data/references/26-frogsfunc_copynumbers_report.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/26-frogsfunc_copynumbers_report.html Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FrogsFunc copy numbers (Step2)</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.0"> + <meta name="version" content="4.0.1"> <!-- 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 445b04a65ed8 -r 37e6f0c959bb test-data/references/27-frogsfunc_functions_report.html --- a/test-data/references/27-frogsfunc_functions_report.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/27-frogsfunc_functions_report.html Tue Jul 19 11:11:16 2022 +0000 |
| [ |
| b'@@ -19,7 +19,7 @@\n \t<head>\n \t\t<title>FrogsFunc functions (Step3)</title>\n \t\t<meta charset="UTF-8">\n-\t\t<meta name="version" content="4.0.0">\n+\t\t<meta name="version" content="4.0.1">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -468,7 +468,7 @@\n \n \n \t\t\tvar detection_categories = ["Function", "Description", "Observation_sum", "SC1703-105_CAGTCT-B6TML_L001_R", "SC1703-106_TTAAAT-B6TML_L001_R", "SC1703-107_AATTGC-B6TML_L001_R", "SC1703-108_ACTCGA-B6TML_L001_R", "SC1703-109_GTTACC-B6TML_L001_R", "SC1703-110_CAGATG-B6TML_L001_R", "SC1703-125_TCGCGC-B6TML_L001_R", "SC1703-126_TAACTT-B6TML_L001_R", "SC1703-127_CTGTAA-B6TML_L001_R", "SC1703-128_CCATTG-B6TML_L001_R", "SC1703-129_TAGGCT-B6TML_L001_R", "SC1703-130_TTCTTG-B6TML_L001_R", "SC1703-131_CCGACC-B6TML_L001_R", "SC1703-132_TTAGCT-B6TML_L001_R", "SC1703-133_CAGAGC-B6TML_L001_R", "SC1703-134_AATATG-B6TML_L001_R", "SC1703-135_TGAGCA-B6TML_L001_R", "SC1703-136_AATCAC-B6TML_L001_R", "SC1703-137_GGTAGC-B6TML_L001_R", "SC1703-138_CTCTCG-B6TML_L001_R", "SC1703-145_AGCGAC-B6TML_L001_R", "SC1703-146_GCCAAG-B6TML_L001_R", "SC1703-147_AGGTTC-B6TML_L001_R", "SC1703-148_TTTTTC-B6TML_L001_R", "SC1703-149_GTCGTG-B6TML_L001_R", "SC1703-150_GCTATC-B6TML_L001_R", "SC1703-151_TATGCG-B6TML_L001_R", "SC1703-41_TCGTTC-B6TML_L001_R", "SC1703-42_GCGATG-B6TML_L001_R", "SC1703-43_ATATAA-B6TML_L001_R", "SC1703-44_ATACTG-B6TML_L001_R", "SC1703-45_GGAGAG-B6TML_L001_R", "SC1703-46_ACGAGA-B6TML_L001_R", "SC1703-47_ATTACA-B6TML_L001_R", "SC1703-48_TGATTT-B6TML_L001_R", "SC1703-49_GGGGTG-B6TML_L001_R", "SC1703-50_ACAAAA-B6TML_L001_R", "SC1703-51_CTCCAG-B6TML_L001_R", "SC1703-52_GGTGTT-B6TML_L001_R", "SC1703-53_CGGGAG-B6TML_L001_R", "SC1703-54_TGGTAG-B6TML_L001_R", "SC1703-62_TGCGGG-B6TML_L001_R", "SC1703-63_TCTATG-B6TML_L001_R", "SC1703-64_GGACGG-B6TML_L001_R", "SC1703-65_AGAGGG-B6TML_L001_R", "SC1703-66_ATGAAC-B6TML_L001_R", "SC1703-67_TACCTG-B6TML_L001_R", "SC1703-68_CTAGAG-B6TML_L001_R", "SC1703-83_CTTGCA-B6TML_L001_R", "SC1703-84_CATGTT-B6TML_L001_R", "SC1703-85_TGGATT-B6TML_L001_R", "SC1703-86_AACGCA-B6TML_L001_R", "SC1703-87_TTCGAG-B6TML_L001_R", "SC1703-88_AAGCTA-B6TML_L001_R", "SC1703-89_AGTTTG-B6TML_L001_R", "SC1703-90_TCCCCA-B6TML_L001_R", "SC1703-91_AACTAG-B6TML_L001_R", "SC1703-92_GTTCGC-B6TML_L001_R", "SC1703-93_TGCCTT-B6TML_L001_R", "SC1703-94_ATAAGA-B6TML_L001_R", "SC1703-95_CACACT-B6TML_L001_R", "SC1703-96_ACAGTT-B6TML_L001_R"] ;\n-\t\t\tvar detection_series = [{"name": 10937.0, "data": ["21568.0", "22912.0", "30967.0", "15764.0", "7394.0", "14257.0", "8139.0", "21831.0", "40099.0", "33944.0", "36207.0", "18113.0", "37099.0", "29436.0", "19640.0", "15087.0", "28286.0", "18217.0", "20304.0", "32524.0", "10460.0", "10795.0", "10171.0", "14299.0", "8535.0", "13752.0", "7508.0", "14924.0", "7729.0", "18573.0", "18865.0", "13270.0", "15035.0", "21741.0", "20772.0", "16731.0", "15853.0", "19760.0", "23086.0", "16225.0", "22163.0", "18355.0", "16365.0", "10974.0", "17803.0", "28371.0", "13969.0", "20106.0", "14717.0", "16212.0", "22396.0", "21263.0", "26409.0", "13764.0", "16760.0", "23047.0", "35566.0", "37117.0", "35318.0", "26832.0", "33037.0", "24795.0", "24795"]}, {"name": 19088.0, "data": ["40567.0", "38318.0", "50204.0", "24510.0", "14219.0", "27066.0", "22529.0", "55798.0", "76863.0", "78641.0", "88958.0", "35444.0", "81237.0", "51887.0", "40345.0", "41090.0", "83814.0", "56914.0", "48196.0", "69476.0", "23294.0", "15391.0", "18587.0", "27786.0", "14210.0", "23046.0", "12200.0", "31362.0", "11706.0", "26710.0", "29946.0", "35204.0", "13957.0", "55274.0", "52190.0", "41080.0", "20386.0", "46839.0", "46825.0", "32982.0", "49318.0", "30293.0", "35316.0", "23344.0", "33890.0", "44339.0", "24590.0", "38844.0", "30516.0", "30049.0", "63704.0", "32959.0", "71044.0", "32393.0", "40039.0", "78044.0", "95183.'..b' 892, \\"44\\": 484, \\"45\\": 259, \\"46\\": 685, \\"47\\": 904, \\"48\\": 426, \\"49\\": 1241, \\"50\\": 1399, \\"51\\": 874, \\"52\\": 1711, \\"53\\": 1532, \\"54\\": 891, \\"55\\": 777, \\"56\\": 224, \\"57\\": 1221, \\"58\\": 798, \\"59\\": 2001, \\"60\\": 1134, \\"61\\": 1332, \\"62\\": 966},\\"EC:6.5.1.6\\":{\\"0\\": 1148, \\"1\\": 1468, \\"2\\": 1044, \\"3\\": 1396, \\"4\\": 552, \\"5\\": 612, \\"6\\": 1846, \\"7\\": 13, \\"8\\": 13, \\"9\\": 15, \\"10\\": 35, \\"11\\": 9, \\"12\\": 24, \\"13\\": 21, \\"14\\": 2666, \\"15\\": 728, \\"16\\": 4407, \\"17\\": 3321, \\"18\\": 9514, \\"19\\": 1597, \\"20\\": 2373, \\"21\\": 969, \\"22\\": 372, \\"23\\": 97, \\"24\\": 697, \\"25\\": 42, \\"26\\": 836, \\"27\\": 399, \\"28\\": 1, \\"29\\": 2, \\"30\\": 6, \\"31\\": 8, \\"32\\": 6, \\"33\\": 7, \\"34\\": 4, \\"35\\": 5184, \\"36\\": 1406, \\"37\\": 2379, \\"38\\": 1471, \\"39\\": 4165, \\"40\\": 2616, \\"41\\": 473, \\"42\\": 1876, \\"43\\": 1757, \\"44\\": 3013, \\"45\\": 1270, \\"46\\": 2225, \\"47\\": 1771, \\"48\\": 3610, \\"49\\": 41, \\"50\\": 20, \\"51\\": 32, \\"52\\": 76, \\"53\\": 34, \\"54\\": 22, \\"55\\": 11, \\"56\\": 15266, \\"57\\": 4545, \\"58\\": 2580, \\"59\\": 2981, \\"60\\": 1403, \\"61\\": 638, \\"62\\": 3822},\\"EC:6.5.1.7\\":{\\"0\\": 1148, \\"1\\": 1468, \\"2\\": 1044, \\"3\\": 1396, \\"4\\": 552, \\"5\\": 612, \\"6\\": 1846, \\"7\\": 13, \\"8\\": 13, \\"9\\": 15, \\"10\\": 35, \\"11\\": 9, \\"12\\": 24, \\"13\\": 21, \\"14\\": 2666, \\"15\\": 728, \\"16\\": 4407, \\"17\\": 3321, \\"18\\": 9514, \\"19\\": 1597, \\"20\\": 2373, \\"21\\": 969, \\"22\\": 372, \\"23\\": 97, \\"24\\": 697, \\"25\\": 42, \\"26\\": 836, \\"27\\": 399, \\"28\\": 1, \\"29\\": 2, \\"30\\": 6, \\"31\\": 8, \\"32\\": 6, \\"33\\": 7, \\"34\\": 4, \\"35\\": 5184, \\"36\\": 1406, \\"37\\": 2379, \\"38\\": 1471, \\"39\\": 4165, \\"40\\": 2616, \\"41\\": 473, \\"42\\": 1876, \\"43\\": 1757, \\"44\\": 3013, \\"45\\": 1270, \\"46\\": 2225, \\"47\\": 1771, \\"48\\": 3610, \\"49\\": 41, \\"50\\": 20, \\"51\\": 32, \\"52\\": 76, \\"53\\": 34, \\"54\\": 22, \\"55\\": 11, \\"56\\": 15266, \\"57\\": 4545, \\"58\\": 2580, \\"59\\": 2981, \\"60\\": 1403, \\"61\\": 638, \\"62\\": 3822})\\"Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)\\")\\"Forming phosphoric-ester bonds\\",((\\"EC:6.6.1.1\\":{\\"0\\": 350, \\"1\\": 336, \\"2\\": 1010, \\"3\\": 520, \\"4\\": 280, \\"5\\": 676, \\"6\\": 632, \\"7\\": 2110, \\"8\\": 982, \\"9\\": 9000, \\"10\\": 2012, \\"11\\": 896, \\"12\\": 3294, \\"13\\": 2382, \\"14\\": 646, \\"15\\": 1364, \\"16\\": 1542, \\"17\\": 1020, \\"18\\": 1678, \\"19\\": 2464, \\"20\\": 1416, \\"21\\": 22, \\"22\\": 396, \\"23\\": 52, \\"24\\": 448, \\"25\\": 64, \\"26\\": 100, \\"27\\": 22, \\"28\\": 1118, \\"29\\": 526, \\"30\\": 562, \\"31\\": 5294, \\"32\\": 142, \\"33\\": 1052, \\"34\\": 1750, \\"35\\": 2044, \\"36\\": 1224, \\"37\\": 206, \\"38\\": 538, \\"39\\": 742, \\"40\\": 764, \\"41\\": 542, \\"42\\": 716, \\"43\\": 1738, \\"44\\": 592, \\"45\\": 696, \\"46\\": 1172, \\"47\\": 736, \\"48\\": 1254, \\"49\\": 2768, \\"50\\": 3600, \\"51\\": 1226, \\"52\\": 6276, \\"53\\": 2998, \\"54\\": 1956, \\"55\\": 6350, \\"56\\": 3722, \\"57\\": 3902, \\"58\\": 3776, \\"59\\": 3310, \\"60\\": 2710, \\"61\\": 1822, \\"62\\": 2832},\\"EC:6.6.1.2\\":{\\"0\\": 175, \\"1\\": 168, \\"2\\": 505, \\"3\\": 260, \\"4\\": 140, \\"5\\": 338, \\"6\\": 316, \\"7\\": 1055, \\"8\\": 491, \\"9\\": 4500, \\"10\\": 1006, \\"11\\": 448, \\"12\\": 1647, \\"13\\": 1191, \\"14\\": 323, \\"15\\": 682, \\"16\\": 771, \\"17\\": 510, \\"18\\": 839, \\"19\\": 1232, \\"20\\": 708, \\"21\\": 11, \\"22\\": 198, \\"23\\": 26, \\"24\\": 224, \\"25\\": 32, \\"26\\": 50, \\"27\\": 11, \\"28\\": 559, \\"29\\": 263, \\"30\\": 281, \\"31\\": 2647, \\"32\\": 71, \\"33\\": 526, \\"34\\": 875, \\"35\\": 1022, \\"36\\": 612, \\"37\\": 103, \\"38\\": 269, \\"39\\": 371, \\"40\\": 382, \\"41\\": 271, \\"42\\": 358, \\"43\\": 869, \\"44\\": 296, \\"45\\": 348, \\"46\\": 586, \\"47\\": 368, \\"48\\": 627, \\"49\\": 1384, \\"50\\": 1800, \\"51\\": 613, \\"52\\": 3138, \\"53\\": 1499, \\"54\\": 978, \\"55\\": 3175, \\"56\\": 1861, \\"57\\": 1951, \\"58\\": 1888, \\"59\\": 1655, \\"60\\": 1355, \\"61\\": 911, \\"62\\": 1416})\\"Forming coordination complexes\\")\\"Forming nitrogen-D-metal bonds\\")\\"Ligases\\")\\"root\\"" ;\n \t\t\t\t/* This string is in newick extended format. The metadata is the count by sample (each sample is referenced by is index position in "samples_names"). */\n \n \t\t\t$(function() {\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/27-frogsfunc_functions_unstrat.tsv --- a/test-data/references/27-frogsfunc_functions_unstrat.tsv Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/27-frogsfunc_functions_unstrat.tsv Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -37,3 +37,1131 @@\n Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.3\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.3\tEC:1.1.1.3\t11333\t24272\t22386\t30290\t15034\t8018\t16378\t6839\t20064\t34189\t31442\t34964\t15798\t34275\t25594\t17300\t17358\t30456\t24738\t19200\t31220\t10758\t9125\t10538\t14493\t8120\t14344\t7126\t11946\t6284\t13380\t12290\t12060\t9149\t18227\t20415\t15386\t12447\t16412\t19666\t14022\t18508\t19750\t21052\t14826\t21764\t27726\t16328\t24540\t11054\t12062\t20260\t15217\t22153\t11324\t12328\t34306\t34262\t35564\t30620\t23636\t28967\t24396\n Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.30\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.30\tEC:1.1.1.30\t233\t1305\t1338\t1495\t598\t348\t395\t2874\t7160\t25\t6914\t9935\t15\t5834\t3173\t2776\t3139\t3049\t7358\t3516\t4819\t89\t768\t158\t205\t63\t204\t72\t4631\t496\t2803\t1551\t6231\t1344\t9366\t7343\t4415\t1522\t7335\t5823\t3464\t5127\t225\t1457\t465\t425\t578\t445\t271\t3593\t3408\t11535\t45\t12854\t4777\t5248\t8442\t12633\t5259\t13924\t9587\t10678\t8315\n Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.305\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.305\tEC:1.1.1.305\t100\t340\t680\t925\t542\t137\t696\t178\t713\t827\t851\t719\t387\t1008\t2445\t1031\t496\t298\t474\t980\t1263\t180\t546\t70\t246\t242\t267\t41\t1388\t952\t2478\t1969\t934\t2855\t1420\t578\t996\t2364\t402\t541\t410\t189\t352\t892\t484\t259\t685\t904\t426\t1241\t1399\t874\t1711\t1532\t891\t777\t224\t1221\t798\t2001\t1134\t1332\t966\n+Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.31\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.31\tEC:1.1.1.31\t3790\t9576\t8217\t11202\t5515\t2732\t4998\t158\t191\t270\t264\t686\t98\t383\t2845\t2569\t813\t807\t743\t1847\t5804\t1862\t2870\t4122\t4327\t2918\t5544\t2418\t363\t727\t44\t26\t731\t350\t216\t157\t23\t180\t173\t44\t135\t392\t7600\t7096\t4187\t9225\t9347\t5538\t8633\t205\t1030\t225\t539\t299\t339\t313\t490\t1423\t2840\t568\t144\t297\t322\n+Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.336\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.336\tEC:1.1.1.336\t100\t340\t680\t925\t542\t137\t696\t178\t713\t827\t851\t719\t387\t1008\t2445\t1031\t496\t298\t474\t980\t1263\t180\t546\t70\t246\t242\t267\t41\t1388\t952\t2478\t1969\t934\t2855\t1420\t578\t996\t2364\t402\t541\t410\t189\t352\t892\t484\t259\t685\t904\t426\t1241\t1399\t874\t1711\t1532\t891\t777\t224\t1221\t798\t2001\t1134\t1332\t966\n+Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.343\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.343\tEC:1.1.1.343\t100\t340\t680\t925\t542\t137\t696\t178\t713\t827\t851\t719\t387\t1008\t2445\t1031\t496\t298\t474\t980\t1263\t180\t546\t70\t246\t242\t267\t41\t1388\t952\t2478\t1969\t934\t2855\t1420\t578\t996\t2364\t402\t541\t410\t189\t352\t892\t484\t259\t685\t904\t426\t1241\t1399\t874\t1711\t1532\t891\t777\t224\t1221\t798\t2001\t1134\t1332\t966\n+Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.346\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.346\tEC:1.1.1.346\t298\t1019\t2040\t2775\t1624\t411\t2090\t535\t2138\t2482\t2554\t2156\t1160\t3023\t7336\t3092\t1490\t892\t1423\t2940\t3790\t539\t1637\t210\t740\t728\t802\t124\t4163\t2854\t7435\t5907\t2804\t8566\t4258\t1735\t2990\t7090\t1207\t1622\t1229\t567\t1056\t2674\t1454\t776\t2054\t2710\t1279\t3723\t4198\t2623\t5133\t4594\t2674\t2331\t672\t3664\t2394\t6004\t3400\t3994\t2899\n+Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.35\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.35\tEC:1.1.1.35\t199\t680\t1360\t1850\t1083\t274\t1393\t356\t1426\t1654\t1702\t1438\t774\t2016\t4890\t2062\t993\t595\t948\t1960\t2526\t360\t1092\t140\t493\t485\t534\t82\t2776\t1903\t4956\t3938\t1869\t5710\t2839\t1156\t1993\t4727\t804\t1082\t820\t378\t704\t1783\t969\t518\t1370\t1807\t852\t2482\t2798\t1748\t3422\t3063\t1782\t1554\t448\t2442\t1596\t4002\t2267\t2663\t1932\n+Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.350\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.350\tEC:1.1.1.350\t100\t340\t680\t925\t542\t137\t696\t178\t713\t827\t851\t719\t387\t1008\t2445\t1031\t496\t298\t474\t980\t1263\t180\t546\t70\t246\t242\t267\t41\t1388\t952\t2478\t1969\t934\t2855\t1420\t578\t996\t2364\t402\t541\t410\t189\t352'..b'2048\t16982\t52319\t99091\t86144\t98198\t43866\t95325\t40862\t27143\t34880\t45262\t60656\t33763\t48904\t12435\t11680\t10898\t16728\t8472\t16242\t7143\t27540\t10948\t30274\t27619\t26474\t16310\t44772\t46258\t33846\t22456\t32593\t37203\t27230\t36219\t24229\t30074\t22270\t25793\t31693\t22232\t34189\t25147\t28143\t54316\t37641\t56222\t28359\t34170\t85747\t75962\t66866\t70422\t50150\t62046\t54953\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);EC:6.5.1.1\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.1\tEC:6.5.1.1\t1148\t1468\t1044\t1396\t552\t612\t1846\t13\t13\t15\t35\t9\t24\t21\t2666\t728\t4407\t3321\t9514\t1597\t2373\t969\t372\t97\t697\t42\t836\t399\t1\t2\t6\t8\t6\t7\t4\t5184\t1406\t2379\t1471\t4165\t2616\t473\t1876\t1757\t3013\t1270\t2225\t1771\t3610\t41\t20\t32\t76\t34\t22\t11\t15266\t4545\t2580\t2981\t1403\t638\t3822\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);EC:6.5.1.2\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.2\tEC:6.5.1.2\t7543\t14696\t14168\t19088\t9518\t5286\t11380\t6681\t19874\t33919\t31178\t34278\t15700\t33892\t22748\t14732\t16544\t29649\t23994\t17352\t25416\t8896\t6255\t6416\t10166\t5202\t8800\t4708\t11583\t5558\t13336\t12264\t11329\t8799\t18011\t20258\t15362\t12267\t16238\t19622\t13887\t18116\t12150\t13956\t10639\t12539\t18378\t10790\t15907\t10850\t11032\t20034\t14678\t21854\t10984\t12016\t33816\t32839\t32724\t30052\t23492\t28670\t24074\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);EC:6.5.1.3\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.3\tEC:6.5.1.3\t100\t340\t680\t925\t542\t137\t696\t178\t713\t827\t851\t719\t387\t1008\t2445\t1031\t496\t298\t474\t980\t1263\t180\t546\t70\t246\t242\t267\t41\t1388\t952\t2478\t1969\t934\t2855\t1420\t578\t996\t2364\t402\t541\t410\t189\t352\t892\t484\t259\t685\t904\t426\t1241\t1399\t874\t1711\t1532\t891\t777\t224\t1221\t798\t2001\t1134\t1332\t966\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);EC:6.5.1.4\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.4\tEC:6.5.1.4\t100\t340\t680\t925\t542\t137\t696\t178\t713\t827\t851\t719\t387\t1008\t2445\t1031\t496\t298\t474\t980\t1263\t180\t546\t70\t246\t242\t267\t41\t1388\t952\t2478\t1969\t934\t2855\t1420\t578\t996\t2364\t402\t541\t410\t189\t352\t892\t484\t259\t685\t904\t426\t1241\t1399\t874\t1711\t1532\t891\t777\t224\t1221\t798\t2001\t1134\t1332\t966\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);EC:6.5.1.6\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.6\tEC:6.5.1.6\t1148\t1468\t1044\t1396\t552\t612\t1846\t13\t13\t15\t35\t9\t24\t21\t2666\t728\t4407\t3321\t9514\t1597\t2373\t969\t372\t97\t697\t42\t836\t399\t1\t2\t6\t8\t6\t7\t4\t5184\t1406\t2379\t1471\t4165\t2616\t473\t1876\t1757\t3013\t1270\t2225\t1771\t3610\t41\t20\t32\t76\t34\t22\t11\t15266\t4545\t2580\t2981\t1403\t638\t3822\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);EC:6.5.1.7\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.7\tEC:6.5.1.7\t1148\t1468\t1044\t1396\t552\t612\t1846\t13\t13\t15\t35\t9\t24\t21\t2666\t728\t4407\t3321\t9514\t1597\t2373\t969\t372\t97\t697\t42\t836\t399\t1\t2\t6\t8\t6\t7\t4\t5184\t1406\t2379\t1471\t4165\t2616\t473\t1876\t1757\t3013\t1270\t2225\t1771\t3610\t41\t20\t32\t76\t34\t22\t11\t15266\t4545\t2580\t2981\t1403\t638\t3822\n+Ligases;Forming nitrogen-D-metal bonds;Forming coordination complexes;EC:6.6.1.1\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.6.1.1\tEC:6.6.1.1\t350\t336\t1010\t520\t280\t676\t632\t2110\t982\t9000\t2012\t896\t3294\t2382\t646\t1364\t1542\t1020\t1678\t2464\t1416\t22\t396\t52\t448\t64\t100\t22\t1118\t526\t562\t5294\t142\t1052\t1750\t2044\t1224\t206\t538\t742\t764\t542\t716\t1738\t592\t696\t1172\t736\t1254\t2768\t3600\t1226\t6276\t2998\t1956\t6350\t3722\t3902\t3776\t3310\t2710\t1822\t2832\n+Ligases;Forming nitrogen-D-metal bonds;Forming coordination complexes;EC:6.6.1.2\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.6.1.2\tEC:6.6.1.2\t175\t168\t505\t260\t140\t338\t316\t1055\t491\t4500\t1006\t448\t1647\t1191\t323\t682\t771\t510\t839\t1232\t708\t11\t198\t26\t224\t32\t50\t11\t559\t263\t281\t2647\t71\t526\t875\t1022\t612\t103\t269\t371\t382\t271\t358\t869\t296\t348\t586\t368\t627\t1384\t1800\t613\t3138\t1499\t978\t3175\t1861\t1951\t1888\t1655\t1355\t911\t1416\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/28-frogsfunc_pathways_report.html --- a/test-data/references/28-frogsfunc_pathways_report.html Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/28-frogsfunc_pathways_report.html Tue Jul 19 11:11:16 2022 +0000 |
| [ |
| b'@@ -19,7 +19,7 @@\n \t<head>\n \t\t<title>FrogsFunc pathways (Step4)</title>\n \t\t<meta charset="UTF-8">\n-\t\t<meta name="version" content="4.0.0">\n+\t\t<meta name="version" content="4.0.1">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -344,11 +344,11 @@\n \t\t\t/* Example:\n \t\t\t\t["LevelA", "LevelB", "LevelC", "Pathway"]\n \t\t\t*/\n-\t\t\tvar samples_names = ["BHT0.LOT01", "BHT0.LOT03", "BHT0.LOT04", "BHT0.LOT05", "BHT0.LOT06", "BHT0.LOT07", "BHT0.LOT08", "BHT0.LOT10", "CDT0.LOT02", "CDT0.LOT04", "CDT0.LOT05", "CDT0.LOT06", "CDT0.LOT07", "CDT0.LOT08", "CDT0.LOT09", "CDT0.LOT10", "DLT0.LOT01", "DLT0.LOT03", "DLT0.LOT04", "DLT0.LOT05", "DLT0.LOT06", "DLT0.LOT07", "DLT0.LOT08", "DLT0.LOT10", "FCT0.LOT01", "FCT0.LOT02", "FCT0.LOT03", "FCT0.LOT05", "FCT0.LOT06", "FCT0.LOT07", "FCT0.LOT08", "FCT0.LOT10", "FST0.LOT01", "FST0.LOT02", "FST0.LOT03", "FST0.LOT05", "FST0.LOT06", "FST0.LOT07", "FST0.LOT08", "FST0.LOT10", "MVT0.LOT01", "MVT0.LOT03", "MVT0.LOT05", "MVT0.LOT06", "MVT0.LOT07", "MVT0.LOT08", "MVT0.LOT09", "MVT0.LOT10", "SFT0.LOT01", "SFT0.LOT02", "SFT0.LOT03", "SFT0.LOT04", "SFT0.LOT05", "SFT0.LOT06", "SFT0.LOT07", "SFT0.LOT08", "VHT0.LOT01", "VHT0.LOT02", "VHT0.LOT03", "VHT0.LOT04", "VHT0.LOT06", "VHT0.LOT07", "VHT0.LOT08", "VHT0.LOT10"] ;\n+\t\t\tvar samples_names = ["SC1703-104_TTGCCC-B6TML_L001_R", "SC1703-105_CAGTCT-B6TML_L001_R", "SC1703-106_TTAAAT-B6TML_L001_R", "SC1703-107_AATTGC-B6TML_L001_R", "SC1703-108_ACTCGA-B6TML_L001_R", "SC1703-109_GTTACC-B6TML_L001_R", "SC1703-110_CAGATG-B6TML_L001_R", "SC1703-125_TCGCGC-B6TML_L001_R", "SC1703-126_TAACTT-B6TML_L001_R", "SC1703-127_CTGTAA-B6TML_L001_R", "SC1703-128_CCATTG-B6TML_L001_R", "SC1703-129_TAGGCT-B6TML_L001_R", "SC1703-130_TTCTTG-B6TML_L001_R", "SC1703-131_CCGACC-B6TML_L001_R", "SC1703-132_TTAGCT-B6TML_L001_R", "SC1703-133_CAGAGC-B6TML_L001_R", "SC1703-134_AATATG-B6TML_L001_R", "SC1703-135_TGAGCA-B6TML_L001_R", "SC1703-136_AATCAC-B6TML_L001_R", "SC1703-137_GGTAGC-B6TML_L001_R", "SC1703-138_CTCTCG-B6TML_L001_R", "SC1703-145_AGCGAC-B6TML_L001_R", "SC1703-146_GCCAAG-B6TML_L001_R", "SC1703-147_AGGTTC-B6TML_L001_R", "SC1703-148_TTTTTC-B6TML_L001_R", "SC1703-149_GTCGTG-B6TML_L001_R", "SC1703-150_GCTATC-B6TML_L001_R", "SC1703-151_TATGCG-B6TML_L001_R", "SC1703-41_TCGTTC-B6TML_L001_R", "SC1703-42_GCGATG-B6TML_L001_R", "SC1703-43_ATATAA-B6TML_L001_R", "SC1703-44_ATACTG-B6TML_L001_R", "SC1703-45_GGAGAG-B6TML_L001_R", "SC1703-46_ACGAGA-B6TML_L001_R", "SC1703-47_ATTACA-B6TML_L001_R", "SC1703-48_TGATTT-B6TML_L001_R", "SC1703-49_GGGGTG-B6TML_L001_R", "SC1703-50_ACAAAA-B6TML_L001_R", "SC1703-51_CTCCAG-B6TML_L001_R", "SC1703-52_GGTGTT-B6TML_L001_R", "SC1703-53_CGGGAG-B6TML_L001_R", "SC1703-54_TGGTAG-B6TML_L001_R", "SC1703-62_TGCGGG-B6TML_L001_R", "SC1703-63_TCTATG-B6TML_L001_R", "SC1703-64_GGACGG-B6TML_L001_R", "SC1703-65_AGAGGG-B6TML_L001_R", "SC1703-66_ATGAAC-B6TML_L001_R", "SC1703-67_TACCTG-B6TML_L001_R", "SC1703-68_CTAGAG-B6TML_L001_R", "SC1703-83_CTTGCA-B6TML_L001_R", "SC1703-84_CATGTT-B6TML_L001_R", "SC1703-85_TGGATT-B6TML_L001_R", "SC1703-86_AACGCA-B6TML_L001_R", "SC1703-87_TTCGAG-B6TML_L001_R", "SC1703-88_AAGCTA-B6TML_L001_R", "SC1703-89_AGTTTG-B6TML_L001_R", "SC1703-90_TCCCCA-B6TML_L001_R", "SC1703-91_AACTAG-B6TML_L001_R", "SC1703-92_GTTCGC-B6TML_L001_R", "SC1703-93_TGCCTT-B6TML_L001_R", "SC1703-94_ATAAGA-B6TML_L001_R", "SC1703-95_CACACT-B6TML_L001_R", "SC1703-96_ACAGTT-B6TML_L001_R"] ;\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 = "((((\\"1CMET2-PWY\\":{\\"0\\": 5950, \\"1\\": 5440, \\"2\\": 5168, \\"3\\": 5935, \\"4\\": 6271, \\"5\\": 5911, \\"6\\": 5765, \\"7\\": 4830, \\"8\\": 2638, \\"9\\": 7761, \\"10\\": 8020, \\"11\\": 6539, \\"12\\": 5460, \\"13\\": 2533, \\"14\\": 7654, \\"15\\": 5076, \\"16\\": 4101, \\"17\\": 4302, \\"18\\": 7722, \\"19\\":'..b' 14095, \\"61\\": 13761, \\"62\\": 15981},\\"PWY0-1297\\":{\\"0\\": 4120, \\"1\\": 6546, \\"2\\": 7531, \\"3\\": 10065, \\"4\\": 5137, \\"5\\": 2902, \\"6\\": 6026, \\"7\\": 4105, \\"8\\": 7854, \\"9\\": 4034, \\"10\\": 8504, \\"11\\": 6313, \\"12\\": 1945, \\"13\\": 7639, \\"14\\": 13569, \\"15\\": 9822, \\"16\\": 9535, \\"17\\": 13078, \\"18\\": 10430, \\"19\\": 11671, \\"20\\": 16151, \\"21\\": 4808, \\"22\\": 3922, \\"23\\": 3686, \\"24\\": 6572, \\"25\\": 3193, \\"26\\": 4114, \\"27\\": 2915, \\"28\\": 6749, \\"29\\": 3515, \\"30\\": 8157, \\"31\\": 7271, \\"32\\": 7428, \\"33\\": 6499, \\"34\\": 9769, \\"35\\": 11046, \\"36\\": 9840, \\"37\\": 7071, \\"38\\": 11295, \\"39\\": 12403, \\"40\\": 8481, \\"41\\": 12071, \\"42\\": 4761, \\"43\\": 7308, \\"44\\": 4845, \\"45\\": 4058, \\"46\\": 10337, \\"47\\": 4789, \\"48\\": 6230, \\"49\\": 7040, \\"50\\": 6899, \\"51\\": 7164, \\"52\\": 5941, \\"53\\": 10995, \\"54\\": 5488, \\"55\\": 5291, \\"56\\": 14261, \\"57\\": 20861, \\"58\\": 18711, \\"59\\": 17844, \\"60\\": 17187, \\"61\\": 19999, \\"62\\": 15112},\\"PWY0-1298\\":{\\"0\\": 3949, \\"1\\": 6308, \\"2\\": 7013, \\"3\\": 9430, \\"4\\": 4860, \\"5\\": 2793, \\"6\\": 5908, \\"7\\": 1353, \\"8\\": 3673, \\"9\\": 4040, \\"10\\": 4320, \\"11\\": 4065, \\"12\\": 1964, \\"13\\": 4711, \\"14\\": 12942, \\"15\\": 8327, \\"16\\": 5612, \\"17\\": 4890, \\"18\\": 6191, \\"19\\": 8101, \\"20\\": 14045, \\"21\\": 4856, \\"22\\": 3602, \\"23\\": 3525, \\"24\\": 6253, \\"25\\": 3022, \\"26\\": 3948, \\"27\\": 2784, \\"28\\": 5051, \\"29\\": 3391, \\"30\\": 6201, \\"31\\": 6250, \\"32\\": 4722, \\"33\\": 5383, \\"34\\": 5939, \\"35\\": 7858, \\"36\\": 4852, \\"37\\": 6690, \\"38\\": 8045, \\"39\\": 10329, \\"40\\": 6978, \\"41\\": 8459, \\"42\\": 4676, \\"43\\": 7232, \\"44\\": 4800, \\"45\\": 4164, \\"46\\": 10091, \\"47\\": 4796, \\"48\\": 6146, \\"49\\": 4789, \\"50\\": 5151, \\"51\\": 4107, \\"52\\": 5651, \\"53\\": 6609, \\"54\\": 3790, \\"55\\": 3513, \\"56\\": 6565, \\"57\\": 11429, \\"58\\": 11842, \\"59\\": 11915, \\"60\\": 7813, \\"61\\": 9501, \\"62\\": 7140})\\"Superpathways\\")\\"Nucleoside and Nucleotide Degradation\\")\\"Degradation/Utilization/Assimilation\\",(((\\"PWY-6700\\":{\\"0\\": 2141, \\"1\\": 3214, \\"2\\": 3064, \\"3\\": 4119, \\"4\\": 1952, \\"5\\": 1313, \\"6\\": 4118, \\"7\\": 2096, \\"8\\": 2267, \\"9\\": 9254, \\"10\\": 3503, \\"11\\": 2256, \\"12\\": 3612, \\"13\\": 4127, \\"14\\": 8179, \\"15\\": 3126, \\"16\\": 7553, \\"17\\": 6448, \\"18\\": 14094, \\"19\\": 4474, \\"20\\": 6332, \\"21\\": 2030, \\"22\\": 1585, \\"23\\": 325, \\"24\\": 1726, \\"25\\": 537, \\"26\\": 1954, \\"27\\": 804, \\"28\\": 3283, \\"29\\": 1932, \\"30\\": 4411, \\"31\\": 6582, \\"32\\": 1835, \\"33\\": 4375, \\"34\\": 4043, \\"35\\": 8964, \\"36\\": 4128, \\"37\\": 6424, \\"38\\": 3353, \\"39\\": 7564, \\"40\\": 4955, \\"41\\": 1277, \\"42\\": 3757, \\"43\\": 4427, \\"44\\": 5222, \\"45\\": 2724, \\"46\\": 5009, \\"47\\": 4226, \\"48\\": 6429, \\"49\\": 4180, \\"50\\": 4899, \\"51\\": 2763, \\"52\\": 7251, \\"53\\": 5297, \\"54\\": 3176, \\"55\\": 6020, \\"56\\": 21380, \\"57\\": 9797, \\"58\\": 6126, \\"59\\": 8497, \\"60\\": 4569, \\"61\\": 4149, \\"62\\": 7972})\\"Queuosine Biosynthesis and Salvage\\",(\\"PWY0-1479\\":{\\"0\\": 286, \\"1\\": 916, \\"2\\": 1719, \\"3\\": 2332, \\"4\\": 1343, \\"5\\": 375, \\"6\\": 1644, \\"7\\": 504, \\"8\\": 1985, \\"9\\": 2361, \\"10\\": 2414, \\"11\\": 2067, \\"12\\": 1103, \\"13\\": 2846, \\"14\\": 5519, \\"15\\": 2551, \\"16\\": 1364, \\"17\\": 852, \\"18\\": 1351, \\"19\\": 2517, \\"20\\": 3275, \\"21\\": 479, \\"22\\": 1302, \\"23\\": 195, \\"24\\": 647, \\"25\\": 559, \\"26\\": 687, \\"27\\": 119, \\"28\\": 3231, \\"29\\": 1919, \\"30\\": 5050, \\"31\\": 4157, \\"32\\": 2343, \\"33\\": 4237, \\"34\\": 3608, \\"35\\": 1625, \\"36\\": 2566, \\"37\\": 4503, \\"38\\": 1144, \\"39\\": 1528, \\"40\\": 1153, \\"41\\": 555, \\"42\\": 938, \\"43\\": 2210, \\"44\\": 1225, \\"45\\": 701, \\"46\\": 1842, \\"47\\": 2027, \\"48\\": 1099, \\"49\\": 2901, \\"50\\": 3211, \\"51\\": 2397, \\"52\\": 4011, \\"53\\": 3969, \\"54\\": 2256, \\"55\\": 2038, \\"56\\": 660, \\"57\\": 3358, \\"58\\": 2245, \\"59\\": 5193, \\"60\\": 3041, \\"61\\": 3600, \\"62\\": 2632})\\"unknow\\")\\"Nucleic Acid Processing\\")\\"Macromolecule Modification\\")\\"root\\"" ;\n \t\t\t/* This string is in newick extended format. The metadata is the count by sample (each sample is referenced by is index position in "samples_names"). */\n \n \t\t\t$(function() {\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb test-data/references/28-frogsfunc_pathways_unstrat.tsv --- a/test-data/references/28-frogsfunc_pathways_unstrat.tsv Mon May 16 15:51:17 2022 +0000 +++ b/test-data/references/28-frogsfunc_pathways_unstrat.tsv Tue Jul 19 11:11:16 2022 +0000 |
| b |
| b'@@ -1,387 +1,262 @@\n-classification\tdb_link\tobservation_name\tBHT0.LOT01\tBHT0.LOT03\tBHT0.LOT04\tBHT0.LOT05\tBHT0.LOT06\tBHT0.LOT07\tBHT0.LOT08\tBHT0.LOT10\tCDT0.LOT02\tCDT0.LOT04\tCDT0.LOT05\tCDT0.LOT06\tCDT0.LOT07\tCDT0.LOT08\tCDT0.LOT09\tCDT0.LOT10\tDLT0.LOT01\tDLT0.LOT03\tDLT0.LOT04\tDLT0.LOT05\tDLT0.LOT06\tDLT0.LOT07\tDLT0.LOT08\tDLT0.LOT10\tFCT0.LOT01\tFCT0.LOT02\tFCT0.LOT03\tFCT0.LOT05\tFCT0.LOT06\tFCT0.LOT07\tFCT0.LOT08\tFCT0.LOT10\tFST0.LOT01\tFST0.LOT02\tFST0.LOT03\tFST0.LOT05\tFST0.LOT06\tFST0.LOT07\tFST0.LOT08\tFST0.LOT10\tMVT0.LOT01\tMVT0.LOT03\tMVT0.LOT05\tMVT0.LOT06\tMVT0.LOT07\tMVT0.LOT08\tMVT0.LOT09\tMVT0.LOT10\tSFT0.LOT01\tSFT0.LOT02\tSFT0.LOT03\tSFT0.LOT04\tSFT0.LOT05\tSFT0.LOT06\tSFT0.LOT07\tSFT0.LOT08\tVHT0.LOT01\tVHT0.LOT02\tVHT0.LOT03\tVHT0.LOT04\tVHT0.LOT06\tVHT0.LOT07\tVHT0.LOT08\tVHT0.LOT10\n-Biosynthesis;Cofactor, Carrier, and Vitamin Biosynthesis;Carrier Biosynthesis;1CMET2-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=1CMET2-PWY\t1CMET2-PWY\t5950\t5440\t5168\t5935\t6271\t5911\t5765\t4830\t2638\t7761\t8020\t6539\t5460\t2533\t7654\t5076\t4101\t4302\t7722\t5315\t6423\t5148\t4972\t4201\t7411\t5969\t3816\t4593\t7459\t4875\t7435\t6701\t6663\t6887\t6995\t6987\t4515\t6512\t7151\t7172\t2292\t2942\t4739\t5373\t4308\t4399\t3464\t863\t3061\t4415\t2502\t4575\t3749\t4883\t3265\t4694\t2578\t3624\t5465\t4868\t6238\t2917\t2712\t4396\n-Degradation/Utilization/Assimilation;Aromatic Compound Degradation;unknow;3-HYDROXYPHENYLACETATE-DEGRADATION-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=3-HYDROXYPHENYLACETATE-DEGRADATION-PWY\t3-HYDROXYPHENYLACETATE-DEGRADATION-PWY\t40\t51\t148\t65\t163\t30\t151\t25\t9\t81\t576\t320\t24\t36\t92\t63\t43\t106\t69\t305\t255\t235\t775\t85\t343\t190\t22\t87\t387\t211\t170\t124\t136\t1020\t950\t918\t312\t292\t542\t723\t24\t74\t235\t132\t242\t228\t40\t10\t5\t128\t40\t82\t42\t2\t34\t14\t39\t26\t50\t39\t48\t229\t24\t39\n-Biosynthesis;Secondary Metabolite Biosynthesis;Siderophore and Metallophore Biosynthesis;AEROBACTINSYN-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=AEROBACTINSYN-PWY\tAEROBACTINSYN-PWY\t8\t0\t5\t7\t3\t0\t0\t0\t0\t0\t10\t16\t0\t0\t0\t4\t11\t4\t23\t20\t32\t0\t4\t0\t13\t55\t90\t86\t2\t118\t21\t41\t4\t531\t478\t404\t18\t14\t8\t2\t7\t13\t37\t35\t14\t121\t0\t0\t61\t33\t6\t27\t4\t1\t7\t1377\t5\t0\t3\t0\t11\t5\t0\t0\n-Superpathways;Superpathways;unknow;ALL-CHORISMATE-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALL-CHORISMATE-PWY\tALL-CHORISMATE-PWY\t81\t217\t453\t212\t189\t138\t591\t206\t260\t2658\t3335\t3199\t294\t836\t1304\t1068\t1414\t1258\t2419\t2383\t2890\t2613\t1433\t1818\t1899\t2119\t1949\t2359\t2895\t2591\t2114\t1913\t655\t3119\t2895\t2831\t1035\t1486\t2326\t2532\t468\t696\t1904\t1120\t827\t1560\t419\t59\t0\t762\t231\t973\t504\t0\t220\t243\t186\t119\t1035\t1953\t950\t479\t332\t415\n-Generation of Precursor Metabolites and Energy;Fermentation;Fermentation to Short-Chain Fatty Acids;ANAEROFRUCAT-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ANAEROFRUCAT-PWY\tANAEROFRUCAT-PWY\t8020\t7085\t8191\t7359\t7571\t8341\t7681\t7679\t3472\t7868\t6299\t5806\t6967\t4276\t5838\t4095\t10145\t9954\t8810\t9642\t9454\t8036\t9267\t8668\t5866\t5128\t5617\t5971\t6011\t6315\t6658\t5102\t8277\t8869\t8508\t8784\t5421\t8880\t7626\t7447\t10397\t10444\t6336\t8291\t7586\t7673\t8534\t10631\t3402\t8475\t8312\t8514\t9136\t402\t4375\t4740\t9669\t9189\t7293\t8439\t8388\t9310\t9633\t7955\n-Generation of Precursor Metabolites and Energy;Glycolysis;unknow;ANAGLYCOLYSIS-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ANAGLYCOLYSIS-PWY\tANAGLYCOLYSIS-PWY\t7815\t7533\t8191\t7366\t7443\t8021\t7501\t7704\t4495\t8543\t8909\t7423\t9754\t4374\t8967\t9323\t9277\t9095\t8891\t9025\t8871\t8002\t8753\t8429\t8115\t6716\t5298\t5913\t8395\t6048\t8091\t7660\t9252\t8680\t8513\t8672\t5865\t9054\t8766\t8476\t9946\t10086\t6491\t8504\t7092\t7671\t8420\t10093\t4005\t8154\t7717\t8269\t8747\t6176\t4542\t5569\t8807\t8559\t7434\t8101\t8385\t8698\t8820\t7768\n-Degradation/Utilization/Assimilation;Amino Acid Degradation;Proteinogenic Amino Acid Degradation;ARGDEG-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ARGDEG-PWY\tARGDEG-PWY\t3\t0\t47\t39\t0\t0\t15\t4\t3\t0\t56\t167\t0\t19\t105\t27\t42\t78\t100\t120\t153\t77\t518\t42\t193\t114\t26\t53\t52\t27\t145\t54\t30\t977\t910\t782\t9\t62\t75\t49\t23\t48\t351\t131\t164\t312\t25\t9\t15\t94\t14\t88\t17\t0\t29\t9\t31\t19\t16\t23\t37\t38\t0\t9\n-Biosynthesis;Amino Acid Biosynthesis;Proteinogenic Amino Acid Biosynthesis;ARGSYN-PWY\th'..b'ways;Superpathways;unknow;TCA-GLYOX-BYPASS\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TCA-GLYOX-BYPASS\tTCA-GLYOX-BYPASS\t598\t1588\t2477\t3255\t1726\t708\t2798\t406\t1450\t1782\t1788\t1464\t854\t2077\t7431\t2987\t2774\t1785\t2970\t3680\t4761\t840\t1519\t252\t1079\t536\t1124\t218\t2637\t1754\t4452\t3798\t1793\t4690\t2788\t3270\t3463\t6414\t1830\t2809\t2100\t837\t1764\t3458\t2372\t1317\t3040\t3305\t2373\t2486\t2761\t1803\t3446\t3103\t1805\t1643\t1753\t5776\t3821\t7107\t3994\t3567\t4586\n+Biosynthesis;Cofactor, Carrier, and Vitamin Biosynthesis;Enzyme Cofactor Biosynthesis;THISYN-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=THISYN-PWY\tTHISYN-PWY\t3841\t5741\t4096\t6508\t3527\t2527\t6526\t555\t1691\t2071\t2087\t2628\t960\t2663\t9145\t3726\t8715\t6174\t16279\t5680\t7259\t2802\t2438\t1457\t2778\t892\t3223\t2092\t2713\t2003\t3521\t2702\t2685\t3852\t2758\t12791\t3949\t7542\t8498\t14310\t8926\t6938\t5339\t7941\t7617\t4541\t10284\t5831\t8176\t2249\t2780\t1952\t3574\t3170\t1990\t1810\t24081\t11810\t6946\t11213\t5799\t5492\t8714\n+Biosynthesis;Amino Acid Biosynthesis;Proteinogenic Amino Acid Biosynthesis;THRESYN-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=THRESYN-PWY\tTHRESYN-PWY\t8321\t16190\t15610\t20760\t10298\t5941\t12051\t7903\t22440\t39038\t34988\t38825\t17514\t37852\t23379\t15923\t17955\t30989\t26602\t18961\t27693\t9212\t6804\t6956\t10880\t5474\t9470\t5159\t12614\t5560\t13401\t13087\t12643\t7737\t20291\t22853\t16683\t11690\t18493\t21868\t15419\t20448\t13325\t15485\t11401\t13870\t20303\t11405\t17275\t11969\t12631\t23086\t16621\t25065\t12474\t15217\t37444\t37149\t36165\t33834\t26298\t31919\t26856\n+Biosynthesis;Aminoacyl-tRNA Charging;Metabolic Clusters;TRNA-CHARGING-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TRNA-CHARGING-PWY\tTRNA-CHARGING-PWY\t7961\t15267\t14557\t19492\t9663\t5582\t11432\t7291\t20721\t35628\t32461\t35812\t16317\t35102\t22041\t15044\t17171\t31289\t24515\t18014\t26206\t9251\t6237\t6759\t10635\t5308\t9076\t4992\t11347\t5106\t12055\t11794\t11421\t6712\t18411\t21354\t15761\t10678\t17425\t20693\t14680\t19724\t12589\t14213\t10696\t13095\t19114\t10602\t16395\t10848\t10945\t21068\t14424\t22629\t11277\t12882\t34757\t34746\t34936\t31103\t24773\t30140\t25313\n+Biosynthesis;Amino Acid Biosynthesis;Proteinogenic Amino Acid Biosynthesis;TRPSYN-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TRPSYN-PWY\tTRPSYN-PWY\t7800\t14293\t12913\t18202\t9097\t4886\t11026\t2350\t4130\t4127\t4567\t3079\t2628\t4177\t17955\t11249\t13239\t28409\t16722\t12865\t20354\t9571\t5269\t6846\t10537\t5406\t9199\t5092\t4039\t3392\t4759\t5727\t4195\t4514\t5312\t12331\t8490\t8908\t8594\t13407\t9285\t9509\t12438\t11931\t10438\t12784\t18365\t10082\t16202\t4504\t3798\t3711\t4760\t5606\t3097\t2664\t25790\t18053\t22967\t13321\t12516\t14004\t13980\n+Biosynthesis;Cofactor, Carrier, and Vitamin Biosynthesis;Carrier Biosynthesis;UBISYN-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=UBISYN-PWY\tUBISYN-PWY\t219\t672\t1130\t1530\t834\t272\t1267\t219\t850\t940\t1023\t858\t449\t1195\t3810\t1507\t1067\t654\t1079\t1655\t2188\t365\t787\t114\t453\t296\t500\t89\t1615\t1082\t2840\t2249\t1102\t3243\t1672\t1247\t1644\t3615\t785\t1150\t854\t350\t712\t1547\t999\t519\t1290\t1559\t909\t1464\t1631\t1054\t1969\t1826\t1057\t920\t529\t2381\t1519\t3352\t1844\t1870\t1897\n+Biosynthesis;Carbohydrate Biosynthesis;Sugar Biosynthesis;UDPNAGSYN-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=UDPNAGSYN-PWY\tUDPNAGSYN-PWY\t5485\t8219\t9012\t11456\t5705\t3973\t8363\t7500\t19812\t38093\t31587\t33958\t16996\t34346\t19848\t13516\t16717\t29688\t24303\t17198\t22471\t7904\t4363\t3684\t7872\t3216\t4983\t3281\t10975\t4751\t11618\t13557\t10340\t6884\t17825\t20880\t15285\t10354\t16168\t19615\t13959\t18128\t7341\t10014\t8342\t6086\t13010\t7093\t11113\t11385\t11520\t19973\t16424\t22277\t11277\t14725\t35375\t33563\t33080\t30177\t24114\t28568\t24814\n+Biosynthesis;Amino Acid Biosynthesis;Proteinogenic Amino Acid Biosynthesis;VALSYN-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=VALSYN-PWY\tVALSYN-PWY\t9349\t18442\t17594\t23322\t11469\t6697\t13560\t9014\t24889\t41827\t38557\t42061\t19107\t41473\t26869\t18589\t21311\t38476\t30443\t22354\t32391\t10855\t7498\t7958\t12546\t6206\t10647\t5772\t14129\t6160\t14862\t14634\t14046\t8321\t22571\t25670\t19657\t13019\t20772\t24771\t17691\t24009\t14784\t17183\t12796\t15523\t22297\t12604\t19485\t13529\t13556\t25414\t17450\t27036\t13918\t15617\t43525\t42801\t42946\t37580\t30760\t37585\t31383\n' |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb tool-data/frogs_picrust2_default_dir.loc.sample --- a/tool-data/frogs_picrust2_default_dir.loc.sample Mon May 16 15:51:17 2022 +0000 +++ b/tool-data/frogs_picrust2_default_dir.loc.sample Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -36,6 +36,6 @@ #-rwxrwxr-x 1 vdarbot vdarbot 600048 avril 1 2021 pro_ref.tre # # EXAMPLE FOR TEST : -#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ -#picrust2_default_dir_ITS ITS <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_ITS/ -#picrust2_default_dir_18S 18S <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_18S/ +#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ +#picrust2_default_dir_ITS ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_ITS/ +#picrust2_default_dir_18S 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_18S/ |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb tool-data/frogs_picrust2_marker_table.loc.sample --- a/tool-data/frogs_picrust2_marker_table.loc.sample Mon May 16 15:51:17 2022 +0000 +++ b/tool-data/frogs_picrust2_marker_table.loc.sample Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -41,5 +41,5 @@ #16S COG COG COG #16S TIGRFAM TIGRFAM TIGRFAM #16S PHENO PHENO PHENO -#ITS EC <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/fungi/ITS_counts.txt.gz <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_ITS_counts.txt.gz -#18S EC <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/fungi/18S_counts.txt.gz <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_18S_counts.txt.gz +#ITS EC <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ITS_counts.txt.gz <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_ITS_counts.txt.gz +#18S EC <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/18S_counts.txt.gz <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_18S_counts.txt.gz |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb tool-data/frogs_picrust2_pathway_map.loc.sample --- a/tool-data/frogs_picrust2_pathway_map.loc.sample Mon May 16 15:51:17 2022 +0000 +++ b/tool-data/frogs_picrust2_pathway_map.loc.sample Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -31,7 +31,7 @@ # # # EXAMPLE FOR TEST : -#pro_metacyc_pathway Metacyc 16S <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt -#fungi_metacyc_pathway Metacyc ITS <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt -#fungi_metacyc_pathway Metacyc 18S <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt -#kegg_modules_pathway Kegg 16S <Galaxy_dir>/database/dependencies/_conda/envs/__picrust2@2.4.1/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv \ No newline at end of file +#pro_metacyc_pathway Metacyc 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt +#fungi_metacyc_pathway Metacyc ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt +#fungi_metacyc_pathway Metacyc 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt +#kegg_modules_pathway Kegg 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv \ No newline at end of file |
| b |
| diff -r 445b04a65ed8 -r 37e6f0c959bb tree.xml --- a/tree.xml Mon May 16 15:51:17 2022 +0000 +++ b/tree.xml Tue Jul 19 11:11:16 2022 +0000 |
| b |
| @@ -38,9 +38,9 @@ <assert_contents> <has_text_matching expression="FROGS\sTree" /> <has_text_matching expression="abundance_removed.*:\s0" /> - <has_text_matching expression="abundance_kept.*:\s74781" /> + <has_text_matching expression="abundance_kept.*:\s300" /> <has_text_matching expression="otu_removed.*:\s0" /> - <has_text_matching expression="otu_kept.*:\s55" /> + <has_text_matching expression="otu_kept.*:\s51" /> </assert_contents> </output> </test> |