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Commit message:
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit af85e2b40a89d997ccbf0310ca51cc71489d334e |
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modified:
affiliation_filters.xml affiliation_postprocess.xml biom_to_stdBiom.xml biom_to_tsv.xml clustering.xml demultiplex.xml deseq2_preprocess.xml deseq2_visualisation.xml frogsfunc_functions.xml frogsfunc_pathways.xml frogsfunc_placeseqs.xml itsx.xml macros.xml normalisation.xml phyloseq_alpha_diversity.xml phyloseq_beta_diversity.xml phyloseq_clustering.xml phyloseq_composition.xml phyloseq_import_data.xml phyloseq_manova.xml phyloseq_structure.xml preprocess.xml remove_chimera.xml static/images/FROGS_DESeq2_html_table.png static/images/FROGS_Phyloseq_biomfile.png static/images/FROGS_Phyloseq_plot_heatmap_red.png static/images/FROGS_affiliation_summary.png static/images/FROGS_cluster_fastidious.png static/images/FROGS_frogsfunc_placeseqs_closest_explained.png static/images/FROGS_frogsfunc_placeseqs_table_JGI.png static/images/FROGS_nwk_treefile.png static/images/FROGS_tree_otufile.png test-data/databases/frogs_picrust2_default_dir.loc test-data/input/frogsfunc.biom 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.fasta test-data/references/05-itsx.html 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/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/21-phylo_clustering.nb.html test-data/references/22-phylo_manova.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/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_HVL_db.loc.sample tool-data/frogs_picrust2_default_dir.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test tree.xml tsv_to_biom.xml |
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added:
affiliation_stats.xml cluster_filters.xml cluster_stats.xml static/images/FROGS_DESeq2_html_ipath.png static/images/FROGS_affiliation_filter_ignore.png static/images/FROGS_affiliation_filter_keep.png static/images/FROGS_affiliation_stats_alignment.png static/images/FROGS_affiliation_stats_bootstrap.png static/images/FROGS_affiliation_stats_rarefaction.png static/images/FROGS_affiliation_stats_sunburst.png static/images/FROGS_affiliation_stats_taxonomies.png static/images/FROGS_cluster_stats_clusterDistrib1.png static/images/FROGS_cluster_stats_sample_dist1.png static/images/FROGS_cluster_stats_sample_dist2.png static/images/FROGS_cluster_stats_seq_dist.png static/images/FROGS_frogsfunc_functions_starplot.png static/images/FROGS_frogsfunc_placeseqs_blast.png static/images/FROGS_frogsfunc_placeseqs_nsti.png static/images/starplot_frogsfrunc_function.png taxonomic_affiliation.xml test-data/1683127225.892718_18537_mafft.stderr test-data/1683127225.892718_18537_mafft_aligned.fasta test-data/1683188955.2635202_141707_rmarkdown.stderr test-data/1683615440.2244859_24853_R.stderr test-data/1683615471.1625206_25567_R.stderr test-data/1683618354.3833234_48737_cleaned.fasta test-data/1683618354.3833234_48737_tmp_convert_fasta.log test-data/1683618354.3833234_48737_tmp_place_seqs.log test-data/1683619172.2099853_50503_cleaned.fasta test-data/1683619172.2099853_50503_tmp_convert_fasta.log test-data/1683619172.2099853_50503_tmp_place_seqs.log test-data/1683625674.1083791_56412_genes_abundances_formatted.tsv test-data/EC_copynumbers_predicted.tsv test-data/affi-filterd.log test-data/affi-stats.log test-data/affiliation_abundance.biom test-data/affiliation_filters.test.log test-data/all_tool_test_output.html test-data/asv_data.Rdata test-data/asv_dds.Rdata test-data/biom_to_tsv.log test-data/chaillou.tsv test-data/cluster_filters.log test-data/cluster_stats.log test-data/databases/frogs_picrust2_db/ITS_counts.txt.gz test-data/databases/frogs_picrust2_db/ec_ITS_counts.txt.gz test-data/deseq_peepro.log test-data/deseq_visu.log test-data/deseq_visu_2.log test-data/filters.tsv test-data/frogsfun test-data/frogsfunc.tsv test-data/frogsfunc_function.biom test-data/frogsfunc_function.fasta test-data/frogsfunc_function.log test-data/frogsfunc_pathways_predictions.tsv test-data/frogsfunc_pathways_strat.tsv test-data/frogsfunc_pathways_summary.html test-data/frogsfunc_pathways_unstrat.tsv test-data/frogsfunc_pathways_unstrat_per_seq.tsv test-data/frogsfunc_placeseq.log test-data/log_chimera.txt test-data/log_cluster_filter.txt test-data/log_clustering.txt test-data/log_itsx.txt test-data/log_itsx_2.txt test-data/log_preprocess.txt test-data/multihits.tsv test-data/phyloseq_alpha_diversity.nb.html test-data/phyloseq_alpha_diversity.tsv test-data/phyloseq_beta test-data/phyloseq_beta.log test-data/phyloseq_import.log test-data/phyloseq_manova.html test-data/phyloseq_manova.nb.html test-data/planemo_test.log test-data/planemo_test.sh test-data/planemo_test_2.log test-data/planemo_test_3.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.lint.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.test.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.lint.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.test.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.lint.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.test.log test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.lint.log test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.test.log test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.lint.log test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.test.log test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.lint.log test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.test.log test-data/planemo_test_4.1.0_vincentdarbot/cluster_stats.lint.log test-data/planemo_test_4.1.0_vincentdarbot/clustering.lint.log test-data/planemo_test_4.1.0_vincentdarbot/clustering.test.log test-data/planemo_test_4.1.0_vincentdarbot/demultiplex.lint.log test-data/planemo_test_4.1.0_vincentdarbot/deseq2_preprocess.lint.log test-data/planemo_test_4.1.0_vincentdarbot/deseq2_visualisation.lint.log test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_functions.lint.log test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_pathways.lint.log test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_placeseqs.lint.log test-data/planemo_test_4.1.0_vincentdarbot/itsx.lint.log test-data/planemo_test_4.1.0_vincentdarbot/macros.lint.log test-data/planemo_test_4.1.0_vincentdarbot/normalisation.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_alpha_diversity.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_beta_diversity.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_clustering.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_composition.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_import_data.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_manova.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_structure.lint.log test-data/planemo_test_4.1.0_vincentdarbot/preprocess.lint.log test-data/planemo_test_4.1.0_vincentdarbot/remove_chimera.lint.log test-data/planemo_test_4.1.0_vincentdarbot/taxonomic_affiliation.lint.log test-data/planemo_test_4.1.0_vincentdarbot/tree.lint.log test-data/planemo_test_4.1.0_vincentdarbot/tsv_to_biom.lint.log test-data/planemo_test_4.log test-data/planemo_test_5.log test-data/planemo_test_6.log test-data/preprocess.log test-data/references/07-impacted_clusters_deleted.tsv test-data/references/07-impacted_clusters_deleted_multihit.tsv test-data/references/07-impacted_clusters_masked.tsv test-data/references/07-impacted_clusters_masked_multihit.tsv test-data/references/25-frogsfunc_copynumbers_marker.tsv test-data/taxo_affi.log test-data/taxo_enrichment.tsv test-data/taxonomic_affiliation.log test-data/test/deseq2_preprocess.log test-data/test/frogsfunc_function.log test-data/test/frogsfunc_pathway.log test-data/test/frogsfunc_pathways.log test-data/test/frogsfunc_placeseqs.log test-data/test/preprocess.log test-data/test/taxo_affi.log test-data/tool_test_output_all.html test-data/tree.log test-data/tsv_to_biom.log |
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removed:
affiliation_OTU.xml affiliations_stat.xml clusters_stat.xml frogsfunc_copynumbers.xml otu_filters.xml static/images/FROGS_affiliation_stat_alignment.png static/images/FROGS_affiliation_stat_bootstrap.png static/images/FROGS_affiliation_stat_rarefaction.png static/images/FROGS_affiliation_stat_sunburst.png static/images/FROGS_affiliation_stat_taxonomies.png static/images/FROGS_cluster_stat_clusterDistrib1.png static/images/FROGS_cluster_stat_sample_dist1.png static/images/FROGS_cluster_stat_sample_dist2.png static/images/FROGS_cluster_stat_seq_dist.png static/images/FROGS_frogsfunc_copynumbers_nsti.png test-data/references/01-prepro-flash.fasta test-data/references/01-prepro-flash.html test-data/references/02-clustering_denoising.fasta test-data/references/02-clustering_fastidious.fasta test-data/references/07-impacted_OTU_deleted.tsv test-data/references/07-impacted_OTU_deleted_multihit.tsv test-data/references/07-impacted_OTU_masked.tsv test-data/references/07-impacted_OTU_masked_multihit.tsv 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 |
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| diff -r 37e6f0c959bb -r b2967b704d6b affiliation_OTU.xml --- a/affiliation_OTU.xml Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,166 +0,0 @@ -<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"> - <requirement type="package" version="2.10">blast</requirement> - <requirement type="package" version="6.6.0">emboss</requirement> - </expand> - <command detect_errors="exit_code"><![CDATA[ - #set $reference_filename = str( $ref_file.fields.path ) - export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-2048}/1024)) && - affiliation_OTU.py - --reference '${reference_filename}' - --taxonomy-ranks $taxonomic_ranks - --input-biom '$biom_abundance' - --input-fasta '$fasta_sequences' - --output-biom '$biom_affiliation' - --summary '$summary' - @CPUS@ - --java-mem \$GALAXY_MEMORY_GB - #if $rdp - --rdp - #end if - ]]></command> - <inputs> - <!-- Database Choice --> - <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> - <options from_data_table="frogs_db"/> - <validator type="no_options" message="A built-in database is not available"/> - </param> - <param argument="--rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allows to perform it also with RDP classifier tool (default No)"/> - <expand macro="taxonomic_ranks"/> - <!-- Files --> - <param format="fasta" name="fasta_sequences" type="data" label="Sequence file" help="The sequences to affiliated (format: FASTA)"/> - <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="The abundance file (format: BIOM)"/> - </inputs> - <outputs> - <data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom"/> - <data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/> - </outputs> - <tests> - <test> - <param name="ref_file" value="ITS1_test"/> - <param name="fasta_sequences" value="references/04-filters.fasta"/> - <param name="biom_abundance" value="references/04-filters.biom"/> - <param name="rdp" value="true"/> - <output name="biom_affiliation" file="references/06-affiliation.biom" compare="sim_size" delta="5"/> - <output name="summary" file="references/06-affiliation.html" compare="diff" lines_diff="0"/> - </test> - </tests> - <help> - -@HELP_LOGO@ - -.. class:: infomark page-header h2 - -What it does - -this tool adds taxonomic affiliation in abundance file. - - -.. class:: infomark page-header h2 - -Inputs/outputs - -.. class:: h3 - -Inputs - -**Sequence file**: - -The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). - -**Abundance file**: - -The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_). - -.. class:: h3 - -Outputs - -**Abundance file** (tax_affiliation.biom): - - The abundance file with affiliation (format `BIOM <http://biom-format.org/>`_). - -**Report file** (report.html): - - This file presents the number of sequences affiliated by blast, and the number of multi-affiliation (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). - - .. image:: FROGS_affiliation_summary.png - :height: 975 - :width: 867 - -.. class:: infomark page-header h2 - -Reference database - -All the databases we format (on demand) for RDPClassifier and NCBI Blast+ are inventoried here: http://genoweb.toulouse.inrae.fr/frogs_databanks/assignation/readme.txt - -.. class:: infomark page-header h2 - -How it works ? - -.. csv-table:: - :header: "Steps", "Description" - :widths: 5, 150 - :class: table table-striped - - "1", "`RDPClassifier <http://rdp.cme.msu.edu/classifier/classifier.jsp>`_ may be used with database to associate to each OTU a taxonomy and a bootstrap (example: *Bacteria;(1.0);Firmicutes;(1.0);Clostridia;(1.0);Clostridiales;(1.0);Clostridiaceae 1;(1.0);Clostridium sensu stricto;(1.0);*)." - "2", "`blastn+ <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_ or `needlall <http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html>`_ is used to find alignment between each OTU and the database. Only the bests hits with the same score are reported. blastn+ is used for merged read pair, and needall is used for artificially combined sequence. For each alignment returned, several metrics are computed: identity percentage, coverage percentage, and alignment length" - "3", "For each OTU with several blastn+/needlall alignment results a consensus is determined on each taxonomic level. If all the taxa at a taxonomic rank are identical the taxon name is reported otherwise *Multi-affiliation* is reported. For example, if you have an OTU with two equivalent hits, associated to *Bacteria;Proteobacteria;Gamma Proteobacteria;Enterobacteriales*, and *Bacteria;Proteobacteria;Beta Proteobacteria;Methylophilales*, the consensus will be *Bacteria;Proteobacteria;Multi-affiliation;Multi-affiliation*." - -.. class:: infomark page-header h2 - -Alignment metrics details on identity percentage calculation - -**- Problem with classical %id computation method** - -* **Case 1: a sequencing of overlapping sequences i.e. 16S V3-V4 amplicon MiSeq sequencing** - -.. image:: FROGS_affiliation_overlapped_percent_id.png - :height: 325 - :width: 807 - -* **Case 2 : a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing** - -.. image:: FROGS_affiliation_combined_percent_id.png - :height: 310 - :width: 887 - -**- Finally, how percentage identity is computed ?** - -With the classical method of %id calculation, filtering on %id will systematically removed “FROGS combined” OTUs. So, we proposed to replace the classical %id by a %id computed on the sequenced bases only. - -.. image:: FROGS_affiliation_percent_id_formula.png - :height: 36 - :width: 637 - -For the precedent use cases we will obtain: - -* Case 1: 16S V3V4 overlapped sequence - - % sequenced bases identity = 400 matches / 400 bp = 100% - -* Case 2: very large ITS1 “FROGS combined” shorter than the real sequence - - % sequenced bases identity = (250 + 250 ) / (600 - 100) = 100% - -This calculation allows to return 100% of identity on sequenced bases for “FROGS combined” shorter or longer than reality in case of perfect sequencing, and a smaller percentage of identity in the case of small overlap repeat kept in FROGS combined sequence. - -.. class:: infomark page-header h2 - - -Advices - -This tool can take large time. It is recommended to filter your OTU abundance and sequence files before this tool (see **FROGS OTU Filters**). - -As you can see the affiliation of each OTU is not human readable in outputed abundance file. We provide a tools to convert these BIOM file in tabulated file, see the **FROGS BIOM to TSV** tool. - - -@HELP_CONTACT@ - - </help> - <expand macro="citations"/> -</tool> |
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| diff -r 37e6f0c959bb -r b2967b704d6b affiliation_filters.xml --- a/affiliation_filters.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/affiliation_filters.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,10 +1,9 @@\n <tool id="FROGS_affiliation_filters" name="FROGS Affiliation Filters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">\n- <description>Filters OTUs on several affiliation criteria</description>\n+ <description>Filters ASVs on several affiliation criteria </description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="requirements"/>\n- <command detect_errors="exit_code">\n+ <expand macro="requirements"/> <command detect_errors="exit_code">\n \t\taffiliation_filters.py\n \t\t\t--input-biom \'$input_biom\'\n \t\t\t--input-fasta \'$input_fasta\'\n@@ -43,11 +42,17 @@\n \t\t\t#end if\n \n \t\t\t#set $sep = \' \'\n- #if $blast.taxon_ignored\n+ #if $blast.keep_or_ignore.taxa_choice == "ignore"\n \t--ignore-blast-taxa\n- \t#for $current in $blast.taxon_ignored\n- \t$sep\'${current.ignore_blast_taxa}\'\n- \t#end for\n+ #for $current in $blast.keep_or_ignore.taxon_ignored\n+ $sep\'${current.ignore_blast_taxa}\'\n+ #end for\n+ #end if\n+ #if $blast.keep_or_ignore.taxa_choice == "keep"\n+ \t--keep-blast-taxa\n+ #for $current in $blast.keep_or_ignore.taxon_kept\n+ $sep\'${current.keep_blast_taxa}\'\n+ #end for\n #end if\n \n \t</command>\n@@ -57,30 +62,57 @@\n <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)"/>\n <expand macro="taxonomic_ranks"/>\n <!-- It is used for optional output fasta -->\n- <param name="mode" type="select" label="Filtering mode" multiple="false" help="Do you want to delete OTU or hide affiliations?" optional="false" display="radio">\n+ <param name="mode" type="select" label="Filtering mode" multiple="false" help="Do you want to delete ASV or hide affiliations?" optional="false" display="radio">\n <option value="hide" selected="true">Hidding mode</option>\n <option value="delete">Deleting mode</option>\n </param>\n <section name="blast" title="Filter on Blast affiliations" expanded="true">\n <param argument="--max-blast-evalue" type="float" min="0.0" max="1.0" optional="true" label="Maximum e-value" help="Fill the field only if you want this treatment"/>\n- <param argument="--min-blast-identity" type="float" min="0.0" max="1.0" optional="true" label="Minimum identity" help="Fill the field only if you want this treatment"/>\n- <param argument="--min-blast-coverage" type="float" min="0.0" max="1.0" optional="true" label="Minimum coverage" help="Fill the field only if you want this treatment"/>\n+ <param argument="--min-blast-identity" type="float" min="0.0" max="100" optional="true" label="Minimum identity" help="Fill the field only if you want this treatment"/>\n+ <param argument="--min-blast-coverage" type="float" min="0.0" max="100" optional="true" label="Minimum coverage" help="Fill the field only if you want this treatment"/>\n <param argument="--min-blast-length" type="integer" min="0" optional="true" label="Minimum alignment length" help="Fill the field only if you want this treatment"/>\n- <repeat name="taxon_ignored" title="Filter blast affiliations including these taxon / word">\n- <param argument="--ignore-blast-taxa" type="text" optional="true" label="Full or partial taxon name" help="Example: "unknown species" or "subsp."">\n- <sanitizer invalid_char="">\n- <valid initial="string.letters,string.digits">\n- <add value="/" />\n- <add value="+" />\n- <add value="-" />\n- <add value="=" />\n- <add value=" " />\n- <ad'..b'mode, Cluster_1 will be removed.\n-In the report.html, it will be considered as "Removed", and if the RDP taxonomy and/or the blast taxonomy is/are not kept thanks to an other OTU, the RDP/blast taxonomy(ies) will be considered as lost.\n+In **deleting mode**, Cluster_1 will be removed.\n+In the report.html, it will be considered as "Removed", and if the RDP taxonomy and/or the blast taxonomy is/are not kept thanks to an other ASV, the RDP/blast taxonomy(ies) will be considered as lost.\n \n-In hidding mode, RDP taxonomy will be removed, blast taxonomy will remain unchanged and Cluster_1 will be kept.\n-In the report.html, it will be considered as "Hidden", and if the RDP taxonomy is not kept thanks to an other OTU, the RDP taxonomy will be considered as lost.\n+In **hidding mode**, RDP taxonomy will be removed, blast taxonomy will remain unchanged and Cluster_1 will be kept.\n+In the report.html, it will be considered as "Hidden", and if the RDP taxonomy is not kept thanks to an other ASV, the RDP taxonomy will be considered as lost.\n \n - Cluster 2:\n \n@@ -250,11 +299,11 @@\n \n The RDP taxonomy respects the RDP boostrap threshold, but none of the blast affiliations respect all the blast criteria.\n \n-In deleting mode, Cluster_1 will be removed.\n-In the report.html, it will be considered as "Removed", and if the two blast taxonomies are not kept thanks to others OTUs, they will be considered as lost. In the same way, if there is no other OTU, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the report.html. And idem for the RDP taxonomy.\n+In **deleting mode**, Cluster_1 will be removed.\n+In the report.html, it will be considered as "Removed", and if the two blast taxonomies are not kept thanks to others ASVs, they will be considered as lost. In the same way, if there is no other ASV, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the report.html. And idem for the RDP taxonomy.\n \n-In hidding mode, RDP taxonomy will be remain unchanged, blast taxonomy will be removed and Cluster_2 will be kept.\n-In the report.html, it will be considered as "Hidden", and if the two taxonomies are not kept thanks to others OTUs, they will be considered as lost. In the same way, if there is no other OTU, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the report.html.\n+In **hidding mode**, RDP taxonomy will be remain unchanged, blast taxonomy will be removed and Cluster_2 will be kept.\n+In the report.html, it will be considered as "Hidden", and if the two taxonomies are not kept thanks to others ASVs, they will be considered as lost. In the same way, if there is no other ASV, affiliated to Sulfurimonas genus but with an ambiguous species, 1 Multi-affilaition will be considered as lost in the report.html.\n \n - Cluster 3:\n \n@@ -262,9 +311,9 @@\n \n The RDP taxonomy respects the RDP boostrap threshold, and one of the two blast affiliations respect all the blast criteria.\n \n-In both deleting and hidding mode, Cluster_1 will be kept.\n+In **the both deleting and hidding** modes, Cluster_1 will be kept.\n In the report.html, it will be considered as "Modified", as the RDP taxonomy will remain unchanged and the blast taxonomy will be updated.\n-If no other OTU is affiliated to the "unknown species" of the Fusobacterium genu, this species will be considered as lost. In the same way if no other OTU is affiliated to Fusobacterium genus but with an ambiguous species, 1 Multi-affilaition at the Species level will be considered as lost in the report.html.\n+If no other ASV is affiliated to the "unknown species" of the Fusobacterium genu, this species will be considered as lost. In the same way if no other ASV is affiliated to Fusobacterium genus but with an ambiguous species, 1 Multi-affilaition at the Species level will be considered as lost in the report.html.\n \n @HELP_CONTACT@\n \n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b affiliation_postprocess.xml --- a/affiliation_postprocess.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/affiliation_postprocess.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,12 +1,12 @@ <tool id="FROGS_affiliation_postprocess" name="FROGS Affiliation postprocess" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Aggregates OTUs based on alignment metrics</description> + <description>Aggregates ASVs based on alignment metrics </description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"> affiliation_postprocess.py - #if $is_HVL.HVL_amplicon + #if $is_HVL.HVL_amplicon == "Yes" --reference '$is_HVL.reference.fields.path' #end if --identity $identity @@ -22,8 +22,11 @@ <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="The sequence file to filter (format: FASTA)."/> <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)"/> <conditional name="is_HVL"> - <param name="HVL_amplicon" type="boolean" label="Is this an amplicon hyper variable in length?" help="Multi-affiliation tag may be resolved by selecting the shortest amplicon reference. For this you need the reference fasta file of your targetted amplicon."/> - <when value="true"> + <param name="HVL_amplicon" type="select" display="radio" label="Is this an amplicon hyper variable in length?" help="Multi-affiliation tag may be resolved by selecting the shortest amplicon reference. For this, you need the reference fasta file of your target amplicon."> + <option value="No">No</option> + <option value="Yes" >Yes</option> + </param> + <when value="Yes"> <param argument="--reference" type="select" label="Using reference database" help="Select reference from the list"> <options from_data_table="frogs_HVL_db"/> <validator type="no_options" message="A built-in database is not available"/> @@ -31,10 +34,10 @@ <column name="value" index="1"/--> </param> </when> - <when value="false"/> + <when value="No"/> </conditional> - <param argument="--identity" type="float" min="0.0" max="100.0" value="99.0" label="Minimum identity for aggregation" help="OTUs will be aggregated if they share the same taxonomy with at least X% identity"/> - <param argument="--coverage" type="float" min="0.0" max="100.0" value="99.0" label="Minimum coverage for aggregation" help="OTUs will be aggregated if they share the same taxonomy with at least X% alignment coverage"/> + <param argument="--identity" type="float" min="0.0" max="100.0" value="99.0" label="Minimum identity for aggregation" help="ASVs will be aggregated if they share the same taxonomy with at least X% identity"/> + <param argument="--coverage" type="float" min="0.0" max="100.0" value="99.0" label="Minimum coverage for aggregation" help="ASVs will be aggregated if they share the same taxonomy with at least X% alignment coverage"/> </inputs> <outputs> <data format="biom1" name="biom_out" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom"/> @@ -62,7 +65,7 @@ What it does -This tool resolves multi-hit ambiguities if exact amplicon length are available and aggregrated OTUs sharing same taxonomy based on alignment metrics thresholds +This tool resolves multi-affiliation ambiguities if exact amplicon length are available and aggregrated ASVs sharing same taxonomy based on alignment metrics thresholds .. class:: infomark page-header h2 @@ -75,11 +78,11 @@ **Abundance file**: -The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_) with taxonomic affiliations metadata. +The abundance of each ASV in each sample (format `BIOM <http://biom-format.org/>`_) with taxonomic affiliations metadata. **Sequence file**: -The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_) of each OTU seed. +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_) of each ASV sequence. **Reference file** (optionnal): @@ -92,24 +95,25 @@ **Abundance file**: - The abundance file of OTUs and aggregated OTUs, with their affiliation (format `BIOM <http://biom-format.org/>`_) and with potentially less ambiguities. + The abundance file of ASVs and aggregated ASVs, with their affiliation (format `BIOM <http://biom-format.org/>`_) and with potentially less ambiguities. **Sequence file**: -The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_) of each aggregated OTU seed. +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_) of each aggregated ASV sequence. **Composition file**: -The aggregation composition file (format text) describing the composition of each resulting OTU. +The aggregation composition file (format text) describing the composition of each resulting ASV. .. class:: infomark page-header h2 How it works ? -If a reference fasta file is provided, for each OTU with multiaffiliation, among the different possible affiliations, we only keep the affiliation of the sequence with the shortest length. The aim is to resolve ambiguities due to potential inclusive sequences such as ITS. +This step is the ASVs aggregation that shares the same taxonomy inferred on alignment metrics. +The process starts with the most abundant ASV. If an ASV shares at least one affiliation with another ASV with at least I% of identity and C% of alignment coverage, the ASVs are aggregated together : the different affiliations, are merged, blast concensus taxonomy is updated and abundance counts are summed. The sequence of the most abundant ASV is kept. -Second step is the OTUs aggregation that shares the same taxonomy inferred on alignment metrics. -The process starts with the most abundant OTU. If an OTU shares at least one affiliation with another OTU with at least I% of identity and C% of alignment coverage, the OTUs are aggregated together : the different affiliations, are merged, blast concensus taxonomy is updated and abundance counts are summed. The seed of the most abundant OTU is kept. +If a reference fasta file is provided, for each ASV with multi-affiliation, among the different possible affiliations, we only keep the affiliation of the sequence with the shortest length. This is useful to resolve ambiguities due to potential inclusive sequences such as ITS. +This step also makes it possible to group ASVs from different copies of the same marker gene, thus having the same affiliation. @HELP_CONTACT@ |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b affiliation_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/affiliation_stats.xml Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,152 @@ +<tool id="FROGS_affiliation_stats" name="FROGS_6_Affiliation_Stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> + <description>Process some metrics on taxonomies </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"> + affiliation_stats.py + --input-biom '$biom' + --output-file '$summary_file' + --taxonomic-ranks $taxonomic_ranks + --rarefaction-ranks $rarefaction_ranks + #if $affiliation.affiliation_type == "FROGS_blast" + --multiple-tag 'blast_affiliations' + --tax-consensus-tag 'blast_taxonomy' + --identity-tag 'perc_identity' + --coverage-tag 'perc_query_coverage' + #else if $affiliation.affiliation_type == "FROGS_rdp" + --taxonomy-tag 'rdp_taxonomy' + --bootstrap-tag 'rdp_bootstrap' + #else + --taxonomy-tag '$affiliation.taxonomy_tag' + #if $affiliation.bootstrap_tag + --bootstrap-tag '$affiliation.bootstrap_tag' + #end if + #if $affiliation.identity_tag and $affiliation.coverage_tag + --identity-tag '$affiliation.identity_tag' + --coverage-tag '$affiliation.coverage_tag' + #end if + #end if + </command> + <inputs> + <!-- Files --> + <param format="biom1" name="biom" type="data" label="Abundance file" help="Abundances and affiliations (format: BIOM)"/> + <!-- Parameters --> + <expand macro="taxonomic_ranks"/> + <param argument="--rarefaction-ranks" type="text" optional="false" value="Class Order Family Genus Species" + label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space."> + <sanitizer invalid_char=""> + <valid initial="string.letters"> + <add value=" " /> + </valid> + </sanitizer> + <validator type="regex">[A-Za-z ]+</validator> + </param> + <conditional name="affiliation"> + <param name="affiliation_type" type="select" label="Affiliation processed" help="Select the type of affiliation processed. If your affiliation has been processed with an external tool: use 'Custom'."> + <option value="FROGS_blast" selected="true">FROGS Blast</option> + <option value="FROGS_rdp">FROGS RDP</option> + <option value="custom">Custom</option> + </param> + <when value="FROGS_blast"/> + <when value="FROGS_rdp"/> + <when value="custom"> + <param argument="--taxonomy-tag" type="text" value="taxonomy" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy"> + <expand macro="sanitizer_validator"/> + </param> + <param argument="--bootstrap-tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap"> + <expand macro="sanitizer_validator"/> + </param> + <param argument="--identity-tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity"> + <expand macro="sanitizer_validator"/> + </param> + <param argument="--coverage-tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment ASVs coverage"> + <expand macro="sanitizer_validator"/> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="biom" value="references/09-normalisation.biom" /> + <param name="rarefaction_ranks" value="Family Genus Species" /> + <conditional name="affiliation"> + <param name="affiliation_type" value="FROGS_blast" /> + <param name="taxonomic_ranks" value="Domain Phylum Class Order Family Genus Species" /> + <param name="taxonomy_tag" value="blast_taxonomy" /> + <param name="identity_tag" value="perc_identity" /> + <param name="coverage_tag" value="perc_query_coverage" /> + </conditional> + <!-- differences may exist due to random function to generat rarefaction curves --> + <output name="summary_file" file="references/11-affiliationsStat.html" compare="sim_size" delta="20" /> + <output name="summary_file" file="references/11-affiliationsStat.html" compare="diff" lines_diff="2" /> + </test> + </tests> + <help> + +@HELP_LOGO@ + +.. class:: infomark page-header h2 + +What it does + +"FROGS Affiliation stats" computes several metrics and generates a HTML file describing ASVs based on their taxonomies and eventually the quality of the affiliations. + + +.. class:: infomark page-header h2 + +Input/output + +.. class:: h3 + +Input + +**Abundance file**: + +The abundance and affiliation of each ASV (format `BIOM <http://biom-format.org/>`_). This file can be produced by FROGS_5_taxonomic_affiliation tool. + + +.. class:: h3 + +Output + +**Report file** (report.html): + + ASVs taxonomies and affiliation metrics (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + + *-Taxonomy distribution*: displays the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample + + .. image:: FROGS_affiliation_stats_taxonomies.png + :height: 380 + :width: 891 + + .. image:: FROGS_affiliation_stats_rarefaction.png + :height: 380 + :width: 794 + + .. image:: FROGS_affiliation_stats_sunburst.png + :height: 380 + :width: 440 + + -Bootstrap distribution: displays for affiliation methods with bootstrap the bootstrap on each taxonomic rank + + .. image:: FROGS_affiliation_stats_bootstrap.png + :height: 568 + :width: 1050 + + -Alignment distribution: displays for affiliation methods with alignment the distribution of identity/coverage + + .. image:: FROGS_affiliation_stats_alignment.png + :height: 570 + :width: 731 + + +@HELP_CONTACT@ + + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b affiliations_stat.xml --- a/affiliations_stat.xml Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,153 +0,0 @@ -<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Process some metrics on taxonomies</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <command detect_errors="exit_code"> - affiliations_stat.py - --input-biom '$biom' - --output-file '$summary_file' - --taxonomic-ranks $taxonomic_ranks - --rarefaction-ranks $rarefaction_ranks - #if $affiliation.affiliation_type == "FROGS_blast" - --multiple-tag 'blast_affiliations' - --tax-consensus-tag 'blast_taxonomy' - --identity-tag 'perc_identity' - --coverage-tag 'perc_query_coverage' - #else if $affiliation.affiliation_type == "FROGS_rdp" - --taxonomy-tag 'rdp_taxonomy' - --bootstrap-tag 'rdp_bootstrap' - #else - --taxonomy-tag '$affiliation.taxonomy_tag' - #if $affiliation.bootstrap_tag - --bootstrap-tag '$affiliation.bootstrap_tag' - #end if - #if $affiliation.identity_tag and $affiliation.coverage_tag - --identity-tag '$affiliation.identity_tag' - --coverage-tag '$affiliation.coverage_tag' - #end if - #end if - </command> - <inputs> - <!-- Files --> - <param format="biom1" name="biom" type="data" label="Abundance file" help="Abundances and affiliations (format: BIOM)"/> - <!-- Parameters --> - <expand macro="taxonomic_ranks"/> - <param argument="--rarefaction-ranks" type="text" optional="false" value="Class Order Family Genus Species" - label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space."> - <sanitizer invalid_char=""> - <valid initial="string.letters"> - <add value=" " /> - </valid> - </sanitizer> - <validator type="regex">[A-Za-z ]+</validator> - </param> - <conditional name="affiliation"> - <param name="affiliation_type" type="select" label="Affiliation processed" help="Select the type of affiliation processed. If your affiliation has been processed with an external tool: use 'Custom'."> - <option value="FROGS_blast" selected="true">FROGS Blast</option> - <option value="FROGS_rdp">FROGS RDP</option> - <option value="custom">Custom</option> - </param> - <when value="FROGS_blast"/> - <when value="FROGS_rdp"/> - <when value="custom"> - <param argument="--taxonomy-tag" type="text" value="taxonomy" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy"> - <expand macro="sanitizer_validator"/> - </param> - <param argument="--bootstrap-tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap"> - <expand macro="sanitizer_validator"/> - </param> - <param argument="--identity-tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity"> - <expand macro="sanitizer_validator"/> - </param> - <param argument="--coverage-tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment OTUs coverage"> - <expand macro="sanitizer_validator"/> - </param> - </when> - </conditional> - </inputs> - <outputs> - <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="summary.html"/> - </outputs> - <tests> - <test> - <param name="biom" value="references/09-normalisation.biom" /> - <param name="rarefaction_ranks" value="Family Genus Species" /> - <conditional name="affiliation"> - <param name="affiliation_type" value="FROGS_blast" /> - <param name="taxonomic_ranks" value="Domain Phylum Class Order Family Genus Species" /> - <param name="taxonomy_tag" value="blast_taxonomy" /> - <param name="identity_tag" value="perc_identity" /> - <param name="coverage_tag" value="perc_query_coverage" /> - </conditional> - <!-- differences may exist due to random function to generat rarefaction curves --> - <output name="summary_file" file="references/11-affiliationsStat.html" compare="sim_size" delta="20" /> - <output name="summary_file" file="references/11-affiliationsStat.html" compare="diff" lines_diff="2" /> - </test> - </tests> - <help> - -@HELP_LOGO@ - -.. class:: infomark page-header h2 - -What it does - -FROGS Affiliations stat computes several metrics and generates a HTML file describing OTUs based on their taxonomies and eventually the quality of the affiliations. - - -.. class:: infomark page-header h2 - -Input/output - -.. class:: h3 - -Input - -**Abundance file**: - -The abundance and affiliation of each OTUs (format `BIOM <http://biom-format.org/>`_). This file can be produced by FROGS Affiliation OTU. - -The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format. - -.. class:: h3 - -Output - -**Report file** (report.html): - - OTUs taxonomies and affiliations metrics (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): - - *-Taxonomy distribution*: displays the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample - - .. image:: FROGS_affiliation_stat_taxonomies.png - :height: 380 - :width: 891 - - .. image:: FROGS_affiliation_stat_rarefaction.png - :height: 380 - :width: 794 - - .. image:: FROGS_affiliation_stat_sunburst.png - :height: 380 - :width: 440 - - -Bootstrap distribution: displays for affiliation methods with bootstrap the bootstrap on each taxonomic rank - - .. image:: FROGS_affiliation_stat_bootstrap.png - :height: 380 - :width: 867 - - -Alignment distribution: displays for affiliation methods with alignment the distribution of identity/coverage - - .. image:: FROGS_affiliation_stat_alignment.png - :height: 380 - :width: 859 - - -@HELP_CONTACT@ - - </help> - <expand macro="citations" /> -</tool> |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b biom_to_stdBiom.xml --- a/biom_to_stdBiom.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/biom_to_stdBiom.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Converts a FROGS BIOM in fully compatible BIOM</description> + <description>Converts a FROGS BIOM in fully compatible BIOM </description> <macros> <import>macros.xml</import> </macros> @@ -62,7 +62,7 @@ How it works ? -FROGS BIOM to std BIOM extracts the blast alignment details in a second file, write a BIOM usable in every tools using BIOM and defined the consensus taxonomy provided by blast as main taxonomy. +**FROGS BIOM to std BIOM** extracts the blast alignment details in a second file, write a BIOM usable in every tools using BIOM and defined the consensus taxonomy provided by blast as main taxonomy. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b biom_to_tsv.xml --- a/biom_to_tsv.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/biom_to_tsv.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGS_biom_to_tsv" name="FROGS BIOM to TSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Converts a BIOM file in TSV file</description> + <description>Converts a BIOM file in TSV file </description> <macros> <import>macros.xml</import> </macros> @@ -11,7 +11,7 @@ --input-fasta '$sequence_file' #end if --output-tsv '$tsv_file' - #if $extract_multi_align + #if $extract_multi_align == "yes" --output-multi-affi '$multi_affi_file' #end if </command> @@ -20,19 +20,22 @@ <param format="biom1" name="biom_file" type="data" label="Abundance file" help="The BIOM file to convert (format: BIOM)" optional="false" /> <param format="fasta" name="sequence_file" type="data" label="Sequences file (optional)" help="The sequences file (format: fasta). If you use this option the sequences will be add in TSV." optional="true" /> <!-- Parameters --> - <param name="extract_multi_align" type="boolean" label="Extract multi-alignments" help="If you have used FROGS affiliation on your data, you can extract information about multiple alignements in a second TSV." checked="true"/> + <param name="extract_multi_align" type="select" display="radio" label="Extract multi-alignments" help="If you have used FROGS_5_taxonomic_affiliation on your data, you can extract information about multiple alignements in a second TSV."> + <option value="yes" selected="true">Yes</option> + <option value="no" >No</option> + </param> </inputs> <outputs> <data format="tsv" name="tsv_file" label="${tool.name}: abundance.tsv" from_work_dir="abundance.tsv"/> <data format="tsv" name="multi_affi_file" label="${tool.name}: multi-affiliations.tsv" from_work_dir="multi_hits.tsv" > - <filter>extract_multi_align</filter> + <filter>extract_multi_align == "yes"</filter> </data> </outputs> <tests> <test> <param name="biom_file" value="references/09-normalisation.biom"/> <param name="sequence_file" value="references/09-normalisation.fasta"/> - <param name="extract_multi_align" value="true"/> + <param name="extract_multi_align" value="yes"/> <output name="tsv_file" value="references/12-biom2tsv.tsv" compare="diff" lines_diff="0"/> <output name="multi_affi_file" value="references/12-biom2tsv-affiliation_multihit.tsv" compare="diff" lines_diff="0"/> </test> @@ -65,27 +68,27 @@ **Abundance file**: - The abundance of each cluster in each sample and theirs metadata (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). + The abundance of each cluster in each sample and its metadata (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). If you add the sequences file, this information is added for each cluster. -**Multiple affiliation file**: +**Multi-affiliation file**: - If you have used *FROGS affiliation* on your data, each OTU can have several affiliations: several alignments with same score on reference database. The multiple affiliation file contains details on these possibles affiliations (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). + If you have used *FROGS_6 taxonomic affiliation* on your data, each ASV can have several affiliations: several alignments with same score on reference database. The multi-affiliation file contains details on these possibles affiliations (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). .. class:: infomark page-header h2 How it works ? -FROGS Biom to Tsv will search if any metadata are available, and the OTU sequence if fasta file is precised. Then it will extract the OTU name, sum the sample abundance, and extract the detailed abundance for each sample. Finally, it will write all these fields separated by tabulation in the TSV file. +**FROGS_Biom_to_TSV** will search if any metadata are available, and the ASV sequence if Sequences file (FASTA format) is precised. Then it will extract the ASV name, sum the sample abundance, and extract the detailed abundance for each sample. Finally, it will write all these fields separated by tabulations in the TSV file. .. class:: infomark page-header h2 Advices -This output tsv file is easily readable in any spreadsheet software. Be aware that these software have a number of line limit (1 048 576 for Excel and LibreOffice calc ate least). If you have more OTU, use **FROGS Filters** to extract for example the most abundant OTU before converting your BIOM abundance table in TSV file. +This output TSV file is easily readable in any spreadsheet software. Be aware that these software have a number of line limit (1 048 576 for Excel and LibreOffice calc ate least). If you have more ASV, use **FROGS Cluster filters** to extract for example the most abundant ASVs before converting your BIOM abundance table in TSV file. @HELP_CONTACT@ |
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| diff -r 37e6f0c959bb -r b2967b704d6b cluster_filters.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cluster_filters.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,285 @@\n+<?xml version="1.0"?>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<tool id="FROGS_cluster_filters" name="FROGS_4 Cluster filters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+\t<description>Filters clusters on several criteria. </description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements">\n+ <requirement type="package" version="2.10">blast</requirement>\n+ </expand>\n+\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\n+\t<command>\n+\n+\t\t\tcluster_filters.py\n+\t\t\t--nb-cpus \\${GALAXY_SLOTS:-1}\n+\t\t\t--input-biom \'$input_biom\'\n+\t\t\t--input-fasta \'$input_fasta\'\n+\t\t\t--output-fasta \'$output_fasta\'\n+\t\t\t--output-biom \'$output_biom\'\n+\t\t\t--excluded \'$output_excluded\'\n+\t\t\t--summary \'$output_summary\'\n+\n+\t\t\t#if $choice_prevalence_method.prevalence_method == "all"\n+\t\t\t\t#if $choice_prevalence_method.min_sample_presence\n+\t\t\t\t\t--min-sample-presence $choice_prevalence_method.min_sample_presence\n+\t\t\t\t#end if\n+\t\t\t#else if $choice_prevalence_method.prevalence_method == "replicate"\n+\t\t\t\t#if $choice_prevalence_method.min_replicate_presence\n+\t\t\t\t\t--min-replicate-presence $choice_prevalence_method.min_replicate_presence\n+\t\t\t\t\t--replicate_file $choice_prevalence_method.replicate_file\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\n+\t\t\t#if $choice_abundance_unit.abundance_unit_type == "count"\n+\t\t\t\t#if $choice_abundance_unit.min_abundance_count\n+\t\t\t\t\t--min-abundance $choice_abundance_unit.min_abundance_count\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\n+\t\t\t#if $choice_abundance_unit.abundance_unit_type == "proportion"\n+\t\t\t\t#if $choice_abundance_unit.min_abundance_proportion\n+\t\t\t\t\t--min-abundance $choice_abundance_unit.min_abundance_proportion\n+\t\t\t\t#end if\n+\t\t\t#end if\n+\n+\t\t\t#if $nb_biggest_clusters\n+\t\t\t\t--nb-biggest-clusters $nb_biggest_clusters\n+\t\t\t#end if\n+\n+\n+\t\t\t#if $contaminantSource.which_contaminantSource == "history"\n+\t\t\t\t##build index on the fly\n+\t\t\t\t--contaminant \'${contaminantSource.ownContaminantFile}\'\n+\t\t\t#else if $contaminantSource.which_contaminantSource == "server"\n+\t\t\t\t##use precomputed indexes\n+\t\t\t\t--contaminant \'${contaminantSource.contaminants_db.fields.path}\'\n+\t\t\t#end if\n+\n+\t</command>\n+\t<inputs>\n+\t\t<!-- Files -->\n+\t\t<param format="fasta" name="input_fasta" type="data" label="Sequence file" help="The sequence file to filter (format: FASTA)" />\n+\t\t<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)" />\n+\n+\t\t<conditional name="choice_prevalence_method">\n+\t\t\t<param name="prevalence_method" type="select" label="Minimum prevalence method">\n+\t\t\t\t<option value="all"> all samples </option>\n+\t\t\t\t<option value="replicate"> replicate identification </option>\n+\t\t\t</param>\n+\t\t\t<when value="all">\n+\t\t\t\t<param name="min_sample_presence" type="integer" optional="true" label="Minimum prevalence" size="5" help="Fill the field only if you want this treatment. Keep cluster if it is present in at least this number of samples.">\n+\t\t\t\t\t<validator type="in_range" min="2" message="To be effective this threshold need to be higher than 1" />\n+\t\t\t\t</param>\n+\t\t\t</when>\n+\t\t\t<when value="replicate">\n+\t\t\t\t<param name="replicate_file" type="data" format="tabular,tsv" optional="True" label="File of replicated sample names" help="Replicate file to link ea'..b'\n+\n+Inputs\n+\n+**Sequence file**:\n+\n+The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n+\n+**Abundance file**:\n+\n+The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_).\n+\n+**Contaminant fasta file** (optional):\n+\n+A sequence fasta file containing the reference sequence of known contaminant\n+\n+**File of replicated sample names** (optional):\n+\n+If you selected " replicate identification " for the minimum prevalence method, this file is needed to identify the group to which the samples belong.\n+\n+If not all samples are present in the "File of replicated sample names", they will not be affected by this filter step and will be kept in the abundance table.\n+\n+The file must consist of only 2 columns, separated by a tabulation. The first column contains the exact names of the samples (exactly those contained in the biom file) and the second column contains the name of the group to which they belong.\n+\n+Please note that group names must not contain accents, spaces or special characters.\n+\n+.. class:: h3\n+\n+Outputs\n+\n+**Sequence file** (sequences.fasta):\n+\n+ The sequences after filtering (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n+\n+**Abundance file** (abundance.biom):\n+\n+ The abundance after filtering (format `BIOM <http://biom-format.org/>`_).\n+\n+**Excluded file** (excluded.txt):\n+\n+ The list of the clusters deleted by filters (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_).\n+\n+**Report file** (report.html):\n+\n+ The filters and the number of removed sequences (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+How it works?\n+\n+The ASVs kept are the ones that satisfy into the BIOM input file the thresholds specified by the user.\n+\n+The BIOM abundance table and the fasta file are written again according to the ASVs kept.\n+\n+The clusters discarded are listed in the excluded file.\n+\n+.. csv-table::\n+ :header: "Steps", "description"\n+ :widths: 5, 150\n+ :class: table table-striped\n+\n+ "1", "Except the filter to select the n most abundant clusters, all the selected filters are run independently. For each filters a list of the clusters removed is generated. Concerning contaminant research, clusters are added to the previous list if it aligns on a contaminant reference sequence with 80% of identity and 80% of coverage"\n+ "2", "All the clusters tagged to remove by at least one filter are removed."\n+ "3", "If the filter to select the N most abundant clusters is filled it is applied."\n+\n+\n+\n+.. class:: infomark page-header h2\n+\n+Advices\n+\n+Please check that the input fasta file and the input BIOM file correspond to the same clusters.\n+\n+Examples for the filters on abundance and occurence of the clusters :\n+\n+-To keep the clusters that are present in 5 samples, fill the **Minimum prevalence method** field with **all samples** option, with "5".\n+\n+-To keep the clusters that are present in half of the replicates, fill the **Minimum prevalence method** field with **replicate identification** option, with a minimum prevalence of "0.5".\n+\n+.. image:: FROGS_otu_filter_replicates_file.png\n+\n+In this example, if we want to keep the clusters that are present in at least 50% of the samples, we set the threshold at 0.5. The process will therefore keep the clusters present in at least \n+\n+ - 2 "rich" samples\n+ - 3 "richAB" samples,\n+ - 1 "lowAB" sample\n+ - 1 "april21" sample\n+\n+and all clusters in sample9 since it is the only representative of the "low" condition.\n+\n+-To display the 20 **biggest** clusters, fill the corresponding field with "20".\n+\n+-To filter on **abundance** of cluster i.e. the cluster size, we advise you to specify 0.005% i.e. 0.00005. It seems to be the optimal threshold (`Bokulich *et al*, 2013 <http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html>`_ ).\n+\n+\n+@HELP_CONTACT@\n+\n+\t</help>\n+\t<expand macro="citations" />\n+</tool>\n+\n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b cluster_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cluster_stats.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,87 @@ +<tool id="FROGS_cluster_stats" name="FROGS_Cluster_Stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> + <description>Process some metrics on clusters </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"> + cluster_stats.py + --input-biom '$biom' + --output-file '$summary_file' + </command> + <inputs> + <param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)"/> + </inputs> + <outputs> + <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="biom" value="references/09-normalisation.biom"/> + <output name="summary_file" value="references/10-clustersStat.html" compare="diff" lines_diff="0"/> + </test> + </tests> + <help> + +@HELP_LOGO@ + +.. class:: infomark page-header h2 + +What it does + +FROGS Cluster stats computes several metrics and generates a HTML file describing clusters based on abundances, samples, ... + + +.. class:: infomark page-header h2 + +Input/output + +.. class:: h3 + +Input + +**Abundance file**: + +The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). + +The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format. + +.. class:: h3 + +Output + +**Report file** (report.html): + + *Cluster distribution* : describes the sizes distribution of all clusters thanks to boxplots and tables + + .. image:: FROGS_cluster_stats_clusterDistrib1.png + :height: 1180 + :width: 900 + + *Sequence distribution* : describes the sequences distribution among clusters + + .. image:: FROGS_cluster_stats_seq_dist.png + + *Sample distribution* : describes clusters distribution among samples and gives an `hierarchical clustering <http://en.wikipedia.org/wiki/Hierarchical_clustering>`_ on samples abundance profile (distance method = `braycurtis <http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis>`_, linkage method = average) + + .. image:: FROGS_cluster_stats_sample_dist1.png + :height: 400 + :width: 700 + + .. image:: FROGS_cluster_stats_sample_dist2.png + :height: 350 + :width: 610 + +.. class:: infomark page-header h2 + +Advices + +This is a very usefull tool to see the evolution of the clusters. Do not hesitate to run this tool after each FROGS step beginning at the clustering step. + + + +@HELP_CONTACT@ + + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 37e6f0c959bb -r b2967b704d6b clustering.xml --- a/clustering.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/clustering.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,5 +1,5 @@\n-<tool id="FROGS_clustering" name="FROGS Clustering swarm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">\n- <description>Single-linkage clustering on sequences</description>\n+<tool id="FROGS_clustering" name="FROGS_2 Clustering swarm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">\n+ <description>Single-linkage clustering on sequences </description>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -16,11 +16,15 @@\n --output-compo \'$swarms_composition\'\n #if $FROGS_guidelines.guidelines_version == "3.2"\n --distance $FROGS_guidelines.distance\n- $FROGS_guidelines.fastidious\n+ #if $FROGS_guidelines.fastidious == "true"\n+ --fastidious\n+ #end if\n #end if\n #if $FROGS_guidelines.guidelines_version == "3.1"\n --distance $FROGS_guidelines.distance\n- $FROGS_guidelines.denoising\n+ #if $FROGS_guidelines.denoising == "true"\n+ --denoising\n+ #end if\n #end if\n </command>\n <inputs>\n@@ -34,12 +38,18 @@\n <option value="3.1">First guidelines until 3.1</option>\n </param>\n <when value="3.2">\n- <param argument="--distance" type="integer" label="Aggregation distance clustering" help="Maximum number of differences between sequences in each aggregation swarm step. (recommended d=1)" value="1" min="1" max="15" optional="false" />\n- <param argument="--fastidious" type="boolean" checked="true" truevalue="--fastidious" falsevalue="" label="Refine OTU clustering" help="Clustering will be performed with the swarm --fastidious option. It is recommended and only usable in association with a distance of 1 (default and recommended: Yes)" />\n+ <param argument="--distance" type="integer" label="Aggregation distance clustering" help="Maximum number of differences between sequences in each aggregation Swarm step. (recommended d=1)" value="1" min="1" max="15" optional="false" />\n+ <param argument="--fastidious" type="select" label="Refine clustering" help="Clustering will be performed with the Swarm --fastidious option. It is recommended and only usable in association with a distance of 1 (default and recommended: Yes)" display="radio" >\n+ <option value="true">Yes, refine clustering with --fastidious swarm option</option>\n+ <option value="false">No, perform clustering without refinment</option>\n+ </param>\n </when>\n <when value="3.1">\n- <param argument="--distance" type="integer" value="3" min="1" max="15" optional="false" label="Aggregation distance clustering" help="Maximum number of differences between sequences in each aggregation swarm step" />\n- <param argument="--denoising" type="boolean" checked="true" truevalue="--denoising" falsevalue="" label="Efficient denoising ? (equals to a first clustering step with d=1)" help="Clustering will be perform in two steps, first with distance = 1 and then with an aggregation distance of next input parameter (default : Yes)" />\n+ <param argument="--distance" type="integer" value="3" min="1" max="15" optional="false" label="Aggregation distance clustering" help="Maximum number of differences between sequences in each aggregation Swarm step" />\n+ <param argument="--denoising" type="select" label="Efficient denoising ? (equals to a first clustering step with d=1)" help="Clustering will be perform in two steps, first with distance = 1 and then with an aggregation distance of next input parameter (default : Yes)" display="radio" >\n+ <option value="true">Yes, perform a first clustering with d=1</option>\n+ <option value="false">No, perform clustering in one step</option>\n+ '..b'/master/README.md#refine-swarm-otus>`_)", "Clusters the pre-clusters sequences (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specified"\n+ "4", "Clusters the reads (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specified", "Clusters the reads (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specified and the (`--fastidious option of Swarm <https://github.com/torognes/swarm/blob/master/README.md#refine-swarm-otus>`_)", "Clusters the pre-clusters sequences (`Swarm <https://github.com/torognes/swarm>`_) with the distance you specified"\n \n **Swarm focus**\n \n-Swarm uses an iterative growth process and the use of sequence abundance values to delineate OTUs.\n+Swarm uses an iterative growth process and the use of sequence abundance values to delineate clusters.\n \n .. image:: FROGS_cluster_swarm.png\n :height: 223\n@@ -158,9 +166,9 @@\n \n In each growth step, the sequence of the previous step is used to find the others sequences with a number of differences inferior or equal to the "Aggregation distance".\n \n-After agregation Swarm refines the clusters by looking at the abundancies along the connections. Theoritically the abundances must decrease when you are going away from the seed (which is often the most abundant sequence). If this abundance raises again, it means that two different clusters are connected by some poorly abundant sequences, so swarm cut the connection.\n+After agregation Swarm refines the clusters by looking at the abundancies along the connections. Theoritically the abundances must decrease when you are going away from the seed (which is often the most abundant sequence). If this abundance raises again, it means that two different clusters are connected by some poorly abundant sequences, so Swarm cut the connection.\n \n-On the other hand, the fastidious option of swarm allows to aggregate small and rare clusters into bigger one if they share sequence with at most 2*d distance. In this cases, d is restricted to 1 so, cluster distance will be 2. (image extracted from `Swarm github <https://github.com/torognes/swarm>`_)\n+On the other hand, the fastidious option of Swarm allows to aggregate small and rare clusters into bigger one if they share sequence with at most 2*d distance. In this cases, d is restricted to 1 so, cluster distance will be 2. (image extracted from `Swarm github <https://github.com/torognes/swarm>`_)\n \n .. image:: FROGS_cluster_fastidious.png\n :height: 319\n@@ -173,11 +181,11 @@\n \n The fastidious strategy is recommended since FROGS 3.2\n \n-The fastidious option is recommended with an aggregating distance of 1. "It will reduce the number of small OTUs while maintaining a high clustering resolution, by postulating the existence of an intermediate amplicon sequences"\n+The fastidious option is recommended with an aggregating distance of 1. "It will reduce the number of small clusters while maintaining a high clustering resolution, by postulating the existence of an intermediate amplicon sequences"\n \n The denoising strategy was recommended until FROGS 3.1\n \n-The denoising step allows to build very fine clusters with minimal differences. In this case, the number of differences between sequences of each crowns is equal to 1. This first clustering is extremly quick. After the denoising, a second swarm is run with an aggregation distance >1 as you have configured, between seeds from this first clustering. We recommended a distance of 3.\n+The denoising step allows to build very fine clusters with minimal differences. In this case, the number of differences between sequences of each crowns is equal to 1. This first clustering is extremly quick. After the denoising, a second Swarm is run with an aggregation distance >1 as you have configured, between seeds from this first clustering. We recommended a distance of 3.\n \n To have some metrics on your clusters, you can use the tool **FROGS Clusters Stat**.\n \n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b clusters_stat.xml --- a/clusters_stat.xml Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,87 +0,0 @@ -<tool id="FROGS_clusters_stat" name="FROGS Clusters stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Process some metrics on clusters</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <command detect_errors="exit_code"> - clusters_stat.py - --input-biom '$biom' - --output-file '$summary_file' - </command> - <inputs> - <param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)"/> - </inputs> - <outputs> - <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="summary.html"/> - </outputs> - <tests> - <test> - <param name="biom" value="references/09-normalisation.biom"/> - <output name="summary_file" value="references/10-clustersStat.html" compare="diff" lines_diff="0"/> - </test> - </tests> - <help> - -@HELP_LOGO@ - -.. class:: infomark page-header h2 - -What it does - -FROGS Clusters stat computes several metrics and generates a HTML file describing clusters based on abundances, samples, ... - - -.. class:: infomark page-header h2 - -Input/output - -.. class:: h3 - -Input - -**Abundance file**: - -The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). - -The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format. - -.. class:: h3 - -Output - -**Report file** (report.html): - - *Cluster distribution* : describes the sizes distribution of all clusters thanks to boxplots and tables - - .. image:: FROGS_cluster_stat_clusterDistrib1.png - :height: 1180 - :width: 900 - - *Sequence distribution* : describes the sequences distribution among clusters - - .. image:: FROGS_cluster_stat_seq_dist.png - - *Sample distribution* : describes clusters distribution among samples and gives an `hierarchical clustering <http://en.wikipedia.org/wiki/Hierarchical_clustering>`_ on samples abundance profile (distance method = `braycurtis <http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis>`_, linkage method = average) - - .. image:: FROGS_cluster_stat_sample_dist1.png - :height: 400 - :width: 700 - - .. image:: FROGS_cluster_stat_sample_dist2.png - :height: 350 - :width: 610 - -.. class:: infomark page-header h2 - -Advices - -This is a very usefull tool to see the evolution of the OTUs. Do not hesitate to run this tool after each FROGS step beginning at the clustering step. - - - -@HELP_CONTACT@ - - </help> - <expand macro="citations" /> -</tool> |
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| diff -r 37e6f0c959bb -r b2967b704d6b demultiplex.xml --- a/demultiplex.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/demultiplex.xml Tue May 23 07:59:04 2023 +0000 |
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| @@ -1,5 +1,5 @@ -<tool id="FROGS_demultiplex" name="FROGS Demultiplex reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Attribute reads to samples in function of inner barcode</description> +<tool id="FROGS_demultiplex" name="FROGS_0 Demultiplex reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> + <description>Attribute reads to samples in function of inner barcode </description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 37e6f0c959bb -r b2967b704d6b deseq2_preprocess.xml --- a/deseq2_preprocess.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/deseq2_preprocess.xml Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -1,5 +1,5 @@ <tool id="FROGSSTAT_DESeq2_Preprocess" name="FROGSSTAT DESeq2 Preprocess" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>import a Phyloseq object and prepare it for DESeq2 differential abundance analysis</description> + <description>import a Phyloseq object and prepare it for DESeq2 differential abundance analysis </description> <macros> <import>macros.xml</import> </macros> @@ -8,27 +8,48 @@ <requirement type="package" version="1.6.6">r-optparse</requirement> </expand> <command detect_errors="exit_code"> - deseq2_preprocess.py --data '$data' + deseq2_preprocess.py + --analysis '$analysis_type.analysis' + #if $analysis_type.analysis == 'ASV' + --data '$data' + --out-Rdata '$dds_asv' + #else: + --input-functions '$input_functions' + --samplefile '$samplefile' + --out-Rdata '$dds_function' + #end if #if $multiple.seconde == 'true' --var '$var1${multiple.mod}${multiple.var2}' #else --var '$var1' #end if - --out-Rdata '$dds' - </command> + + </command> <inputs> - <!-- Files --> - <param format="rdata" name="data" type="data" label="Phyloseq object " help="This is the result of FROGSSTAT Phyloseq Import Data with normalise option set to NO (DESeq2 is more powerful on unnormalised counts) (format RData)"/> - <!-- Parameters --> - <param name="var1" type="text" label="Experimental variable" help="The factor suspected to have an effect on OTU abundances. Ex: Treatment, etc."> + <!-- Files --> + <conditional name="analysis_type"> + <param name="analysis" type="select" label="Type of analysis" help="Type of data to perform the differential analysis. ASV: DESeq2 is run on the ASV abundance table. FUNCTION: DESeq2 is run on predicted function abundance table from FROGSFUNC_2_function tool." display='radio'> + <option value="ASV" selected="true">ASV</option> + <option value="FUNCTION">FUNCTION</option> + </param> + <when value="ASV"> + <param format="rdata" name="data" type="data" label="Phyloseq object " help="This is the result of FROGSSTAT_Phyloseq_Import_Data without normalisation (DESeq2 is more powerful on unnormalised counts) (format RData)"/> + </when> + <when value="FUNCTION"> + <param format="tsv" name="input_functions" type="data" label="Function abundances file " help="Input file of predicted function abundances (frogsfunc_functions_unstrat.tsv from FROGSFUNC_2_function tool)."/> + <param format="tabular,tsv" argument="--samplefile" type="data" label="Metadata asociated to samples (format: TSV)" help="The file must contain the metadata that characterise each sample."/> + </when> + </conditional> + <!-- Parameters --> + <param name="var1" type="text" label="Experimental variable" help="The factor that could have an effect on ASV/FUNCTION abundances. Ex: Treatment, etc."> <expand macro="sanitizer_validator"/> </param> - <conditional name="multiple"> - <param name="seconde" type="select" label="Do you want to correct for a confounding factor?" help="If yes, specifiy counfouding factor"> + <conditional name="multiple"> + <param name="seconde" type="select" label="Do you want to correct a confounding factor?" help="If yes, specify the counfouding factor"> <option value="true">True</option> <option value="false" selected="true">False</option> </param> - <when value="false"/> + <when value="false"/> <when value="true"> <param name="var2" type="text" label="Variable 2" help="Confounding factor. Ex: Gender, etc."> <expand macro="sanitizer_validator"/> @@ -41,13 +62,24 @@ </conditional> </inputs> <outputs> - <data format="rdata" name="dds" label="${tool.name}: dds.Rdata" from_work_dir="DESeq2_preprocess.Rdata"/> + <data format="rdata" name="dds_asv" label="${tool.name}: asv_dds.Rdata" from_work_dir="asv_dds.Rdata"> + <filter> analysis_type['analysis'] == 'ASV'</filter> + </data> + <data format="rdata" name="dds_function" label="${tool.name}: function_dds.Rdata" from_work_dir="function_dds.Rdata"> + <filter> analysis_type['analysis'] == 'FUNCTION'</filter> + </data> + <data format="rdata" name="phyloseq" label="${tool.name}: function_data.Rdata" from_work_dir="function_data.Rdata"> + <filter> analysis_type['analysis'] == 'FUNCTION'</filter> + </data> </outputs> <tests> <test> - <param name="data" value="references/16-phylo_import.Rdata" /> <param name="var1" value="EnvType"/> - <output name="dds" file="references/23-deseq2_preprocess.Rdata" compare="sim_size" delta="50"/> + <conditional name="analysis_type"> + <param name="analysis" value="ASV"/> + <param name="data" value="references/16-phylo_import.Rdata" /> + </conditional> + <output name="dds_asv" file="references/23-deseq2_preprocess.Rdata" compare="sim_size" delta="50"/> </test> </tests> <help> @@ -68,34 +100,48 @@ Input -**phyloseq object** (format rdata): -A phyloseq object stored in a rdata file. -This file is the result of FROGSSTAT Phyloseq Import Data. +Two cases : + +-1. for **ASV**: A **phyloseq object** stored in a Rdata file. This file is the result of FROGSSTAT Phyloseq Import Data. We need unnormalised data to analyse the abundance differencies. .. class:: warningmark We need unnormalised data to analyse the abundance differencies. + +-2. For **FUNCTION**: two files: + - the files that contains predicted **function abundances**, it is named frogsfunc_functions_unstrat.tsv and produced by FROGSFUNC_2_function tool. + - the file that must contain the **metadata** that characterise each sample i.e. the conditions of experiment with sample ID in the first column as: + + .. image:: FROGS_Phyloseq_samplefile.png + :height: 115 + :width: 369 + + .. class:: h3 Ouput -**dds object** (format rdata): -A DESeq2 dataset (dds) stored in rdata file. -This result will be one of the input of the FROGSSTAT DESeq Visualisation tool. +Two cases : + +1. For **ASV**: a **dds.object** that is a DESeq2 dataset (dds) stored in Rdata file. This result will be one of the input of the FROGSSTAT DESeq Visualisation tool. +2. For **FUNCTION**: + - a **dds.object** that is a DESeq2 dataset (dds) stored in Rdata file. This result will be one of the input of the FROGSSTAT DESeq Visualisation tool. + - a **abundance.Rdata** taht contains information of data in one phyloseq object. + .. class:: infomark page-header h2 How it works ? -The DESeq function performs a default analysis through the steps: +The DESeq2 function performs a default analysis through the steps: - 1. estimation of size factors: ‘estimateSizeFactors’ + 1. estimation of size factors: ‘estimateSizeFactors’ - 2. estimation of dispersion: ‘estimateDispersions’ + 2. estimation of dispersion: ‘estimateDispersions’ - 3. Negative Binomial GLM fitting and Wald statistics: - ‘nbinomWaldTest’ + 3. Negative Binomial GLM fitting and Wald statistics: + ‘nbinomWaldTest’ You must precise at least on variable on which the differential abundances will be compared. |
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| diff -r 37e6f0c959bb -r b2967b704d6b deseq2_visualisation.xml --- a/deseq2_visualisation.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/deseq2_visualisation.xml Tue May 23 07:59:04 2023 +0000 |
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| @@ -1,5 +1,5 @@ -<tool id="FROGSSTAT_DESeq2_Visualisation" name="FROGSTAT Deseq2 Visualisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>to extract and visualise differentially abundant OTUs</description> +<tool id="FROGSSTAT_DESeq2_Visualisation" name="FROGSSTAT DESeq2 Visualisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> + <description>to extract and visualise differentially abundant ASVs or functions </description> <macros> <import>macros.xml</import> </macros> @@ -9,24 +9,33 @@ </expand> <command detect_errors="exit_code"> deseq2_visualisation.py - --phyloseqData '$phyloseqData' + --analysis '$analysis' + --abundanceData '$abundanceData' --dds '$dds' --var '$var' #if $varType.vartType_selected == "qual": --mod1 '$varType.mod1' --mod2 '$varType.mod2' #end if + #if $analysis == "FUNCTION": + --ipath-over '$over' + --ipath-under '$under' + #end if --padj $padj --html '$html' </command> <inputs> <!-- Files --> - <param format="rdata" argument="--phyloseqData" type="data" label="Phyloseq object (format: RData)" help="This is the result of FROGS Phyloseq Import Data, used in FROGSSTAT DESeq2 Preprocess tool" /> - <param format="rdata" argument="--dds" type="data" label="DESeq2 object (format: RData)" help="This is the result of FROGSSTAT DESeq2 Preprocess tool"/> + <param name="analysis" type="select" label="Type of analysis" help="Type of data to perform the differential analysis. ASV: DESeq2 is run on the ASV abundance table. FUNCTION: DESeq2 is run on predicted function abundance table from FROGSFUNC_2_function tool." display='radio'> + <option value="ASV" selected="true">ASV</option> + <option value="FUNCTION">FUNCTION</option> + </param> + <param format="rdata" argument="--abundanceData" type="data" label="Data object (format: data.RData)" help="For ASV: asv_data.Rdata from FROGSSTAT_Phyloseq_Import_Data tool - For FUNCTION: function_data.Rdata from FROGSSTAT_DESeq2_Preprocess tool." /> + <param format="rdata" argument="--dds" type="data" label="DESeq2 object (format: dds.RData)" help="This is the result of FROGSSTAT_DESeq2_Preprocess tool asv_dds.Rdata or function_dds.Rdata"/> <!-- Parameters --> - <param argument="var" type="text" value="" label="Experimental variable" help="The suspected factor to have an effect on OTU abundances (one of the variables used in FROGS DESeq2 Preprocess tool). Ex : Treatment"/> + <param argument="var" type="text" value="" label="Experimental variable" help="The factor that could have an effect on ASV/FUNCTION abundances. Ex : Treatment"/> <conditional name="varType"> - <param type="select" name="vartType_selected" label="Is your variable quantitative or qualitative?" help="If qualitative, choose 2 conditions to compare"> + <param type="select" name="vartType_selected" label="The experimental variable is it quantitative or qualitative?" help="If qualitative, choose 2 conditions to compare"> <option value="qual">Qualitative</option> <option value="quant">Quantitative</option> </param> @@ -40,14 +49,20 @@ </when> <when value="quant"/> </conditional> - <param argument="--padj" type="float" value="0.05" label="Adjusted p-value threshold" help="Threshold used for statistical significance of the differentially abundant OTU analysis"/> + <param argument="--padj" type="float" value="0.05" label="Adjusted p-value threshold" help="Threshold used for statistical significance of the differentially abundant ASV/FUNCTION analysis"/> </inputs> <outputs> <data format="html" name="html" label="${tool.name}: report.nb.html" from_work_dir="report.nb.html"/> + <data format="tsv" name="over" label="${tool.name}: ipath_over.tsv" from_work_dir="ipath_over.tsv"> + <filter>analysis == "FUNCTION"</filter> + </data> + <data format="tsv" name="under" label="${tool.name}: ipath_under.tsv" from_work_dir="ipath_under.tsv"> + <filter>analysis == "FUNCTION"</filter> + </data> </outputs> <tests> <test> - <param name="phyloseqData" value="references/16-phylo_import.Rdata"/> + <param name="abundanceData" value="references/16-phylo_import.Rdata"/> <param name="dds" value="references/23-deseq2_preprocess.Rdata"/> <param name="var" value="EnvType" /> <conditional name="varType"> @@ -90,27 +105,36 @@ Input -**phyloseq object** (format rdata): -One phyloseq object stored in a rdata file. -This file is the result of FROGSSTAT Phyloseq Import Data. +**-Data object-** (format data.Rdata): +One *phyloseq* object stored in a Rdata file. +This file is the result of : -**dds object** (format rdata): -A DESeq2 dataset (dds) stored in rdata file. -This file is the result of FROGSSTAT DESeq2 preprocess. + 1. for **ASV**: asv.dds.Rdata from FROGSSTAT_Phyloseq_Import_Data tool + 2. for **FUNCTION**: DESeq2_preprocess_tool output for FUNCTION parameter. + +**-DESeq2 object-** (format dds.Rdata): +A DESeq2 dataset (dds) stored in Rdata file. +This file is the result of FROGSSTAT_DESeq2_preprocess tool. .. class:: h3 Ouput -**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): visualisation of "Differential Abundance". +**-2 TSV files-** +- ipath_under.tsv +- ipath_over.tsv +To visualise and explore metabolic pathways with `IPATH3 website <https://pathways.embl.de/>`_ , use the two files **ipath_under.tsv** and **ipath_over.tsv** as inputs. + + +**-html file-** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): visualisation of *Differential Abundance* of ASV or FUNCTIONS depending on the case. The html file contains Table, Pie Chart, MA plot, Volcano plot and Heatmap plot. If the experimental variable is qualitative, only samples corresponding to the 2 compared conditions are shown in the Heatmap. Otherwise, samples are sorted in increasing order of the experimental variable. -* Table containing the differentially abundant OTUs. +* Table containing the differentially abundant ASVs. .. image:: FROGS_DESeq2_html_table.png - :height: 216 - :width: 789 + :height: 448 + :width: 641 * Pie Chart, MA plot and Volcano plot @@ -126,17 +150,23 @@ :height: 506 :width: 633 -* Heatmap plot corresponding to the differentially abundant OTUs. +* Heatmap plot corresponding to the differentially abundant ASVs. .. image:: FROGS_DESeq2_html_heatmap_plot.png :height: 576 :width: 768 +* Differentially abundant functions visualized with iPath 3 (FUNCTION analysis only). + + .. image:: FROGS_DESeq2_html_ipath.png + :height: 720 + :width: 584 + .. class:: infomark page-header h2 How it works ? -Based on the variable you precise to construct the model in FROGSSTAT DESeq2 Preprocess, this tool will construct table and graphs to visualise differentially abundant OTU between condition of the selected variables. +Based on the variable you precise to construct the model in FROGSSTAT DESeq2 Preprocess, this tool will construct table and graphs to visualise differentially abundant ASV or functions between condition of the selected variables. You may first precise the variable used to construct the model during the FROGSSTAT DESeq Preprocess step. If you precised variable with a confounding factor (a second variable), you may choose between one of the variables, but remember that you will see the result of this variable corrected by the confounding factor (and reversely) not just the selected variable itself. |
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| diff -r 37e6f0c959bb -r b2967b704d6b frogsfunc_copynumbers.xml --- a/frogsfunc_copynumbers.xml Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,181 +0,0 @@\n-<?xml version="1.0"?>\n-<!--\n-# Copyright (C) 2022 INRAE\n-#\n-# This program is free software: you can redistribute it and/or modify\n-# it under the terms of the GNU General Public License as published by\n-# the Free Software Foundation, either version 3 of the License, or\n-# (at your option) any later version.\n-#\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n-# GNU General Public License for more details.\n-#\n-# You should have received a copy of the GNU General Public License\n-# along with this program. If not, see <http://www.gnu.org/licenses/>.\n--->\n-<tool id="FROGSFUNC_step2_copynumbers" name="FROGSFUNC_step2_copynumbers" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n-\t<description>Predicts number of marker and function copy number in each OTU. </description>\n-\n-\t<macros>\n- <import>macros.xml</import>\n- </macros>\n- \n- <expand macro="requirements_frogsfunc" />\n- \n- <stdio>\n- <exit_code range="1:" />\n- <exit_code range=":-1" />\n- </stdio>\n- <command >\n-\t frogsfunc_copynumbers.py\n- --input-biom $input_biom\n-\t \t\t--tree $input_tree\n-\t \t\t#if $category.value == "16S"\n-\t \t\t\t--in-trait $function.fields.name\n-\t \t\t#end if\n-\t \t\t--hsp-method $hsp_method\n-\t \t\t--output-marker $out_marker\n-\t \t\t--output-function $out_function\n-\t \t\t#if $category.value != "16S"\n-\t \t\t--observed-marker-table $function.fields.path\n-\t \t\t--observed-trait-table $function.fields.traits\n-\t \t\t#end if\n- --html $summary_file\n-\t</command> \n-\t<inputs>\n-\t <!-- Input files -->\n- <param argument="--input-biom" format="biom1" name="input_biom" type="data" label="Biom file" help="The abundance file to analyse i.e. FROGSFUNC_step1_placeseqs tool output file (frogsfunc_placeseqs.biom)." optional="false"/>\n-\t <param argument="--tree" format="nhx" name="input_tree" type="data" label="Tree file" help="The file contains the tree information from FROGSFUNC_step1_placeseqs tool (frogsfunc_placeseqs_tree.nwk)." optional="false"/>\n-\t \t<!-- Parameters-->\n-\t <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio">\n- <options from_data_table="frogs_picrust2_marker_table">\n- <column name=\'name\' index=\'0\' />\n- <column name=\'value\' index=\'0\' />\n- <filter type="unique_value" column=\'0\'/>\n- <validator type="no_options" message="A built-in database is not available" />\n- </options>\n-\t\t</param>\n-\n-\t\t<param name="function" type="select" label="Function table" multiple="true" optional="false" help=" 16S : at least \'EC\' or/and \'KO\' should be chosen (EC for Metacyc pathway analysis or/and KO for KEGG pathway analysis) - others values are optionnal. ITS and 18S : \'EC\' only available." >\n-\t\t\t<options from_data_table="frogs_picrust2_marker_table">\n-\t\t\t\t<column name=\'name\' index=\'1\' />\n-\t\t\t\t<column name=\'value\' index=\'1\' />\n-\t\t\t\t<column name=\'path\' index=\'2\' />\n-\t\t\t\t<column name=\'traits\' index=\'3\' />\n- <filter type="param_value" ref="category" column="0" /> \n- \t\t<validator type="expression" message="\'EC\' is the default database used by PICRUSt2. \'EC\' or \'KO\' must be at least selected. Other tables are optionnal">"EC" in value or "KO" in value</validator> \n- </options>\n- </param>\n-\t\t<param argument="--hsp-method" name="hsp_method" type="select" label="HSP method" help=\'Hidden-state prediction method to use: maximum parsimony (mp), empirical probabilities (emp_prob), continuous traits prediction using subtree averaging (subtree_average), continuous traits prediction with phylogentic independent contrast (pic), continuous traits reconstruction using squared-change parsimony (scp) (default: mp).\' multiple="false" display="ra'..b'output name="out_function" file="references/26-frogsfunc_copynumbers_predicted_functions.tsv" compare="diff" lines_diff="0" />\n-\t\t\t<output name="out_marker" file="references/26-frogsfunc_copynumbers_marker.tsv" compare="diff" lines_diff="0" />\n- <output name="summary_file" file="references/26-frogsfunc_copynumbers_report.html" compare="diff" lines_diff="0" />\n-\t\t</test>\n-\t</tests>\n-\n- <help>\n-\n-@HELP_LOGO@\n-\n-.. class:: infomark page-header h2\n-\n-What it does\n-\n-Prediction of functional abundances (and marker copy number) based solely on the sequences of marker genes with `PICRUSt2 <https://github.com/picrust/picrust2>`_. The available marker genes are 16S, ITS and 18S.\n-\n-FROGSFUNC_step2_copynumber is the second step of PICRUSt2. It runs hidden-state prediction (hsp) to predict function abundances with `castor-R <https://cran.r-project.org/web/packages/castor/index.html>`_ of each OTUs placed in the PICRUSt2 reference phylogenetic tree (FROGSFUNC_step1_placeseqs outputs). \n-\n-\n-.. class:: infomark page-header h2\n-\n-Inputs/Outputs\n-\n-.. class:: h3\n-\n-Inputs\n-\n-**Tree file** (format newick `nwk <https://en.wikipedia.org/wiki/Newick_format>`_):\n-\n- The file contains the tree informations from FROGSFUNC_step1_placeseqs (FROGSFUNC_step1_placeseqs output : frogsfunc_placeseqs_tree.nwk) \n-\n-\n-**OTUs biom file**:\n-\n- The abundance file to analyse i.e. FROGSFUNC_step1_placeseqs tool output file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). (frogsfunc_placeseqs.biom)\n-\n-\n-**Function table choice**:\n-\n-Which default pre-calculated count table to use ?\n-- For 16S rRNA gene you can choose between: \'EC\', \'KO\', \'PFAM\', \'COG\', \'TIGRFAM\', and/or \'PHENO\'. You must select at least \'EC\' or \'KO\' because for next FROGSFUNC tools, the information from Metacyc (EC) or KEGG (KO) are requiered.\n-- For ITS and 18S markers, \'EC\' is only available.\n-\n-For more informations about the different databases:\n-\n- - EC : https://enzyme.expasy.org/\n- - KO : https://www.genome.jp/kegg/ko.html\n- - PFAM : http://pfam.xfam.org/\n- - COG : https://www.ncbi.nlm.nih.gov/research/cog-project/\n- - TIGRFAM : https://tigrfams.jcvi.org/cgi-bin/index.cgi\n- - PHENO : https://phenodb.org/\n-\t \n-.. class:: h3\n-\n-Outputs\n-\n-**Copy number marker file**:\n-\n-.. image:: FROGS_frogsfunc_copynumbers_marker.png\n-\n-Output table of predicted marker gene copy numbers per sequence. (frogsfunc_copynumbers_marker.tsv)\n-\n-Marker gene copy number prediction is used to normalize the counting matrices of metabolic functions. For example, if the OTU has two 16S copies, the abundance of metabolic function for this OTU will be divided by 2.\n-\n-\n-**Predicted function file**:\n-\n-.. image:: FROGS_frogsfunc_copynumbers_function.png\n-\n-Output table with predicted function abundances per sequence. (frogsfunc_copynumbers_predicted_functions.tsv)\n-\n-**Report file**:\n-\n-.. image:: FROGS_frogsfunc_copynumbers_nsti.png\n- :height: 350\n- :width: 639\n-\n-Nearest Sequenced Taxon Index (NSTI) is the phylogenetic distance between the OTU and the nearest sequenced reference genome. This metric can be used to identify OTUs that are highly distant from all reference sequences but the predictions for these sequences are less reliable. The higher the NSTI score, the less the affiliations are relevant. Any OTUs with a NSTI value higher than 2 are typically either from uncharacterized phyla or off-target sequences.\n-\n-The graph shows the number of kept OTUs and sequences according to the NSTI threshold. It is a decision support graphic to help choosing the NSTI threshold. This NSTI threshold will be asked to set in the next tool FROGSFUNC_step3_functions. A good practice is to choose a NSTI threshold that retains a good number of sequences and as low as possible i.e. while ensuring that the taxonomies derived from FROGS and PICRUSt2 do not diverge too much.\n-\n-@HELP_CONTACT@\n-\n-\t</help>\n-\n-\n-\t<expand macro="citations" />\n-\t\n-</tool>\n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b frogsfunc_functions.xml --- a/frogsfunc_functions.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/frogsfunc_functions.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -15,14 +15,15 @@\n # You should have received a copy of the GNU General Public License\n # along with this program. If not, see <http://www.gnu.org/licenses/>.\n -->\n-<tool id="FROGSFUNC_step3_functions" name="FROGSFUNC_step3_functions" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n- <description>Calculates functions abundances in each sample.</description>\n+<tool id="FROGSFUNC_step3_functions" name="FROGSFUNC_2_functions" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+ <description>Calculates functions abundances in each sample. </description>\n \n- <macros>\n+ <macros>\n <import>macros.xml</import>\n- </macros>\n+ </macros>\n \n- <expand macro="requirements_frogsfunc" />\n+ <expand macro="requirements_frogsfunc" />\n+\n \n <stdio>\n <exit_code range="1:" />\n@@ -30,49 +31,130 @@\n </stdio>\n <command >\n frogsfunc_functions.py\n+ @CPUS@\n --input-biom $input_biom\n- --function $function\n- --marker $marker\n+ --input-fasta $input_fasta\n+ --input-tree $input_tree\n+ --input-marker $input_marker\n+ --marker-type $category.value\n+ #if $category.value == "16S"\n+ --functions $functions\n+ #end if\n+ #if $category.value != "16S"\n+ --input-function-table $functions.fields.traits\n+ #end if \n --max-nsti $max_nsti\n- --function-abund $function_abund\n- --seqtab $seqtab\n- --weighted $weighted\n- --excluded $excluded\n- --html $summary_file\n+ --min-blast-ident $min_blast_ident\n+ --min-blast-cov $min_blast_cov\n+\t \t\t--hsp-method $hsp_method\n+ --output-biom $output_biom\n+ --output-fasta $output_fasta\n+ --output-function-abund "frogsfunc_functions_unstrat.tsv"\n+ --output-otu-norm $output_otu_norm\n+ --output-weighted $output_weighted\n+ --output-excluded $output_excluded\n+ --summary $summary_file\n+\n </command> \n <inputs>\n <!-- Input files -->\n- <param argument="--input-biom" format="biom1" name="input_biom" type="data" label="Biom file" help="The abundance file i.e. FROGSFUNC_step1_placeseqs tool output file (frogsfunc_placeseqs.biom)." optional="false"/>\n- <param argument=\'--function\' format="tsv" type="data" label="Function file" help="Copy number table of functions present in the predicted genome for each OTU i.e. FROGSFUNC_step2_copynumbers tool output file (frogsfunc_copynumbers_predicted_functions.tsv)." optional="false"/>\n- <param argument=\'--marker\' format="tsv" type="data" label="Marker file" help="Table of predicted marker copy number i.e. FROGSFUNC_step2_copynumbers output (frogsfunc_copynumbers_marker.tsv)." optional="false"/>\n+ <param argument="--input-biom" format="biom1" type="data" label="Biom file" help="The abundance file i.e. FROGSFUNC_1_placeseqs_copynumber tool output file (frogsfunc_placeseqs.biom)." optional="false"/>\n+ \t<param argument="--input-fasta" format="fasta" type="data" label="Sequence file" help="The fasta file i.e. from FROGSFUNC_1_placeseqs_copynumber tool output file (frogsfunc_placeseqs.fasta)." optional="false"/>\n+ <param argument="--input-tree" format="nhx" type="data" label="Tree file" help="The file contains the tree information from FROGSFUNC_1_placeseqs_copynumber tool (frogsfunc_placeseqs_tree.nwk)." optional="false"/>\n+ <param argument="--input-marker" format="tsv" type="data" label="Marker file" help="Table of predicted marker copy number i.e. FROGSFUNC_1_placeseqs_copynumber output (frogsfunc_marker.tsv)." optional="false"/>\n \n <!-- Parameters-->\n- <param argument="--max-nsti" name="max_nsti" type="float" label="NSTI cut-off" help="Any sequence with an NSTI above this threshold will be out. (default: 2)" value="2" min="0" optional="false" /> \n+\t <para'..b'and 1).\n+\n+**-HSP method-**:\n+\n+ Hidden-state prediction method to use.\n+\n \n-\n .. class:: h3\n \n Outputs\n \n-**Report file**: (report.html)\n+**-Fasta file-**:\n+\n+ Sequence file without excluded ASVs (NSTI, blast perc identity or blast perc coverage thresholds). (FROGSFUNC_2_functions.fasta)\n+\n+**-ASV abundance Biom file-**:\n+\n+ ASV abundance data i a biom file without excluded ASVs (NSTI, %identity or %coverage thresholds alignment). (FROGSFUNC_2_functions.biom)\n+\n+**-Function abundance file-**:\n+ \n+ It is the function abundance predictions of metagenome, per sample. (frogsfunc_functions_unstrat_DATABASENAME.tsv, for exemple: FROGSFUNC_2_functions_unstrat_EC.tsv)\n+ \n+Table column description:\n+ - classification: the hierarchy classification of the gene function. \n+ - db_link: the url on the link accession ID (*observation_name*) of the function. \n+ - observation_name: Accession identifier\n+ - observation_sum: Total abundance of functions across all samples.\n+ - last columns: Abundances of these functions in each samples.\n+\n+**-ASV normalized abundance table-**:\n+\n+ Table with normalized abundances per marker copy number from FROGSFUNC_1 step. (FROGSFUNC_2_functions_marker_norm.tsv)\n+\n+**-Weighted NSTI file-**:\n+\n+ Output file with the mean of NSTI value per sample. (FROGSFUNC_2_functions_weighted_nsti.tsv)\n+\n+**-Excluded sequences file-**:\n+ \n+Information about removed sequences that have a NSTI value aboved the NSTI threshold chosen in this step:\n+ - ASV: ASV name id.\n+ - FROGS_taxonomy\n+ - PICRUSt2_taxonomy\n+ - exclusion_paramater: The paramater(s) that excluded the ASVs.\n+ - value_parameter: The values associated with the paramater(s).\n+\n+**-Copy number marker file - one per chosen target function database (EC, KO, PFAM, COG, TIGRFAM,PHENO)-**:\n+\n+Output table of predicted function copy numbers per ASV. There are as many tables as chosen target function database (EC, KO, PFAM, COG, TIGRFAM,PHENO) (exemple : FROGSFUNC_step3_functions: EC_copynumbers_predicted.tsv and FROGSFUNC_step3_functions: PHENO_copynumbers_predicted.tsv )\n+\n+**-Report file-**: (report.html)\n \n .. image:: FROGS_frogsfunc_functions_piechart.png\n- :height: 500\n- :width: 1352\n+ :height: 375\n+ :width: 1014\n+\n+ASVs are excluded if the associated NSTI is above the threshold, or if the alignment values are below the thresholds.\n+\n \n-OTUs are out if the NSTI associated is above the threshold.\n+.. image:: FROGS_frogsfunc_functions_starplot.png\n+ :height: 466\n+ :width: 806\n+\n+Number of different taxonomic ranks before (green) and after (orange) application of the filters. \n+\n \n .. image:: FROGS_frogsfunc_functions_table.png\n :height: 580\n- :width: 1352\n+ :width: 1452\n \n \n .. image:: FROGS_frogsfunc_functions_sunburst.png\n \n \n-Gene families/function from KEGG or Metacyc databases are classified according to 3 hierarchy levels. The graph shows the proportion of each level within the selected samples.\n-\n-**Function abundance file**:\n- \n- It is the function abundance predictions of metagenome, per sample. (frogsfunc_functions_unstrat.tsv)\n- \n- - Classification column: the hierarchy classification of the gene function. \n- - db_link column: the url on the link accession ID (*observation_name*) of the function. \n- - observation_name: Accession identifier \n- - last columns: Abundances of these functions in each samples.\n-\n-**Excluded sequences**:\n-\n- Information (FROGS taxonomy, PICRUSt2 taxonomy, NSTI) about removed sequences that have a NSTI value aboved the NSTI threshold chosen in this step.\n-\n-**Normalized OTU abundance table**:\n-\n- Table with normalized abundance per marker copy number. (frogsfunc_functions_marker_norm.tsv)\n-\n-**Weighted NSTI file**:\n-\n- It is the table with average NSTI calculated per sample. (frogsfunc_functions_weighted_nsti.tsv)\n+Gene families/function from KEGG or Metacyc databases are classified according to 4 hierarchy levels. The graph shows the proportion of each level within the selected samples.\n \n \n \n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b frogsfunc_pathways.xml --- a/frogsfunc_pathways.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/frogsfunc_pathways.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -15,8 +15,8 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGSFUNC_step4_pathways" name="FROGSFUNC_step4_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>Calculates pathway abundances in each sample. </description> +<tool id="FROGSFUNC_step4_pathways" name="FROGSFUNC_3_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>Calculates pathway abundances in each sample. </description> <macros> <import>macros.xml</import> @@ -35,17 +35,11 @@ --normalisation #end if --map $map_file.value - - #if $category.value == "16S" - #if $map_file.fields.name == "Kegg" - --no-regroup - #end if - #end if - --html $summary_file + --summary $summary_file </command> <inputs> <!-- Input files --> - <param argument="--input-file" format="tsv" name="input_file" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table)." optional="false"/> + <param argument="--input-file" format="tsv" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_2_functions tool, FROGSFUNC_2_functions_unstrat_EC.tsv for Metacyc database or FROGSFUNC_2_functions_unstrat_KO.tsv for Kegg database (unstratified table)." optional="false"/> <!-- References --> <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio"> @@ -56,7 +50,7 @@ <validator type="no_options" message="A built-in database is not available" /> </options> </param> - <param name="map_file" type='select' label="Pathway reference" help="For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_step2_copynumbers tool. For ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'> + <param name="map_file" type='select' label="Pathway reference" help="For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_1_placeseqs_copynumbers tool. For ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'> <options from_data_table="frogs_picrust2_pathway_map"> <column name='name' index='1'/> <column name='value' index='3'/> @@ -70,7 +64,7 @@ </inputs> <outputs> <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/> - <data format="tsv" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/> + <data format="tsv" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/> </outputs> <tests> @@ -91,10 +85,10 @@ What it does -FROGSFUNC_step4_pathway is the last step of `PICRUSt2 <https://github.com/picrust/picrust2>`_. This script infers MetaCyc/KEGG pathway abundances based on EC/KO number abundances. +**FROGSFUNC_3_pathways** is the last step of `PICRUSt2 <https://github.com/picrust/picrust2>`_. This script infers MetaCyc/KEGG pathway abundances based on **EC** or **KO** number abundances. - - Regroups EC/KO numbers to MetaCyc/KEGG reactions. - - Infers which MetaCyc/KEGG pathways are present based on these reactions with `MinPath <http://omics.informatics.indiana.edu/MinPath/>`_. + - Regroups EC or KO numbers to MetaCyc or KEGG reactions, depending of the unstrat abundances input file. + - Infers which MetaCyc or KEGG pathways are present based on these reactions with `MinPath <http://omics.informatics.indiana.edu/MinPath/>`_. - Calculates and returns the abundance of pathways identified as present. .. class:: infomark page-header h2 @@ -105,23 +99,23 @@ Input -**Function prediction abundance file**: +**-Function prediction abundance file (EC or KO)-**: - TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table). + TSV function abundances table from FROGSFUNC_2_functions tool, frogsfunc_functions_unstrat_EC.tsv or frogsfunc_functions_unstrat_KO.tsv (unstratified table). -**Taxonomic marker:** +**-Taxonomic marker-**: - Output table of predicted marker gene copy numbers per sequence from FROGSFUNC_step2_copynumbers tool. (frogsfunc_copynumbers_marker.tsv) + Output table of predicted marker gene copy numbers per sequence from FROGSFUNC_1_placeseqs tool. (frogsfunc_marker.tsv) -**Pathway reference:** +**-Pathway reference-**: Mapping of pathways to reactions. - - For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_step2_copynumbers tool. If you want both, run this tool twice. + - For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_2_functions tool. If you want both, run this tool twice. - For ITS or 18S marker, Metacyc is the only valid option. -**Do you want to normalize the final output table ?**: +**-Do you want to normalize the final output table ?-**: If this option is set, the pathway abundances file (frogsfunc_functions_unstrat.tsv) is normalized: values are divided by sum of columns, then multiplied by 10^6 (Count Per Million values). @@ -133,16 +127,14 @@ Outputs -**HTML report**: +**-HTML report-**: The HTML file summarizes information about pathway abundances within each sample. .. image:: FROGS_frogsfunc_pathways_sunburst.png - - -**Pathways abundances tables - unstratified**: +**-Pathways abundances tables - unstratified-**: It is the pathways abundance predictions of metagenome, per sample. (frogsfunc_pathways_unstrat.tsv) |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b frogsfunc_placeseqs.xml --- a/frogsfunc_placeseqs.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/frogsfunc_placeseqs.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -15,16 +15,16 @@\n # You should have received a copy of the GNU General Public License\n # along with this program. If not, see <http://www.gnu.org/licenses/>.\n -->\n-<tool id="FROGSFUNC_step1_placeseqs" name="FROGSFUNC_step1_placeseqs" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n-\t<description>Places the OTUs into a reference phylogenetic tree.</description>\n+<tool id="FROGSFUNC_step1_placeseqs" name="FROGSFUNC_1_placeseqs_and_copynumbers" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+\t<description>Places ASVs into a reference phylogenetic tree. </description>\n \n- <macros>\n+ <macros>\n <import>macros.xml</import>\n- </macros>\n+ </macros>\n \n- <expand macro="requirements_frogsfunc">\n- <requirement type="package" version="3.1.2">ete3</requirement>\n- </expand>\n+ <expand macro="requirements_frogsfunc" >\n+\t<requirement type="package" version="4.5.2">dendropy</requirement>\n+ </expand>\n \n <stdio>\n <exit_code range="1:" />\n@@ -36,60 +36,69 @@\n \t \t\t--input-biom $input_biom\n \t \t\t--min-align $min_align\n \t \t\t--placement-tool $placement_tool\n-\t \t\t--out-tree $out_tree \n+\t \t\t--output-tree $output_tree \n \t \t\t--excluded $excluded\n-\t \t\t--insert-biom $insert_biom\n-\t \t\t--insert-fasta $insert_fasta\n+\t \t\t--output-biom $output_biom\n+\t \t\t--output-fasta $output_fasta\n \t \t\t--closests-ref $closests_ref\n-\t \t\t--html $summary_file\n+\t\t\t--output-marker $output_marker\n+\t \t\t--summary $summary_file\n \n \t \t\t#if $marker.name != "16S"\n \t \t\t--ref-dir ${marker.value}\n+\t\t\t--input-marker-table ${marker.fields.traits}\n \t \t\t#end if\n \t</command> \n \t<inputs>\n \t<!-- Input files -->\n-\t\t<param argument="--input-fasta" format="fasta" name="input_fasta" type="data" label="Sequence file" help="The sequence file to analyse (format: fasta)." optional="false"/>\n-\t\t<param argument="--input-biom" format="biom1" name="input_biom" type="data" label="Biom file" help="The abundance file to analyse (format: biom). Taxonomic affiliations must be inside (FROGS Affiliation OTU step)." optional="false"/>\n+\t\t<param argument="--input-fasta" format="fasta" type="data" label="Sequence file" help="The sequence file to analyse (format: fasta)." optional="false"/>\n+\t\t<param argument="--input-biom" format="biom1" type="data" label="Biom file" help="The abundance file to analyse (format: biom). Taxonomic affiliations must be inside (FROGS taxonomic_affiliation step)." optional="false"/>\n \n \t<!-- Parameters -->\n <param argument="--ref-dir" name="marker" type="select" label="Taxonomy marker" display="radio" help="Taxonomic marker of interest.">\n \t\t\t<options from_data_table="frogs_picrust2_default_dir">\n \t \t\t<column name="name" index="1"/>\n \t \t<column name="value" index="2"/>\n+\t\t\t\t<column name="traits" index="3"/>\n+ <filter type="unique_value" column=\'1\'/>\n \t\t\t\t\t<validator type="no_options" message="A built-in database is not available" />\n \t\t\t</options>\n \t\t</param>\n- <param argument="--placement-tool" name="placement_tool" type="select" label="Placement tool" help="Placement tool for insertion of sequences into the reference tree. SEPP is a low-memory alternative to EPA-ng for placing sequences." multiple="false" display="radio">\n- \t<option value="epa-ng">epa-ng</option>\n- \t<option value="sepp">sepp</option>\n+ <param argument="--placement-tool" type="select" label="Placement tool" help="Placement tool for insertion of sequences into the reference tree. SEPP is a low-memory alternative to EPA-ng for placing sequences, and is only available for 16S analysis." multiple="false" display="radio">\n+\t\t\t<options from_data_table="frogs_picrust2_default_dir"> \t\n+\t\t\t\t<column name=\'name\' index=\'4\' />\n+\t\t\t\t<column name=\'value\' index=\'4\' />\n+ <filter type="param_value" ref="marker" column="2" /> \n+\t\t\t</options>\n \t\t</param>\n-\t\t<param argument="--min-align" name="min_align" type="float" label="Minimum alignment length" help="Proportion of the to'..b'e the explanatory illustration at the bottom of this page).\n \n * **PICRUSt2 closest reference name** : Genome Name / Sample Name.\n \n-* **PICRUSt2 closest taxonomy** : Taxonomy (JGI) of the closest reference sequence from the OTU inserted in the reference tree under the following format: Kingdom;Phylum;Class;Order;Family;Genus;Species\n+* **PICRUSt2 closest taxonomy** : Taxonomy (JGI) of the closest reference sequence from the ASV inserted in the reference tree under the following format: Kingdom;Phylum;Class;Order;Family;Genus;Species\n \n-* **NSTI** : Nearest Sequenced Taxon Index (`NSTI <https://www.nature.com/articles/nbt.2676>`_) is the phylogenetic distance between the OTU and the nearest sequenced reference genome. This metric can be used to identify OTUs that are highly distant from all reference sequences (the predictions for these sequences are less reliable!). The higher the NSTI score, the less the affiliations are relevant. Any OTUs with a NSTI value higher than 2 are typically either from uncharacterized phyla or off-target sequences.\n+* **NSTI** : Nearest Sequenced Taxon Index (`NSTI <https://www.nature.com/articles/nbt.2676>`_) is the phylogenetic distance between the ASV and the nearest sequenced reference genome. This metric can be used to identify ASVs that are highly distant from all reference sequences (the predictions for these sequences are less reliable!). The higher the NSTI score, the less the affiliations are relevant. Any ASVs with a NSTI value higher than 2 are typically either from uncharacterized phyla or off-target sequences.\n \n * **NSTI confidence** : According to the NSTI score, we guide you in the confidence you can bring to the issue affiliation of PICRUSt2.\n \n * **Lowest same taxonomic rank between FROGS and PICRUSt2** : Comparison between FROGS and PICRUSt2 taxonomic affiliations. Lowest common taxonomic rank between FROGS and PICRUSt2 affiliations.\n \n-* **Comment** : " identical taxonomy " if the FROGS and PICRUSt2 taxonomic affiliations are identical. " identical sequence " if the OTU sequence is strictly the same as the reference sequence.\n+* **Comment** : " identical taxonomy " if the FROGS and PICRUSt2 taxonomic affiliations are identical. " identical sequence " if the ASV sequence is strictly the same as the reference sequence.\n \n .. image:: FROGS_frogsfunc_placeseqs_closest_explained.png\n+ :height: 269\n+ :width: 825\n+ \n+Closest reference sequence (from JGI database) from one ASV sequence.\n \n-Closest reference sequence (from JGI database) from one cluster sequence.\n+.. image:: FROGS_frogsfunc_placeseqs_nsti.png\n+ :height: 295\n+ :width: 778\n+\n+Nearest Sequenced Taxon Index (NSTI) is the phylogenetic distance between the ASV and the nearest sequenced reference genome. This metric can be used to identify ASVs that are highly distant from all reference sequences but the predictions for these sequences are less reliable. The higher the NSTI score, the less the affiliations are relevant. Any ASV with a NSTI value higher than 2 are typically either from uncharacterized phyla or off-target sequences.\n+\n+The graph shows the number of kept ASVs and sequences according to the NSTI threshold. It is a decision support graphic to help choose the NSTI threshold. This NSTI threshold will be asked to set in the next tool FROGSFUNC_2_functions. A good practice is to choose a NSTI threshold that retains a good number of sequences and as low as possible i.e. while ensuring that the taxonomies derived from FROGS and PICRUSt2 do not diverge too much.\n+\n+.. image:: FROGS_frogsfunc_placeseqs_blast.png\n+ :height: 295\n+ :width: 920\n+\n+The graph depicts the blast percentages of identity and coverage against the closest PICRUSt2 sequence (ordinate), against the NSTI score (abcsissa). Thus, the ASVs with the best predictions will be located at the top left of the graph.\n \n @HELP_CONTACT@\n \n </help>\n <expand macro="citations" />\n-</tool>\n\\ No newline at end of file\n+</tool>\n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b itsx.xml --- a/itsx.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/itsx.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGS_itsx" name="FROGS ITSx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Extract the highly variable ITS1 and ITS2 subregions from ITS sequences</description> + <description>Extract the highly variable ITS1 and ITS2 subregions from ITS sequences </description> <macros> <import>macros.xml</import> </macros> @@ -9,7 +9,6 @@ <command detect_errors="exit_code"> itsx.py @CPUS@ - --region '$region' --input-fasta '$input_fasta' --input-biom '$input_biom' --out-fasta '$out_fasta' @@ -17,17 +16,34 @@ --out-removed '$out_excluded' --summary '$summary_file' --organism-groups '$organism_groups' - $trim_sequence + + #if $trim_sequence.check_its_only == "yes" + --check-its-only + #else + --region $trim_sequence.region + #end if + </command> <inputs> <!-- Files --> <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="The sequence file to filter (format: FASTA)." /> <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)" /> - <param argument="--region" type="select" label="ITS region" help="Which fungal ITS region is targeted: either ITS1 or ITS2 ?"> - <option value="ITS1">ITS1</option> - <option value="ITS2">ITS2</option> - </param> - <param argument="--check-its-only" name="trim_sequence" type="boolean" checked="false" truevalue="" falsevalue="--check-its-only" label="Trim conserved sequence (SSU, 5.8S, LSU) ?" help="If Yes, only part of the sequences with ITS signature will be kept, SSU, LSU or 5.8S regions will be trimmed (default : No)" /> + + <conditional name="trim_sequence"> + <param argument="--check-its-only" type="select" label="Trim conserved sequence (SSU, 5.8S, LSU) ?" help="If Yes, only part of the sequences with ITS signature will be kept, SSU, LSU or 5.8S regions will be trimmed (default : No)" display="radio"> + <option value="yes" selected="true">No, keep conserved regions</option> + <option value="no" >Yes, trim conserved regions</option> + + </param> + <when value="yes"/> + <when value="no"> + <param argument="--region" type="select" label="ITS region" help="Which fungal ITS region is targeted: either ITS1 or ITS2 ?" display="radio"> + <option value="ITS1">ITS1</option> + <option value="ITS2">ITS2</option> + </param> + </when> + </conditional> + <param argument="--organism-groups" type="select" multiple="true" display="checkboxes" label="Choose pertinent organisms to scan:" help="Save a lot of time by checking pertinent organism group model to scan"> <option value="F" selected="true">Fungi</option> <option value="A">Alveolata</option> @@ -63,7 +79,9 @@ <param name="input_fasta" value="references/04-filters.fasta" /> <param name="input_biom" value="references/04-filters.biom" /> <param name="region" value="ITS1" /> - <param name="trim_sequence" value="true" /> + <conditional name="trim_sequence"> + <param name="check_its_only" value="yes"/> + </conditional> <output name="out_abundance_biom" file="references/05-itsx.biom" compare="sim_size" delta="0" /> <output name="out_fasta" file="references/05-itsx.fasta" compare="diff" lines_diff="0" /> <output name="out_excluded" file="references/05-itsx-excluded.fasta" compare="diff" lines_diff="0" /> |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b macros.xml --- a/macros.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/macros.xml Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">4.0.1</token> + <token name="@TOOL_VERSION@">4.1.0</token> <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> @@ -23,7 +23,8 @@ <xml name="requirements_frogsfunc"> <expand macro="requirements"> - <requirement type="package" version="2.4.1">picrust2</requirement> + <requirement type="package" version="2.5.1">picrust2</requirement> + <requirement type="package" version="3.1.2">ete3</requirement> <yield /> </expand> </xml> @@ -39,10 +40,12 @@ <validator type="regex">[A-Za-z ]+</validator> </param> </xml> + <xml name="sanitizer_validator"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="+" /> + <add value="*" /> <add value="-" /> <add value="=" /> <add value=" " /> @@ -51,7 +54,7 @@ <add value="." /> </valid> </sanitizer> - <validator type="regex">[A-Za-z0-9 =-_+,.]+</validator> + <validator type="regex">[A-Za-z0-9+*-= _,.]+</validator> </xml> <token name="@HELP_LOGO@"> @@ -87,7 +90,7 @@ pages = {1287-1294}, year = {2018}, month = {04}, - abstract = "{Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own.This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr.Supplementary data are available at Bioinformatics online.}", + abstract = "{Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own.This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of ASVs and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of ASVs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr.Supplementary data are available at Bioinformatics online.}", issn = {1367-4803}, doi = {10.1093/bioinformatics/btx791}, url = {https://doi.org/10.1093/bioinformatics/btx791}, |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b normalisation.xml --- a/normalisation.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/normalisation.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -16,7 +16,7 @@ # along with this program. If not, see <http://www.gnu.org/licenses/>. --> <tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>Normalise OTU abundance.</description> + <description>Normalise ASV abundance. </description> <macros> <import>macros.xml</import> @@ -36,8 +36,8 @@ #if $sampling_method.sampling_by_min == "yes" --sampling-by-min #else - --num-reads $sampling_method.num_reads - #if $sampling_method.delete_samples + --num-reads '$sampling_method.num_reads' + #if $sampling_method.delete_samples == "true" --delete-samples #end if #end if @@ -46,16 +46,20 @@ --summary-file '$summary_file' </command> <inputs> - <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." /> - <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." /> + <param format="fasta" argument="--input-fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." /> + <param format="biom1" argument="--input-biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." /> <conditional name="sampling_method"> - <param name="sampling_by_min" type="select" label="Sampling method" help='Sampling by the number of sequences of the smallest sample, or select a number manually' display='radio'> + <param argument="--sampling-by-min" type="select" label="Sampling method" help="Sampling by the number of sequences of the smallest sample, or select a number manually" display="radio"> <option value="yes" selected="true">Sampling by the number of sequences of the smallest sample</option> <option value="no">Select a number of sequences</option> </param> + <when value="yes"/> <when value="no"> - <param name="num_reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." /> - <param name="delete_samples" type="boolean" label="Remove samples that have an initial number of reads below the number of reads to sample ?" /> + <param argument="--num-reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." /> + <param argument="--delete-samples" type="select" label="Remove samples that have an initial number of reads below the number of reads to sample ?" display="radio"> + <option value="false">No, subsampling threshold need to at most equal to the smallest sample</option> + <option value="true">Yes, subsampling threshold may be greater than the smallest sample</option> + </param> </when> </conditional> </inputs> @@ -101,7 +105,7 @@ **Abundance file**: -The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_). +The abundance of each ASV in each sample (format `BIOM <http://biom-format.org/>`_). **Sampling method**: |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b otu_filters.xml --- a/otu_filters.xml Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,297 +0,0 @@\n-<?xml version="1.0"?>\n-<!--\n-# Copyright (C) 2015 INRA\n-#\n-# This program is free software: you can redistribute it and/or modify\n-# it under the terms of the GNU General Public License as published by\n-# the Free Software Foundation, either version 3 of the License, or\n-# (at your option) any later version.\n-#\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n-# GNU General Public License for more details.\n-#\n-# You should have received a copy of the GNU General Public License\n-# along with this program. If not, see <http://www.gnu.org/licenses/>.\n--->\n-<tool id="FROGS_OTU_filters" name="FROGS OTU Filters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n-\t<description>Filters OTUs on several criteria.</description>\n-\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n-\n- <expand macro="requirements">\n- <requirement type="package" version="2.10">blast</requirement>\n- </expand>\n-\n- <stdio>\n- <exit_code range="1:" />\n- <exit_code range=":-1" />\n- </stdio>\n-\n-\t<command>\n-\n-\t\t\totu_filters.py\n-\t\t\t--nb-cpus \\${GALAXY_SLOTS:-1}\n-\t\t\t--input-biom \'$input_biom\'\n-\t\t\t--input-fasta \'$input_fasta\'\n-\t\t\t--output-fasta \'$output_fasta\'\n-\t\t\t--output-biom \'$output_biom\'\n-\t\t\t--excluded \'$output_excluded\'\n-\t\t\t--summary \'$output_summary\'\n-\n-\t\t\t#if $choice_prevalence_method.prevalence_method == "all"\n-\t\t\t\t#if $choice_prevalence_method.min_sample_presence\n-\t\t\t\t\t--min-sample-presence $choice_prevalence_method.min_sample_presence\n-\t\t\t\t#end if\n-\t\t\t#else if $choice_prevalence_method.prevalence_method == "replicate"\n-\t\t\t\t#if $choice_prevalence_method.min_replicate_presence\n-\t\t\t\t\t--min-replicate-presence $choice_prevalence_method.min_replicate_presence\n-\t\t\t\t\t--replicate_file $choice_prevalence_method.replicate_file\n-\t\t\t\t#end if\n-\t\t\t#end if\n-\n-\t\t\t#if $choice_abundance_unit.abundance_unit_type == "count"\n-\t\t\t\t#if $choice_abundance_unit.min_abundance_count\n-\t\t\t\t\t--min-abundance $choice_abundance_unit.min_abundance_count\n-\t\t\t\t#end if\n-\t\t\t#end if\n-\n-\t\t\t#if $choice_abundance_unit.abundance_unit_type == "proportion"\n-\t\t\t\t#if $choice_abundance_unit.min_abundance_proportion\n-\t\t\t\t\t--min-abundance $choice_abundance_unit.min_abundance_proportion\n-\t\t\t\t#end if\n-\t\t\t#end if\n-\n-\t\t\t#if $nb_biggest_otu\n-\t\t\t\t--nb-biggest-otu $nb_biggest_otu\n-\t\t\t#end if\n-\n-\n-\t\t\t#if $contaminantSource.which_contaminantSource == "history"\n-\t\t\t\t##build index on the fly\n-\t\t\t\t--contaminant \'${contaminantSource.ownContaminantFile}\'\n-\t\t\t#else if $contaminantSource.which_contaminantSource == "server"\n-\t\t\t\t##use precomputed indexes\n-\t\t\t\t--contaminant \'${contaminantSource.contaminants_db.fields.path}\'\n-\t\t\t#end if\n-\n-\t</command>\n-\t<inputs>\n-\t\t<!-- Files -->\n-\t\t<param format="fasta" name="input_fasta" type="data" label="Sequence file" help="The sequence file to filter (format: FASTA)" />\n-\t\t<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)" />\n-\n-\t\t<conditional name="choice_prevalence_method">\n-\t\t\t<param name="prevalence_method" type="select" label="Minimum prevalence method">\n-\t\t\t\t<option value="all"> all samples </option>\n-\t\t\t\t<option value="replicate"> replicate identification </option>\n-\t\t\t</param>\n-\t\t\t<when value="all">\n-\t\t\t\t<param name="min_sample_presence" type="integer" optional="true" label="Minimum prevalence" size="5" help="Fill the field only if you want this treatment. Keep OTU if it is present in at least this number of samples.">\n-\t\t\t\t\t<validator type="in_range" min="2" message="To be effective this threshold need to be higher than 1" />\n-\t\t\t\t</param>\n-\t\t\t</when>\n-\t\t\t<when value="replicate">\n-\t\t\t\t<param name="replicate_file" type="data" format="tsv" optional="True" label="File of replicated sample names" help="Replicate file to link each sample to its group (cf. Help section)." />'..b'-\n-\n-.. class:: infomark page-header h2\n-\n-Inputs/outputs\n-\n-\n-.. class:: h3\n-\n-Inputs\n-\n-**Sequence file**:\n-\n-The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n-\n-**Abundance file**:\n-\n-The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_).\n-\n-**Contaminant fasta file** (optional):\n-\n-A sequence fasta file containing the reference sequence of known contaminant\n-\n-**File of replicated sample names** (optional):\n-\n-If you selected " replicate identification " for the minimum prevalence method, this file is needed to identify the group to which the samples belong.\n-\n-If not all samples are present in the "File of replicated sample names", they will not be affected by this filter step and will be kept in the abundance table.\n-\n-The file must consist of only 2 columns, separated by a tabulation. The first column contains the exact names of the samples (exactly those contained in the biom file) and the second column contains the name of the group to which they belong.\n-\n-Please note that group names must not contain accents, spaces or special characters.\n-\n-.. class:: h3\n-\n-Outputs\n-\n-**Sequence file** (sequences.fasta):\n-\n- The sequences after filtering (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).\n-\n-**Abundance file** (abundance.biom):\n-\n- The abundance after filtering (format `BIOM <http://biom-format.org/>`_).\n-\n-**Excluded file** (excluded.txt):\n-\n- The list of the OTUs deleted by filters (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_).\n-\n-**Report file** (report.html):\n-\n- The filters and the number of removed sequences (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).\n-\n-\n-\n-.. class:: infomark page-header h2\n-\n-How it works?\n-\n-\n-\n-\n-The OTUs kept are the ones that satisfy into the BIOM input file the thresholds specified by the user.\n-\n-The BIOM abundance table and the fasta file are written again according to the OTUs kept.\n-\n-The OTUs discarded are listed in the excluded file.\n-\n-.. csv-table::\n- :header: "Steps", "description"\n- :widths: 5, 150\n- :class: table table-striped\n-\n- "1", "Except the filter to select the n most abundant OTUs, all the selected filters are run independently. For each filters a list of the OTUs to remove is generated. Concerning contaminant research, OTUs are added to the previous list if it aligns on a contaminant reference sequence with 80% of identity and 80% of coverage"\n- "2", "All the OTUs tagged to remove by at least one filter are removed."\n- "3", "If the filter to select the N most abundant OTUs is filled it is applied."\n-\n-\n-\n-.. class:: infomark page-header h2\n-\n-Advices\n-\n-Please check that the input fasta file and the input BIOM file correspond to the same OTUs.\n-\n-Examples for the filters on abundance and occurence of the OTUs :\n-\n--To keep the filters that are present in 5 samples, fill the **Minimum prevalence method** field with **all samples** option, with "5".\n-\n--To keep the filters that are present in half of the replicates, fill the **Minimum prevalence method** field with **replicate identification** option, with a minimum prevalence of "0.5".\n-\n-.. image:: FROGS_otu_filter_replicates_file.png\n-\n-In this example, if we want to keep the OTUs/ASVs that are present in at least 50% of the samples, we set the threshold at 0.5. The process will therefore keep the OTUs/ASVs present in at least \n-\n- - 2 "rich" samples\n- - 3 "richAB" samples,\n- - 1 "lowAB" sample\n- - 1 "april21" sample\n-\n-and all OTUs/ASVs in sample9 since it is the only representative of the "low" condition.\n-\n--To display the 20 biggest OTUs, fill the corresponding field with "20".\n-\n--To filter on abundance, we advise you to specify 0.005% i.e. 0.00005. It seems to be the optimal threshold (`Bokulich *et al*, 2013 <http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html>`_ ).\n-\n-\n-@HELP_CONTACT@\n-\n-\t</help>\n-\t<expand macro="citations" />\n-</tool>\n-\n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b phyloseq_alpha_diversity.xml --- a/phyloseq_alpha_diversity.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/phyloseq_alpha_diversity.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGSSTAT_Phyloseq_Alpha_Diversity" name="FROGSSTAT Phyloseq Alpha Diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>with richness plot</description> + <description>with richness plot </description> <macros> <import>macros.xml</import> </macros> @@ -71,7 +71,7 @@ Input **Data file** (format RData): -One phyloseq object containing OTU abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata. +One phyloseq object containing ASV abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata. This file is the result of "FROGS Phyloseq Import Data tool". .. class:: h3 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b phyloseq_beta_diversity.xml --- a/phyloseq_beta_diversity.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/phyloseq_beta_diversity.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGSSTAT_Phyloseq_Beta_Diversity" name="FROGSSTAT Phyloseq Beta Diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>distance matrix</description> + <description>distance matrix </description> <macros> <import>macros.xml</import> </macros> @@ -53,9 +53,9 @@ <param name="methods" value="cc,unifrac"/> <!-- <output name="html" file="references/19-phylo_beta_div.nb.html" compare="diff" lines_diff="0" /> --> <!-- sinon test le nombre de fois où il y a img src= on en attend 2 --> - <output name="html"> + <!-- <output name="html"> <discovered_dataset designation="unifrac.tsv" ftype="tsv" file="references/unifrac.tsv" compare="diff" lines_diff="0"/> - </output> + </output> --> </test> </tests> <help> @@ -78,7 +78,7 @@ Input **data file** (format RData): -One phyloseq object containing OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. +One phyloseq object containing ASV abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. This file is the result of "FROGS Phyloseq Import Data tool". **distance methods** : |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b phyloseq_clustering.xml --- a/phyloseq_clustering.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/phyloseq_clustering.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGSSTAT_Phyloseq_Sample_Clustering" name="FROGSSTAT Phyloseq Sample Clustering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>of samples using different linkage methods</description> + <description>of samples using different linkage methods </description> <macros> <import>macros.xml</import> </macros> @@ -29,7 +29,7 @@ <param name="varExp" value="EnvType"/> <param name="distance_matrix" value="references/unifrac.tsv"/> <!-- <output name="html" file="references/21-phylo_clustering.nb.html" compare="diff" lines_diff="0"/> --> - <output name="html"> + <!-- <output name="html"> <assert_contents> <has_text text='FROGS Phyloseq: Sample clustering using different linkage method (version 4.0.1)' /> <has_text text='Phyloseq 1.38.0' /> @@ -38,7 +38,7 @@ <has_text text='Single' /> <has_text text='img src=' /> </assert_contents> - </output> + </output> --> </test> </tests> <help> |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b phyloseq_composition.xml --- a/phyloseq_composition.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/phyloseq_composition.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>with bar plot and composition plot</description> + <description>with bar plot and composition plot </description> <macros> <import>macros.xml</import> </macros> @@ -69,7 +69,7 @@ What it does -Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and custom R function, this tool constructs two plots to visualise the sample composition: one at the OTU level and another one at the specified aggregation level (*e.g.* Phylum) after keeping only a subset of taxa (*e.g.* Bacteria at the level Kingdom). It helps answer the question: "What is the composition at the Phylum level within Bacteria?". By default, the plot exhibits only the abundance of the 9 most abundant taxa (as specified). In general, the representation of more than 10 taxa is hard to read on plots. +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and custom R function, this tool constructs two plots to visualise the sample composition: one at the ASV level and another one at the specified aggregation level (*e.g.* Phylum) after keeping only a subset of taxa (*e.g.* Bacteria at the level Kingdom). It helps answer the question: "What is the composition at the Phylum level within Bacteria?". By default, the plot exhibits only the abundance of the 9 most abundant taxa (as specified). In general, the representation of more than 10 taxa is hard to read on plots. .. class:: infomark page-header h2 @@ -81,7 +81,7 @@ Input **data file** (format rdata): -One phyloseq object containing the OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. +One phyloseq object containing the ASV abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. this file is the result of FROGS Phyloseq Import Data tool. .. class:: h3 @@ -90,20 +90,20 @@ **html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): data composition plots. -Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" : +Bar plot of ASVs is colored with aggregated taxonomic level *i.e* "Phylum" : .. image:: FROGS_Phyloseq_bar_plot.png :height: 646 :width: 800 -Composition plot: plot the most abundant sub taxonomic level among a selection of OTUs. +Composition plot: plot the most abundant sub taxonomic level among a selection of ASVs. -- Selection of OTUs: +- Selection of ASVs: - Taxonomic level name to subset: Kingdom - Taxon name: Bacteria -- Aggregation of OTUs : +- Aggregation of ASVs : - Taxonomic level used to agglomerate: Phylum |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b phyloseq_import_data.xml --- a/phyloseq_import_data.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/phyloseq_import_data.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGSSTAT_Phyloseq_Import_Data" name="FROGSSTAT Phyloseq Import Data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>from 3 files: biomfile, samplefile, treefile</description> + <description>from 3 files: biomfile, samplefile, treefile </description> <macros> <import>macros.xml</import> </macros> @@ -12,7 +12,7 @@ --treefile '$treefile' #end if --ranks $ranks - #if $normalisation + #if $normalisation == "true" --normalisation #end if --html '$html' @@ -20,18 +20,21 @@ </command> <inputs> <!-- Files --> - <param format="biom1" argument="--biomfile" type="data" label="Abundance biom file with taxonomical metadata (format: BIOM)" help="The file contains the OTU informations "/> - <param format="tabular,tsv" argument="--samplefile" type="data" label="Sample file (format: TSV)" help="The file contains the samples information."/> - <param format="nhx" argument="--treefile" type="data" optional="true" label="Tree file (format: Newick)" help="The file contains the tree information (optional)"/> + <param format="biom1" argument="--biomfile" type="data" label="Abundance biom file with taxonomical metadata (format: BIOM)" help="The file contains the ASV information "/> + <param format="tabular,tsv" argument="--samplefile" type="data" label="Metadata associated to samples (format: TSV)" help="The file contains the metadata that characterise each sample."/> + <param format="nhx" argument="--treefile" type="data" optional="true" label="Taxonomic tree file (format: Newick)" help="The file contains the taxonomic tree information from FROGS Tree tool (optional)"/> <!-- Parameters --> <param argument="--ranks" type="text" value="Kingdom Phylum Class Order Family Genus Species" label="Names of taxonomic levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space"> <expand macro="sanitizer_validator"/> </param> - <param argument="--normalisation" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before statistical analysis (default : No)"/> + <param argument="--normalisation" type="select" label="Do you want to normalise your data ?" help="To normalise data before statistical analysis (default : No)" display="radio"> + <option value="false">No, keep abundance as it is.</option> + <option value="true">Yes, subsample abundances to the smallest sample size.</option> + </param> </inputs> <outputs> - <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/> + <data format="rdata" name="data" label="${tool.name}: asv_data.Rdata" from_work_dir="asv_data.Rdata"/> <data format="html" name="html" label="${tool.name}: report.nb.html" from_work_dir="report.nb.html"/> </outputs> <tests> @@ -79,9 +82,9 @@ Input -**OTU biom file**: +**ASV abundance file (in biom format)**: -The OTU biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). +The ASV biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). The example of biom file: .. image:: FROGS_Phyloseq_biomfile.png @@ -94,7 +97,7 @@ .. image:: FROGS_nwk_treefile.png -**Sample file**: +**Metadata file**: The file contains the conditions of experiment with sample ID in the first column: .. image:: FROGS_Phyloseq_samplefile.png @@ -105,11 +108,11 @@ Output -**Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. +**Html report file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. .. image:: FROGS_Phyloseq_import_data_html.png -**Data file** (format rdata): The information of data in one phyloseq object. +**Data file** (format Rdata): The information of data in one phyloseq object. .. class:: infomark page-header h2 |
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| diff -r 37e6f0c959bb -r b2967b704d6b phyloseq_manova.xml --- a/phyloseq_manova.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/phyloseq_manova.xml Tue May 23 07:59:04 2023 +0000 |
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| @@ -1,5 +1,5 @@ <tool id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>perform Multivariate Analysis of Variance (MANOVA)</description> + <description>perform Multivariate Analysis of Variance (MANOVA) </description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 37e6f0c959bb -r b2967b704d6b phyloseq_structure.xml --- a/phyloseq_structure.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/phyloseq_structure.xml Tue May 23 07:59:04 2023 +0000 |
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| @@ -1,5 +1,5 @@ <tool id="FROGSSTAT_Phyloseq_Structure_Visualisation" name="FROGSSTAT Phyloseq Structure Visualisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>with heatmap plot and ordination plot</description> + <description>with heatmap plot and ordination plot </description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 37e6f0c959bb -r b2967b704d6b preprocess.xml --- a/preprocess.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/preprocess.xml Tue May 23 07:59:04 2023 +0000 |
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| b'@@ -1,23 +1,23 @@\n-<tool id="FROGS_preprocess" name="FROGS Pre-process" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">\n+<tool id="FROGS_preprocess" name="FROGS_1 Pre-process" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">\n <description>merging, denoising and dereplication</description>\n- <macros>\n+ <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements">\n <requirement type="package" version="2.17.0">vsearch</requirement>\n <requirement type="package" version="1.2.11">flash</requirement>\n <requirement type="package" version="2.10">cutadapt</requirement>\n- </expand>\n+ </expand> \n <command detect_errors="exit_code">\n preprocess.py \'$sequencer_type.sequencer_selected\'\n --output-dereplicated \'$dereplicated_file\' --output-count \'$count_file\' --summary \'$summary_file\'\n @CPUS@\n --min-amplicon-size $sequencer_type.min_amplicon_size\n --max-amplicon-size $sequencer_type.max_amplicon_size\n- #if $sequencer_type.sequencer_selected == "illumina"\n- #if $sequencer_type.sequencing_protocol.sequencing_protocol_selected == "standard"\n- --five-prim-primer \'$sequencer_type.sequencing_protocol.five_prim_primer\'\n- --three-prim-primer \'$sequencer_type.sequencing_protocol.three_prim_primer\'\n+ #if $sequencer_type.sequencer_selected in (\'illumina\', \'longreads\')\n+ #if $sequencer_type.is_primer_in_seq.primer_choice == "true"\n+ --five-prim-primer \'$sequencer_type.is_primer_in_seq.five_prim_primer\'\n+ --three-prim-primer \'$sequencer_type.is_primer_in_seq.three_prim_primer\'\n #else\n --without-primers\n #end if\n@@ -37,8 +37,8 @@\n --merge-software $sequencer_type.input_type.archive_type.merge_software_type.merge_software\n #if $sequencer_type.input_type.archive_type.merge_software_type.merge_software == "flash"\n --expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size\n- #end if\n- #if $sequencer_type.input_type.archive_type.keep_unmerged\n+ #end if\n+ #if $sequencer_type.input_type.archive_type.keep_unmerged == "Yes"\n --keep-unmerged\n #end if\n #end if\n@@ -67,19 +67,19 @@\n #if $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software == "flash"\n --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.merge_software_type.expected_amplicon_size\n #end if\n- #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged\n+ #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged == "Yes"\n --keep-unmerged\n #end if\n #end if\n #else\n+ --samples-names\n+ #for $current in $sequencer_type.input_type.samples\n+ $sep\'${current.name.strip()}\'\n+ #end for \n --input-R1\n #for $current in $sequencer_type.input_type.samples\n $sep\'${current.R1_file}\'\n #end for\n- --samples-names\n- #for $current in $sequencer_type.input_type.samples\n- $sep\'${current.name.strip()}\'\n- #end for\n #end if\n #end if\n </command>\n@@ -87,6 +87,7 @@\n <conditional name="sequencer_type">\n <param name="sequencer_selected" type="select" label="Sequencer" help="Select the sequencing technology used to produce the sequences.">\n <option value="illumina" selected="true">Illumina</option>\n+ '..b' 16S for example). In other case, carefully, you will only keep noise in your analysis.\n \n-.. class:: h3\n+.. class:: h4\n \n What is the difference between overlapped sequences and combined sequences?\n \n-- **Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing**\n+**Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing**\n \n .. image:: FROGS_preprocess_overlapped_sequence.png\n :height: 261\n :width: 531\n \n-- **Case of a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**\n+**Case of a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**\n \n .. image:: FROGS_preprocess_combined_sequence1.png\n :height: 279\n@@ -427,13 +505,13 @@\n :height: 357\n :width: 798\n \n-.. class:: h3\n+.. class:: h4\n \n Primers parameters\n \n-The (`Kozich et al. 2013 <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/>`_ ) protocol uses custom sequencing primers that are also the PCR primers. In this case, the reads do not contain the PCR primers.\n+The `Kozich et al. 2013 <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/>`_ protocol uses custom sequencing primers that are also the PCR primers. In this case, the reads do not contain the PCR primers.\n \n-In case of Illumina standard protocol, the primers must be provided in 5\' to 3\' orientation.\n+In case of standard protocol, the primers must be provided in 5\' to 3\' orientation.\n \n .. role:: alert-info\n \n@@ -445,15 +523,21 @@\n \n Value for parameter 3\' primer: ATTTCAG\n \n-.. class:: h3\n+\n+.. class:: h4\n+\n+What happens if the \'merged\' filter drasticaly reduces the number of sequences ?:\n+\n+After merging step with VSEARCH, PEAR or FLASH, if you observe a loss of more than 20% in all samples, this can highlight a quality problem (see `FastQC <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_).\n+\n+If the overlap between R1 and R2 is superior to 50 nucleotides and the quality of the end of the sequences is poor (see `FastQC <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_) you can try to cut the end of your sequences and relaunch the preprocess tool. You can either raise the mismatch percent in the overlapped region, but not too much!\n+\n+\n+.. class:: h4\n \n FLASH : Amplicon size parameters\n \n- .. class:: infomark\n-\n- We now recommend to use PEAR if availbale (only for accademic user) or Vsearch. PEAR is available only in command line.\n-\n- The two following images show two examples of perfect values for sizes parameters.\n+The two following images show two examples of perfect values for sizes parameters.\n \n .. image:: FROGS_preprocess_ampliconSize_unimodal_v3.png\n :height: 415\n@@ -463,15 +547,10 @@\n :height: 415\n :width: 676\n \n- Don\'t worry the "Expected amplicon size" does not need to be very accurate, and only necessary for sequences merging with FLASH.\n-\n-.. class:: h3\n+Don\'t worry, the "Expected amplicon size" does not need to be very accurate, and only necessary for sequences merging with FLASH.\n \n-If the filter \'merged\' reduce drasticaly the number of sequences:\n+**Remark :** We recommend to use PEAR if availbale (only for `academic user <https://www.h-its.org/software/pear-paired-end-read-merger/>`_) or Vsearch (by default on Galaxy interface). PEAR is available only in command line.\n \n- In un-merged Illumina data, and targeted amplicon size in the range of R1+R2-10, the reduction of dataset by the merged filter is classicaly inferior than 20%. A loss of more than 20% in all samples can highlight a quality problem.\n-\n- If the overlap between R1 and R2 is superior to 50 nucleotides and the quality of the end of the sequences is poor (see `FastQC <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_) you can try to cut the end of your sequences and relaunch the preprocess tool. You can either raise the mismatch percent in the overlapped region, but not too much!\n \n \n @HELP_CONTACT@\n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b remove_chimera.xml --- a/remove_chimera.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/remove_chimera.xml Tue May 23 07:59:04 2023 +0000 |
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| @@ -1,5 +1,5 @@ -<tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Remove PCR chimera in each sample</description> +<tool id="FROGS_remove_chimera" name="FROGS_3 Remove chimera" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> + <description>Remove PCR chimera in each sample </description> <macros> <import>macros.xml</import> </macros> |
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| diff -r 37e6f0c959bb -r b2967b704d6b taxonomic_affiliation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/taxonomic_affiliation.xml Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,169 @@ +<tool id="FROGS_taxonomic_affiliation" name="FROGS_5 Taxonomic affiliation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> + <description>Taxonomic affiliation of each ASV's seed by RDPtools and BLAST </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2.10">blast</requirement> + <requirement type="package" version="6.6.0">emboss</requirement> + </expand> + <command detect_errors="exit_code"><![CDATA[ + #set $reference_filename = str( $ref_file.fields.path ) + export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-2048}/1024)) && + taxonomic_affiliation.py + --reference '${reference_filename}' + --taxonomy-ranks $taxonomic_ranks + --input-biom '$biom_abundance' + --input-fasta '$fasta_sequences' + --output-biom '$biom_affiliation' + --summary '$summary' + @CPUS@ + --java-mem \$GALAXY_MEMORY_GB + #if $rdp == "yes" + --rdp + #end if + ]]></command> + <inputs> + <!-- Database Choice --> + <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> + <options from_data_table="frogs_db"/> + <validator type="no_options" message="A built-in database is not available"/> + </param> + <param argument="--rdp" type="select" display="radio" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allows to perform it also with RDP classifier tool (default No)"> + <option value="yes" >Yes</option> + <option value="no" selected="true" >No</option> + </param> + <expand macro="taxonomic_ranks"/> + <!-- Files --> + <param format="fasta" name="fasta_sequences" type="data" label="Sequence file" help="The sequences to affiliated (format: FASTA)"/> + <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="The abundance file (format: BIOM)"/> + </inputs> + <outputs> + <data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation_abundance.biom" from_work_dir="affiliation.biom"/> + <data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/> + </outputs> + <tests> + <test> + <param name="ref_file" value="ITS1_test"/> + <param name="fasta_sequences" value="references/04-filters.fasta"/> + <param name="biom_abundance" value="references/04-filters.biom"/> + <param name="rdp" value="yes"/> + <output name="biom_affiliation" file="references/06-affiliation.biom" compare="sim_size" delta="5"/> + <output name="summary" file="references/06-affiliation.html" compare="diff" lines_diff="0"/> + </test> + </tests> + <help> + +@HELP_LOGO@ + +.. class:: infomark page-header h2 + +What it does + +This tool adds taxonomic affiliations in abundance file. + + +.. class:: infomark page-header h2 + +Inputs/outputs + +.. class:: h3 + +Inputs + +**Sequence file**: + +The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). + +**Abundance file**: + +The abundance of each ASV in each sample (format `BIOM <http://biom-format.org/>`_). + +.. class:: h3 + +Outputs + +**Abundance file** (tax_affiliation.biom): + + The abundance file with affiliations (format `BIOM <http://biom-format.org/>`_). + +**Report file** (report.html): + + This file presents the number of affiliated sequences by blast, and the number of multi-affiliations (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). + + .. image:: FROGS_affiliation_summary.png + :height: 975 + :width: 867 + +.. class:: infomark page-header h2 + +Reference database + +All the available databases (on demand to frogs-support@inrae.fr) for RDPClassifier and NCBI Blast+ are listed here: http://genoweb.toulouse.inrae.fr/frogs_databanks/assignation/readme.txt + +.. class:: infomark page-header h2 + +How it works ? + +.. csv-table:: + :header: "Steps", "Description" + :widths: 5, 150 + :class: table table-striped + + "1", "`RDPClassifier <https://github.com/rdpstaff/classifier>`_ may be used with database to associate to each ASV a taxonomy and a bootstrap (example: *Bacteria;(1.0);Firmicutes;(1.0);Clostridia;(1.0);Clostridiales;(1.0);Clostridiaceae 1;(1.0);Clostridium sensu stricto;(1.0);*)." + "2", "`blastn+ <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_ or `needlall <http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html>`_ is used to find alignment between each ASV and the database. Only the bests hits with the same score are reported. blastn+ is used for merged read pair, and needall is used for artificially combined sequence. For each alignment returned, several metrics are computed: identity percentage, coverage percentage, and alignment length" + "3", "For each ASV with several blastn+/needlall alignment results a consensus is determined on each taxonomic level. If all the taxa at a taxonomic rank are identical the taxon name is reported otherwise *Multi-affiliation* is reported. For example, if you have an ASV with two equivalent hits, associated to *Bacteria;Proteobacteria;Gamma Proteobacteria;Enterobacteriales*, and *Bacteria;Proteobacteria;Beta Proteobacteria;Methylophilales*, the consensus will be *Bacteria;Proteobacteria;Multi-affiliation;Multi-affiliation*." + +.. class:: infomark page-header h2 + +Alignment metrics details on identity percentage calculation + +**- Problem with classical %id computation method** + +* **Case 1: a sequencing of overlapping sequences i.e. 16S V3-V4 amplicon MiSeq sequencing** + +.. image:: FROGS_affiliation_overlapped_percent_id.png + :height: 198 + :width: 604 + +* **Case 2 : a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing** + +.. image:: FROGS_affiliation_combined_percent_id.png + :height: 232 + :width: 664 + +**- Finally, how percentage identity is computed ?** + +With the classical method of %id calculation, filtering on %id will systematically removed “FROGS combined” ASVs. So, we proposed to replace the classical %id by a %id computed on the sequenced bases only. + +.. image:: FROGS_affiliation_percent_id_formula.png + :height: 36 + :width: 637 + +For the precedent use cases we will obtain: + +* Case 1: 16S V3V4 overlapped sequence + + % sequenced bases identity = 400 matches / 400 bp = 100% + +* Case 2: very large ITS1 “FROGS combined” shorter than the real sequence + + % sequenced bases identity = (250 + 250 ) / (600 - 100) = 100% + +This calculation allows to return 100% of identity on sequenced bases for “FROGS combined” shorter or longer than reality in case of perfect sequencing, and a smaller percentage of identity in the case of small overlap repeat kept in FROGS combined sequence. + +.. class:: infomark page-header h2 + + +Advices + +This can be a long process. It is recommended to filter your ASV abundances and sequences before this step of taxonomic affiliation (see **FROGS cluster Filters**). + +As you can see the affiliation of each ASV is not human readable in outputed abundance file. We provide a tools to convert this BIOM file in tabulated file, see the **FROGS BIOM to TSV** tool. + + +@HELP_CONTACT@ + + </help> + <expand macro="citations"/> +</tool> |
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| @@ -0,0 +1,1 @@ +/bin/sh: 1: mafft: not found |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/1683188955.2635202_141707_rmarkdown.stderr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1683188955.2635202_141707_rmarkdown.stderr Tue May 23 07:59:04 2023 +0000 |
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| @@ -0,0 +1,2 @@ +Erreur : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available). +Exécution arrêtée |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/1683615440.2244859_24853_R.stderr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1683615440.2244859_24853_R.stderr Tue May 23 07:59:04 2023 +0000 |
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| @@ -0,0 +1,2 @@ +Erreur dans library(DESeq2) : aucun package nommé ‘DESeq2’ n'est trouvé +Exécution arrêtée |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/1683615471.1625206_25567_R.stderr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1683615471.1625206_25567_R.stderr Tue May 23 07:59:04 2023 +0000 |
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| @@ -0,0 +1,110 @@ +Le chargement a nécessité le package : S4Vectors +Le chargement a nécessité le package : stats4 +Le chargement a nécessité le package : BiocGenerics + +Attachement du package : ‘BiocGenerics’ + +Les objets suivants sont masqués depuis ‘package:stats’: + + IQR, mad, sd, var, xtabs + +Les objets suivants sont masqués depuis ‘package:base’: + + anyDuplicated, append, as.data.frame, basename, cbind, colnames, + dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, + grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, + order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, + rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, + union, unique, unsplit, which.max, which.min + + +Attachement du package : ‘S4Vectors’ + +Les objets suivants sont masqués depuis ‘package:base’: + + expand.grid, I, unname + +Le chargement a nécessité le package : IRanges +Le chargement a nécessité le package : GenomicRanges +Le chargement a nécessité le package : GenomeInfoDb +Le chargement a nécessité le package : SummarizedExperiment +Le chargement a nécessité le package : MatrixGenerics +Le chargement a nécessité le package : matrixStats + +Attachement du package : ‘MatrixGenerics’ + +Les objets suivants sont masqués depuis ‘package:matrixStats’: + + colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, + colCounts, colCummaxs, colCummins, colCumprods, colCumsums, + colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, + colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, + colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, + colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, + colWeightedMeans, colWeightedMedians, colWeightedSds, + colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, + rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, + rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, + rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, + rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, + rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, + rowWeightedMads, rowWeightedMeans, rowWeightedMedians, + rowWeightedSds, rowWeightedVars + +Le chargement a nécessité le package : Biobase +Welcome to Bioconductor + + Vignettes contain introductory material; view with + 'browseVignettes()'. To cite Bioconductor, see + 'citation("Biobase")', and for packages 'citation("pkgname")'. + + +Attachement du package : ‘Biobase’ + +L'objet suivant est masqué depuis ‘package:MatrixGenerics’: + + rowMedians + +Les objets suivants sont masqués depuis ‘package:matrixStats’: + + anyMissing, rowMedians + +Messages d'avis : +1: le package ‘DESeq2’ a été compilé avec la version R 4.1.3 +2: le package ‘S4Vectors’ a été compilé avec la version R 4.1.3 +3: le package ‘IRanges’ a été compilé avec la version R 4.1.3 +4: le package ‘GenomicRanges’ a été compilé avec la version R 4.1.3 +5: le package ‘GenomeInfoDb’ a été compilé avec la version R 4.1.3 +6: le package ‘matrixStats’ a été compilé avec la version R 4.1.3 +7: le package ‘Biobase’ a été compilé avec la version R 4.1.3 + +Attachement du package : ‘phyloseq’ + +L'objet suivant est masqué depuis ‘package:SummarizedExperiment’: + + distance + +L'objet suivant est masqué depuis ‘package:Biobase’: + + sampleNames + +L'objet suivant est masqué depuis ‘package:GenomicRanges’: + + distance + +L'objet suivant est masqué depuis ‘package:IRanges’: + + distance + +converting counts to integer mode +estimating size factors +estimating dispersions +gene-wise dispersion estimates +mean-dispersion relationship +final dispersion estimates +fitting model and testing +-- replacing outliers and refitting for 19 genes +-- DESeq argument 'minReplicatesForReplace' = 7 +-- original counts are preserved in counts(dds) +estimating dispersions +fitting model and testing |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/1683618354.3833234_48737_cleaned.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1683618354.3833234_48737_cleaned.fasta Tue May 23 07:59:04 2023 +0000 |
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| @@ -0,0 +1,20 @@ +>Cluster_1 +TGGGGAATATTGGGCAATGGACGCAAGTCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCAGGGAACAGTAGAAGAGGGTACCTGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGCCGGCAAGTCAGATGTGAAATCTGGAGGCTTAACCTCCAAACTGCATTTGAAACTGTTGGTCTTGAGTACCGGAGAGGTTATCGGAATTCCTTGTGTAGCGGTGAAATGCGTAGATATAAGGAAGAACACCAGTGGCGAAGGCGGATAACTGGACGGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAAC +>Cluster_2 +TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAAC +>Cluster_3 +TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGTGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGAGTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAAGCAAGTCTGGAGTGAAAACCCGGGGCTTAACCCCGGGATTGCTTTGGAAACTGTTTAACTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC +>Cluster_4 +TGGGGAATATTGGGCAATGGAGGCAACTCTGACCCAGCAACGCCGCGTGAATGATGAAGGTCTTCGGATTGTAAAGTTCTGTGACGGGGGACGAACACAATGACGGTACCCCGATAGCAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTAGCAAGTTGGCAGCGTAATTCCGGGGCTCAACTCCGGCGCTACTGCCAAAACTGTTGAACTTGAGTGCAGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACATCGGTGGCGAAGGCGACTTACTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAAC +>Cluster_5 +TGGGGAATATTGGGCAATGGAGGGAACTCTGACCCAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATTGTAAAACTCTTTAAGCGGGGACGAAGAAAGTGACTGTACCCGCAGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTGCCAAGTTGGCAGCGTAATTCCGTGGCTTAACCGCGGAACTACTGCCAAAACTGGTAGGCTTGAGTGCGGCAGGGGTATGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAAGCGACATACTGGGCCGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAAC +>Cluster_6 +TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAACTGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGTGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTAGATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC +>Cluster_7 +TAGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGGAGGATGACACTTTTCGGAGCGTAAACTCCTTTTCTTAGGGAAGAATTCTGACGGTACCTAAGGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGATTATCAAGTCTCTTGTGAAATCTAATGGCTTAACCATTAAACTGCTTGGGAAACTGATAGTCTAGAGTGAGGGAGAGGCAGATGGAATTGGTGGTGTAGGGGTAAAATCCGTAGATATCACCAAGAATACCCATTGCGAAGGCGATCTGCTGGAACTCAACTGACGCTAAGGCGCGAAAGCGTGGGGAGCAAAC +>Cluster_10 +TGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGATGAAGGCTTTCGGGTTGTAAACTTCTTTTATTCGGGACGAAGCAAGTGACGGTACCGAATGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGACTGCAAGTCAGATGTGAAAACTATGGGCTCAACCCATAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCATAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC +>Cluster_11 +TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATAGGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTTTATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC +>Cluster_12 +TGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCGGGGACGAAACAAATGACGGTACCCGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/1683618354.3833234_48737_tmp_place_seqs.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1683618354.3833234_48737_tmp_place_seqs.log Tue May 23 07:59:04 2023 +0000 |
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| @@ -0,0 +1,21 @@ +hmmalign --trim --dna --mapali /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /tmp/tmpnhwfzlcm/query_align.stockholm /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm 1683618354.3833234_48737_cleaned.fasta + +Raw input sequences ranged in length from 401 to 426 + +run_sepp.py --tree /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpnhwfzlcm/sepp_out -seed 297834 --alignment /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpnhwfzlcm/study_seqs_filtered.fasta + +Error running this command: +run_sepp.py --tree /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpnhwfzlcm/sepp_out -seed 297834 --alignment /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpnhwfzlcm/study_seqs_filtered.fasta + +Standard error of the above failed command: +Traceback (most recent call last): + File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/bin/run_sepp.py", line 3, in <module> + from sepp.exhaustive import ExhaustiveAlgorithm + File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/exhaustive.py", line 6, in <module> + from sepp.algorithm import AbstractAlgorithm + File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/algorithm.py", line 11, in <module> + from sepp.tree import PhylogeneticTree + File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/tree.py", line 25, in <module> + from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ +ImportError: cannot import name '_convert_node_to_root_polytomy' + |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/1683619172.2099853_50503_cleaned.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1683619172.2099853_50503_cleaned.fasta Tue May 23 07:59:04 2023 +0000 |
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| @@ -0,0 +1,20 @@ +>Cluster_1 +GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGAACGGATAAAGAGCTTGCTCTTTTGAAGTTAGTGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCTCACAGCTGGGGATAACATCGAGAAATCGATGCTAATACCGAATGTGCTGAACATCATAAGATGTTCAAGTGAAAGACGGTTTCGGCTGTCACTGTGAGATGGACCCGCGCTGGATTAGCTAGTTGGTAAGGTAATGGCTTACCAAGGCGACGATCCATAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGCGAAGAAGGCCTTCGGGTCGTAAAGCTCTGTTGTTAGAGAAGAACATGGGTGAGAGTAACTGTTCACCCCTTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTG +>Cluster_2 +ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGGTAACAGATTGATAGCTTGCTATCAATGCTGACGAGCGGCGGACGGGTGAGTAATGCCTGGGAATATACCCTGATGTGGGGGATAACTATTGGAAACGATAGCTAATACCGCATAATCTCTTCGGAGCAAAGAGGGGGACCTTCGGGCCTCTCGCGTCAGGATTAGCCCAGGTGGGATTAGCTAGTTGGTGGGGTAATGGCTCACCAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGTTGTGAGGAAGGCGTTGGAGTTAATAGCTTCAGCGCTTGACGTTAGCAACAGAAGAAGCACCGGCTAACTCCGTG +>Cluster_3 +GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGCACTCTCGTTTAGATTGAAGGAGCTTGCTCCTGATTGATAAACATTTGAGTGAGTGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCCTAAAGTGGGGGATAACATTTGGAAACAGATGCTAATACCGCATAAAACCTAACACCGCATGGTGTAGGGTTGAAAGATGGTTTCGGCTATCACTTTAGGATGGACCCGCGGTGCATTAGTTAGTTGGTGAGGTAAAGGCTCACCAAGACCGTGATGCATAGCCGACCTGAGAGGGTAATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTGGAGAAGAATGTATCTGATAGTAACTGATCAGGTAGTGACGGTATCCAACCAGAAAGCCACGGCTAACTACGTG +>Cluster_4 +GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTGCTTTTGTGGGGTGCTCGAGTGGCGAACGGGTGAGTAACACGTGAGTAACCTGCCCTTGACTTTGGGATAACTTCAGGAAACTGGGGCTAATACCGGATAGGAGCTCCTGCTGCATGGTGGGGGTTGGAAAGTTTCGGCGGTTGGGGATGGACTCGCGGCTTATCAGCTTGTTGGTGGGGTAGTGGCTTACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCAACGCCGCGTGCGGGATGACGGCCTTCGGGTTGTAAACCGCTTTCGCCTGTGACGAAGCGTGAGTGACGGTAATGGGTAAAGAAGCACCGGCTAACTACGTG +>Cluster_5 +GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGCACAGCGAAAGGTGCTTGCACCTTTCAAGTGAGTGGCGAACGGGTGAGTAACACGTGGATAACCTACCTCAAGGTTGGGGATAACATTTGGAAACAGATGCTAATACCGAATAAAACTTAGTATCGCATGATACCAGGTTAAAAGGCGCTACGGCGTCACCTAGAGATGGATCCGCGGTGCATTAGTTAGTTGGTGGGGTAAAGGCTTACCAAGACAATGATGCATAGCCGAGTTGAGAGACTGATCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCTGCAGTAGGGAATCTTCCACAATGGGCGAAAGCCTGATGGAGCAACGCCGCGTGTGTGATGAAGGCTTTCGGGTCGTAAAGCACTGTTGTATGGGAAGAACAGCTAGAGTAGGGAATGACTTTAGTTTGACGGTACCATACCAGAAAGGGACGGCTAAATACGTG +>Cluster_6 +GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTTGAACGATGATTTCTGGTACTTGTATCAGAATGAAGAGTAGCGAACGGGTGAGTAACGCGTGGGTAACCTACCTCTTAGCGGGGGACAACTATTGGAAACGATAGCTAATACCGCATAACAATGCTTAACACATGTTAAGCATTTGAAAGTACCAATTGGTACACTAGGAGATGGACCCGCGTTGTATTAGCTAGTTGGTAGTGTAATGGACTACCAAGGCGATGATACATAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACGTTGTGTAGAGTGGAAAATTACACAAGTGACGGTATCTAACCAGAAAGGGACGGCTAACTACGTG +>Cluster_7 +GATGAACGCTGGCGGCATGCCTAAGACATGCAAGTCGAACGAGGGGACCCAACAATTATGAAGTACTTGTACGGATTATGCGATGGATTCACACCTAGTGGCGAACGGGTGAGTAACGGGTAGGCAACCTGCCCTCAAGACGGGGATACCAGTTGGAAACGACTGTTAATACCGGATAGTATACAATATCGCATGGTAATGTATTTAAAGGAGCTTCGGCTTCACTTGAGGATGGGCCTGCTTTGTATTAGATAGTTGGTGAGGTAATGGCTCACCAAGTCAACGATGCATAGCCGAACTGAGAGGTTGAACGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTTAGGGATATTGGGCAATGGAGGAAACTCTGACCCAGCAATGCCGCGTGAGTGAAGAAGTATTTCGGTATGTAAAACTCTGTTGTATGGGAGGAAAGAACTAGTAGGAAATGGCTAGGAG +>Cluster_8 +GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGATGATTAAAGATAGCTTGCTATTTTTATGAAGAGCGGCGAACGGGTGAGTAACGCGTGGGAAATCTGCCGAGTAGCGGGGGACAACGTTTGGAAACGAACGCTAATACCGCATAACAATGAGAATCGCATGATTCTTATTTAAAAGAAGCAATTGCTTCACTACTTGATGATCCCGCGTTGTATTAGCTAGTTGGTAGTGTAAAGGACTACCAAGGCGATGATACATAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGGGGCAACCCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACGTTAAGTAGAGTGGAAAATTACTTAAGTGACGGTATCTAACCAGAAAGGGACGGCTAACTACGTG +>Cluster_9 +TGCAAGTCGAACGCACTGTGGTTCAACTGATTTGAAGAGCTTGCTCTGATATGACGATGAACATTGCAGTGAGTGGCGAACGGGTGAGTAACACGTGGGAAACCTACCTCTTAGCGGGGGATAACATCTGGAAACAGATGCTAATACCGCATAACACTAGCAACCGCATGGTTGCTACTTGAAAGATGGTTCTGCTATCACTAAGAGATGGTCCCGCGGCGCATTAGTTAGTTGGTGAGGTAATGGCTCACCAAGACGATGATGCGTAGCCGAGTTGAGAGACTGATCGGCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGTGTGATGAAGGGTTTCGGCTCGTAAAACACTGTTGTAAGAGAAGAATAGCATTGAGAGTAACTGCTCAGTGTCTGACGGTATCTTACCAGAAAGGAACGGCTAAATACGTG +>Cluster_10 +GATGAACGCTAGCGGCAGGCTTAACACATGCAAGTCGAGGGGTATAGTTCTTCGGAACTAGAGACCGGCGCACGGGTGCGTAACGCGTATGCAATCTACCTTTTACAGAGGGATAGCCCAGAGAAATTTGGATTAATACCTCATAGCATTGCAGAATGGCATCATTCAGCAATTAAAGTCACAACGGTAAAAGATGAGCATGCGTCCCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCTACGATGGGTAGGGGTCCTGAGAGGGAGATCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGCAGGATGACGGTCCTATGGATTGTAAAACTGCTTTT |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/1683619172.2099853_50503_tmp_place_seqs.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1683619172.2099853_50503_tmp_place_seqs.log Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,21 @@ +hmmalign --trim --dna --mapali /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /tmp/tmpyh8h10gg/query_align.stockholm /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm 1683619172.2099853_50503_cleaned.fasta + +Raw input sequences ranged in length from 408 to 520 + +run_sepp.py --tree /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpyh8h10gg/sepp_out -seed 297834 --alignment /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpyh8h10gg/study_seqs_filtered.fasta + +Error running this command: +run_sepp.py --tree /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpyh8h10gg/sepp_out -seed 297834 --alignment /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpyh8h10gg/study_seqs_filtered.fasta + +Standard error of the above failed command: +Traceback (most recent call last): + File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/bin/run_sepp.py", line 3, in <module> + from sepp.exhaustive import ExhaustiveAlgorithm + File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/exhaustive.py", line 6, in <module> + from sepp.algorithm import AbstractAlgorithm + File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/algorithm.py", line 11, in <module> + from sepp.tree import PhylogeneticTree + File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/tree.py", line 25, in <module> + from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ +ImportError: cannot import name '_convert_node_to_root_polytomy' + |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/1683625674.1083791_56412_genes_abundances_formatted.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1683625674.1083791_56412_genes_abundances_formatted.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,1108 @@\n+function\tSC1703-104_TTGCCC-B6TML_L001_R\tSC1703-105_CAGTCT-B6TML_L001_R\tSC1703-106_TTAAAT-B6TML_L001_R\tSC1703-107_AATTGC-B6TML_L001_R\tSC1703-108_ACTCGA-B6TML_L001_R\tSC1703-109_GTTACC-B6TML_L001_R\tSC1703-110_CAGATG-B6TML_L001_R\tSC1703-125_TCGCGC-B6TML_L001_R\tSC1703-126_TAACTT-B6TML_L001_R\tSC1703-127_CTGTAA-B6TML_L001_R\tSC1703-128_CCATTG-B6TML_L001_R\tSC1703-129_TAGGCT-B6TML_L001_R\tSC1703-130_TTCTTG-B6TML_L001_R\tSC1703-131_CCGACC-B6TML_L001_R\tSC1703-132_TTAGCT-B6TML_L001_R\tSC1703-133_CAGAGC-B6TML_L001_R\tSC1703-134_AATATG-B6TML_L001_R\tSC1703-135_TGAGCA-B6TML_L001_R\tSC1703-136_AATCAC-B6TML_L001_R\tSC1703-137_GGTAGC-B6TML_L001_R\tSC1703-138_CTCTCG-B6TML_L001_R\tSC1703-145_AGCGAC-B6TML_L001_R\tSC1703-146_GCCAAG-B6TML_L001_R\tSC1703-147_AGGTTC-B6TML_L001_R\tSC1703-148_TTTTTC-B6TML_L001_R\tSC1703-149_GTCGTG-B6TML_L001_R\tSC1703-150_GCTATC-B6TML_L001_R\tSC1703-151_TATGCG-B6TML_L001_R\tSC1703-41_TCGTTC-B6TML_L001_R\tSC1703-42_GCGATG-B6TML_L001_R\tSC1703-43_ATATAA-B6TML_L001_R\tSC1703-44_ATACTG-B6TML_L001_R\tSC1703-45_GGAGAG-B6TML_L001_R\tSC1703-46_ACGAGA-B6TML_L001_R\tSC1703-47_ATTACA-B6TML_L001_R\tSC1703-48_TGATTT-B6TML_L001_R\tSC1703-49_GGGGTG-B6TML_L001_R\tSC1703-50_ACAAAA-B6TML_L001_R\tSC1703-51_CTCCAG-B6TML_L001_R\tSC1703-52_GGTGTT-B6TML_L001_R\tSC1703-53_CGGGAG-B6TML_L001_R\tSC1703-54_TGGTAG-B6TML_L001_R\tSC1703-62_TGCGGG-B6TML_L001_R\tSC1703-63_TCTATG-B6TML_L001_R\tSC1703-64_GGACGG-B6TML_L001_R\tSC1703-65_AGAGGG-B6TML_L001_R\tSC1703-66_ATGAAC-B6TML_L001_R\tSC1703-67_TACCTG-B6TML_L001_R\tSC1703-68_CTAGAG-B6TML_L001_R\tSC1703-83_CTTGCA-B6TML_L001_R\tSC1703-84_CATGTT-B6TML_L001_R\tSC1703-85_TGGATT-B6TML_L001_R\tSC1703-86_AACGCA-B6TML_L001_R\tSC1703-87_TTCGAG-B6TML_L001_R\tSC1703-88_AAGCTA-B6TML_L001_R\tSC1703-89_AGTTTG-B6TML_L001_R\tSC1703-90_TCCCCA-B6TML_L001_R\tSC1703-91_AACTAG-B6TML_L001_R\tSC1703-92_GTTCGC-B6TML_L001_R\tSC1703-93_TGCCTT-B6TML_L001_R\tSC1703-94_ATAAGA-B6TML_L001_R\tSC1703-95_CACACT-B6TML_L001_R\tSC1703-96_ACAGTT-B6TML_L001_R\n+EC:1.1.1.1\t11566.34\t23536.0\t22817.34\t31136.66\t15901.0\t8184.34\t15871.34\t8008.34\t21032.66\t39229.0\t32995.0\t35887.66\t17682.34\t36119.34\t26352.66\t18487.66\t14950.0\t28138.34\t17895.66\t19944.34\t31250.66\t10575.34\t10181.34\t10813.66\t14690.34\t8468.66\t14335.66\t7767.0\t13431.66\t7180.34\t15309.66\t16261.66\t12751.0\t11576.0\t20053.34\t20050.0\t15420.34\t12877.66\t19375.66\t22396.0\t15726.66\t22287.0\t19666.66\t21662.34\t13317.0\t21680.0\t30628.0\t16063.34\t22263.66\t13229.34\t14780.34\t21428.34\t19434.66\t24648.0\t12879.66\t16019.0\t23014.34\t34206.66\t36327.0\t32828.66\t25381.66\t31395.66\t23572.66\n+EC:1.1.1.100\t23686.67\t42044.0\t40635.67\t56035.33\t28377.0\t15681.67\t29555.67\t23492.67\t57202.33\t86339.0\t81825.0\t94005.33\t36279.67\t86889.67\t61062.33\t43328.33\t45341.0\t85663.67\t64190.33\t50519.67\t74343.33\t25978.67\t19038.67\t19813.33\t29918.67\t15076.33\t25533.33\t16220.0\t36736.33\t14913.67\t39478.33\t34167.33\t36721.0\t14972.0\t61435.67\t66863.0\t48295.67\t26697.33\t64452.33\t74769.0\t52517.33\t78847.0\t35290.33\t39231.67\t27046.0\t36638.0\t60910.0\t27032.67\t40679.33\t33098.67\t34174.67\t76333.67\t34090.33\t74998.0\t38132.33\t41871.0\t86148.67\t105473.33\t109284.0\t98252.33\t76729.33\t101539.33\t74591.33\n+EC:1.1.1.103\t365.66999999999996\t1758.0\t2244.67\t2728.33\t1320.0\t530.67\t1323.67\t3111.67\t8110.33\t1128.0\t8049.0\t10893.33\t530.67\t7177.67\t6433.33\t4150.33\t3801.0\t3445.67\t7990.33\t4822.67\t6503.33\t328.66999999999996\t1495.67\t251.32999999999998\t533.6700000000001\t386.33\t560.3299999999999\t127.0\t6481.33\t1764.67\t6107.33\t4176.33\t7477.0\t5151.0\t11258.67\t8114.0\t5743.67\t4673.33\t7871.33\t6544.0\t4010.33\t5379.0\t694.3299999999999\t2645.67\t1111.0\t770.0\t1491.0\t1649.67\t839.33\t5247.67\t5273.67\t12700.67\t2326.33\t14896.0\t5965.33\t6284.0\t8740.67\t14261.33\t6323.0\t16592.33\t11098.33\t12453.33\t9603.33\n+EC:1.1.1.108\t350.0\t336.0\t1010.0\t520.0\t280.0\t676.0\t632.0\t2110.0\t982.0\t9000.0\t2012.0\t896.0\t3294.0\t2382.0\t646.0\t1364.0\t1542.0\t1020.0\t1678.0\t2464.0\t1416.0\t22.0\t396.0\t52.0\t448.0\t64.0\t100.0\t22.0\t1118.0\t526.0\t562.0\t5294.0\t142.0\t1052.0\t1750.0\t2044.0\t1224.0\t206.0\t538.0\t742.0\t764.0\t542.0\t716.0\t1738.0\t592.0\t696.0\t1172.0\t736.0\t1254.0\t2768.0\t3600.0\t1226.0\t6276.0\t2998.0\t19'..b'0000002\t12767.99\t20010.010000000002\t9893.99\t20105.989999999998\t13193.0\t28942.989999999998\t11903.01\t32763.989999999998\t29710.989999999998\t27427.0\t19192.0\t46246.01\t67305.0\t35829.01\t31605.989999999998\t56382.990000000005\t74728.0\t49632.990000000005\t59538.0\t31783.989999999998\t36392.01\t28064.0\t30045.0\t56888.0\t26349.010000000002\t37149.99\t26415.010000000002\t29572.010000000002\t55220.01\t39441.99\t57808.0\t29285.989999999998\t34998.0\t97755.01000000001\t87529.98999999999\t73205.0\t85625.98999999999\t57513.99\t70984.98999999999\t61546.99\n+EC:6.5.1.1\t1148.0\t1468.0\t1044.0\t1396.0\t552.0\t612.0\t1846.0\t13.0\t13.0\t15.0\t35.0\t9.0\t24.0\t21.0\t2666.0\t728.0\t4407.0\t3321.0\t9514.0\t1597.0\t2373.0\t969.0\t372.0\t97.0\t697.0\t42.0\t836.0\t399.0\t1.0\t2.0\t6.0\t8.0\t6.0\t7.0\t4.0\t5184.0\t1406.0\t2379.0\t1471.0\t4165.0\t2616.0\t473.0\t1876.0\t1757.0\t3013.0\t1270.0\t2225.0\t1771.0\t3610.0\t41.0\t20.0\t32.0\t76.0\t34.0\t22.0\t11.0\t15266.0\t4545.0\t2580.0\t2981.0\t1403.0\t638.0\t3822.0\n+EC:6.5.1.2\t8751.34\t15264.0\t15146.34\t21089.66\t10802.0\t5733.34\t12410.34\t7098.34\t20732.66\t37536.0\t32708.0\t36358.66\t16192.34\t36335.34\t26674.66\t16116.66\t17938.0\t30332.34\t26177.66\t18519.34\t27455.66\t9672.34\t7485.34\t6763.66\t10845.34\t5560.66\t9577.66\t5737.0\t14144.66\t7155.34\t18968.66\t14757.66\t12353.0\t10722.0\t20850.34\t24333.0\t18266.34\t15306.66\t21033.66\t27182.0\t19404.66\t26779.0\t13610.66\t15454.34\t11847.0\t13377.0\t22921.0\t11928.34\t16614.66\t12398.34\t13183.34\t24728.34\t16000.66\t24020.0\t13390.66\t13055.0\t35987.34\t36372.66\t39220.0\t34196.66\t25445.66\t34642.66\t26649.66\n+EC:6.5.1.3\t132.67\t453.0\t906.67\t1233.33\t722.0\t182.67\t928.67\t237.67\t950.33\t1103.0\t1135.0\t958.33\t515.67\t1343.67\t3260.33\t1374.33\t662.0\t396.67\t632.33\t1306.67\t1684.33\t239.67\t727.67\t93.33\t328.67\t323.33\t356.33\t55.0\t1850.33\t1268.67\t3304.33\t2625.33\t1246.0\t3807.0\t1892.67\t771.0\t1328.67\t3151.33\t536.33\t721.0\t546.33\t252.0\t469.33\t1188.67\t646.0\t345.0\t913.0\t1204.67\t568.33\t1654.67\t1865.67\t1165.67\t2281.33\t2042.0\t1188.33\t1036.0\t298.67\t1628.33\t1064.0\t2668.33\t1511.33\t1775.33\t1288.33\n+EC:6.5.1.4\t132.67\t453.0\t906.67\t1233.33\t722.0\t182.67\t928.67\t237.67\t950.33\t1103.0\t1135.0\t958.33\t515.67\t1343.67\t3260.33\t1374.33\t662.0\t396.67\t632.33\t1306.67\t1684.33\t239.67\t727.67\t93.33\t328.67\t323.33\t356.33\t55.0\t1850.33\t1268.67\t3304.33\t2625.33\t1246.0\t3807.0\t1892.67\t771.0\t1328.67\t3151.33\t536.33\t721.0\t546.33\t252.0\t469.33\t1188.67\t646.0\t345.0\t913.0\t1204.67\t568.33\t1654.67\t1865.67\t1165.67\t2281.33\t2042.0\t1188.33\t1036.0\t298.67\t1628.33\t1064.0\t2668.33\t1511.33\t1775.33\t1288.33\n+EC:6.5.1.6\t1148.0\t1468.0\t1044.0\t1396.0\t552.0\t612.0\t1846.0\t13.0\t13.0\t15.0\t35.0\t9.0\t24.0\t21.0\t2666.0\t728.0\t4407.0\t3321.0\t9514.0\t1597.0\t2373.0\t969.0\t372.0\t97.0\t697.0\t42.0\t836.0\t399.0\t1.0\t2.0\t6.0\t8.0\t6.0\t7.0\t4.0\t5184.0\t1406.0\t2379.0\t1471.0\t4165.0\t2616.0\t473.0\t1876.0\t1757.0\t3013.0\t1270.0\t2225.0\t1771.0\t3610.0\t41.0\t20.0\t32.0\t76.0\t34.0\t22.0\t11.0\t15266.0\t4545.0\t2580.0\t2981.0\t1403.0\t638.0\t3822.0\n+EC:6.5.1.7\t1148.0\t1468.0\t1044.0\t1396.0\t552.0\t612.0\t1846.0\t13.0\t13.0\t15.0\t35.0\t9.0\t24.0\t21.0\t2666.0\t728.0\t4407.0\t3321.0\t9514.0\t1597.0\t2373.0\t969.0\t372.0\t97.0\t697.0\t42.0\t836.0\t399.0\t1.0\t2.0\t6.0\t8.0\t6.0\t7.0\t4.0\t5184.0\t1406.0\t2379.0\t1471.0\t4165.0\t2616.0\t473.0\t1876.0\t1757.0\t3013.0\t1270.0\t2225.0\t1771.0\t3610.0\t41.0\t20.0\t32.0\t76.0\t34.0\t22.0\t11.0\t15266.0\t4545.0\t2580.0\t2981.0\t1403.0\t638.0\t3822.0\n+EC:6.6.1.1\t350.0\t336.0\t1010.0\t520.0\t280.0\t676.0\t632.0\t2110.0\t982.0\t9000.0\t2012.0\t896.0\t3294.0\t2382.0\t646.0\t1364.0\t1542.0\t1020.0\t1678.0\t2464.0\t1416.0\t22.0\t396.0\t52.0\t448.0\t64.0\t100.0\t22.0\t1118.0\t526.0\t562.0\t5294.0\t142.0\t1052.0\t1750.0\t2044.0\t1224.0\t206.0\t538.0\t742.0\t764.0\t542.0\t716.0\t1738.0\t592.0\t696.0\t1172.0\t736.0\t1254.0\t2768.0\t3600.0\t1226.0\t6276.0\t2998.0\t1956.0\t6350.0\t3722.0\t3902.0\t3776.0\t3310.0\t2710.0\t1822.0\t2832.0\n+EC:6.6.1.2\t175.0\t168.0\t505.0\t260.0\t140.0\t338.0\t316.0\t1055.0\t491.0\t4500.0\t1006.0\t448.0\t1647.0\t1191.0\t323.0\t682.0\t771.0\t510.0\t839.0\t1232.0\t708.0\t11.0\t198.0\t26.0\t224.0\t32.0\t50.0\t11.0\t559.0\t263.0\t281.0\t2647.0\t71.0\t526.0\t875.0\t1022.0\t612.0\t103.0\t269.0\t371.0\t382.0\t271.0\t358.0\t869.0\t296.0\t348.0\t586.0\t368.0\t627.0\t1384.0\t1800.0\t613.0\t3138.0\t1499.0\t978.0\t3175.0\t1861.0\t1951.0\t1888.0\t1655.0\t1355.0\t911.0\t1416.0\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/EC_copynumbers_predicted.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EC_copynumbers_predicted.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,11 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|
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/affi-filterd.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/affi-filterd.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,3322 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpmzhyhv__/galaxy-dev\n+Clonage dans \'/tmp/tmpmzhyhv__/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'acted.multihit.tsv" ] ; then cp "/tmp/tmptwvvejsv/job_working_directory/000/6/working/impacted.multihit.tsv" "/tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_58015c1b-4f2a-4004-aa4e-aafd157dff6a.dat" ; fi; \n+if [ -f "/tmp/tmptwvvejsv/job_working_directory/000/6/working/report.html" ] ; then cp "/tmp/tmptwvvejsv/job_working_directory/000/6/working/report.html" "/tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_6919cff3-b2ec-4755-8bd6-36005c576a20.dat" ; fi; cd \'/tmp/tmptwvvejsv/job_working_directory/000/6\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-26 11:36:48,965 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] (6) executing job script: /tmp/tmptwvvejsv/job_working_directory/000/6/galaxy_6.sh\n+galaxy.web_stack DEBUG 2023-04-26 11:36:48,977 [pN:main.1,p:213974,tN:Thread-9] server_name set to: main.1\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-26 11:36:54,124 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 213974\n+galaxy.jobs.runners.local DEBUG 2023-04-26 11:36:54,125 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmptwvvejsv/job_working_directory/000/6/galaxy_6.sh\n+\n+galaxy.jobs DEBUG 2023-04-26 11:36:55,753 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_eb946f9d-6a69-44d9-9e07-5cdfb2e8f303.dat to /tmp/tmptwvvejsv/files/e/b/9/dataset_eb946f9d-6a69-44d9-9e07-5cdfb2e8f303.dat\n+galaxy.jobs DEBUG 2023-04-26 11:36:55,753 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_203c65c0-5cdd-41b8-acf5-30686db81fac.dat to /tmp/tmptwvvejsv/files/2/0/3/dataset_203c65c0-5cdd-41b8-acf5-30686db81fac.dat\n+galaxy.jobs DEBUG 2023-04-26 11:36:55,754 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_f4c6a30a-8a47-406c-bab8-1af4180c5d8f.dat to /tmp/tmptwvvejsv/files/f/4/c/dataset_f4c6a30a-8a47-406c-bab8-1af4180c5d8f.dat\n+galaxy.jobs DEBUG 2023-04-26 11:36:55,754 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_58015c1b-4f2a-4004-aa4e-aafd157dff6a.dat to /tmp/tmptwvvejsv/files/5/8/0/dataset_58015c1b-4f2a-4004-aa4e-aafd157dff6a.dat\n+galaxy.jobs DEBUG 2023-04-26 11:36:55,754 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_6919cff3-b2ec-4755-8bd6-36005c576a20.dat to /tmp/tmptwvvejsv/files/6/9/1/dataset_6919cff3-b2ec-4755-8bd6-36005c576a20.dat\n+galaxy.model.metadata DEBUG 2023-04-26 11:36:55,789 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 9\n+galaxy.model.metadata DEBUG 2023-04-26 11:36:55,805 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 10\n+galaxy.model.metadata DEBUG 2023-04-26 11:36:55,821 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 11\n+galaxy.model.metadata DEBUG 2023-04-26 11:36:55,855 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 12\n+galaxy.model.metadata DEBUG 2023-04-26 11:36:55,889 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 13\n+\n+galaxy.jobs DEBUG 2023-04-26 11:36:56,762 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] job_wrapper.finish for job 6 executed (1014.947 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 2 test(s) executed passed.\n+FROGS_affiliation_filters (Test #1): passed\n+FROGS_affiliation_filters (Test #2): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/affi-stats.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/affi-stats.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1853 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpvm6ztn8s/galaxy-dev\n+Clonage dans \'/tmp/tmpvm6ztn8s/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'read-0] Job wrapper for Job [2] prepared (109.492 ms)\n+galaxy.tool_util.deps DEBUG 2023-04-26 11:49:32,617 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] Using dependency frogs version 4.1.0 of type conda\n+galaxy.tool_util.deps DEBUG 2023-04-26 11:49:32,617 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] Using dependency frogs version 4.1.0 of type conda\n+galaxy.jobs.command_factory INFO 2023-04-26 11:49:32,635 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] Built script [/tmp/tmpvm6ztn8s/job_working_directory/000/2/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; affiliation_stats.py --input-biom \'/tmp/tmpvm6ztn8s/files/e/9/2/dataset_e921953b-5d8b-4280-86cf-3a17cbd1b979.dat\' --output-file \'/tmp/tmpvm6ztn8s/job_working_directory/000/2/outputs/galaxy_dataset_f6c8fb33-f2bb-4d6a-9fb6-5e68a72509ac.dat\' --taxonomic-ranks Domain Phylum Class Order Family Genus Species --rarefaction-ranks Family Genus Species --multiple-tag \'blast_affiliations\' --tax-consensus-tag \'blast_taxonomy\' --identity-tag \'perc_identity\' --coverage-tag \'perc_query_coverage\']\n+galaxy.jobs.runners DEBUG 2023-04-26 11:49:32,725 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpvm6ztn8s/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpvm6ztn8s/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmpvm6ztn8s/job_working_directory/000/2/working/summary.html" ] ; then cp "/tmp/tmpvm6ztn8s/job_working_directory/000/2/working/summary.html" "/tmp/tmpvm6ztn8s/job_working_directory/000/2/outputs/galaxy_dataset_f6c8fb33-f2bb-4d6a-9fb6-5e68a72509ac.dat" ; fi; cd \'/tmp/tmpvm6ztn8s/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-26 11:49:32,749 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] (2) executing job script: /tmp/tmpvm6ztn8s/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-26 11:49:39,274 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 215091\n+galaxy.jobs.runners.local DEBUG 2023-04-26 11:49:39,274 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpvm6ztn8s/job_working_directory/000/2/galaxy_2.sh\n+galaxy.jobs DEBUG 2023-04-26 11:49:39,326 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpvm6ztn8s/job_working_directory/000/2/outputs/galaxy_dataset_f6c8fb33-f2bb-4d6a-9fb6-5e68a72509ac.dat to /tmp/tmpvm6ztn8s/files/f/6/c/dataset_f6c8fb33-f2bb-4d6a-9fb6-5e68a72509ac.dat\n+galaxy.model.metadata DEBUG 2023-04-26 11:49:39,407 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 2\n+galaxy.jobs DEBUG 2023-04-26 11:49:39,540 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 2 executed (230.314 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_affiliation_stats (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/affiliation_abundance.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/affiliation_abundance.biom Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +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": "2023-04-14T07:56:49", "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": 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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/biom_to_tsv.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biom_to_tsv.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1999 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp_alx6hte/galaxy-dev\n+Clonage dans \'/tmp/tmp_alx6hte/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; biom_to_tsv.py --input-biom \'/tmp/tmp_alx6hte/files/0/b/a/dataset_0baedaa9-8f4a-45da-8053-1ec4e7a1a1e0.dat\' --input-fasta \'/tmp/tmp_alx6hte/files/0/2/0/dataset_020940d9-f049-4320-a3d7-e944a3ccbd81.dat\' --output-tsv \'/tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_23178c6b-2652-4e59-bde8-755de1e116d4.dat\' --output-multi-affi \'/tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_172a24d1-ad2e-46fe-9fb0-afdcf88c2ff2.dat\']\n+\n+galaxy.jobs.runners DEBUG 2023-04-26 10:42:03,389 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmp_alx6hte/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp_alx6hte/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmp_alx6hte/job_working_directory/000/3/working/abundance.tsv" ] ; then cp "/tmp/tmp_alx6hte/job_working_directory/000/3/working/abundance.tsv" "/tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_23178c6b-2652-4e59-bde8-755de1e116d4.dat" ; fi; \n+if [ -f "/tmp/tmp_alx6hte/job_working_directory/000/3/working/multi_hits.tsv" ] ; then cp "/tmp/tmp_alx6hte/job_working_directory/000/3/working/multi_hits.tsv" "/tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_172a24d1-ad2e-46fe-9fb0-afdcf88c2ff2.dat" ; fi; cd \'/tmp/tmp_alx6hte/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-26 10:42:03,419 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] (3) executing job script: /tmp/tmp_alx6hte/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-26 10:42:11,015 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 207856\n+galaxy.jobs.runners.local DEBUG 2023-04-26 10:42:11,015 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmp_alx6hte/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-04-26 10:42:11,045 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_23178c6b-2652-4e59-bde8-755de1e116d4.dat to /tmp/tmp_alx6hte/files/2/3/1/dataset_23178c6b-2652-4e59-bde8-755de1e116d4.dat\n+galaxy.jobs DEBUG 2023-04-26 10:42:11,046 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_172a24d1-ad2e-46fe-9fb0-afdcf88c2ff2.dat to /tmp/tmp_alx6hte/files/1/7/2/dataset_172a24d1-ad2e-46fe-9fb0-afdcf88c2ff2.dat\n+galaxy.model.metadata DEBUG 2023-04-26 10:42:11,091 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.model.metadata DEBUG 2023-04-26 10:42:11,105 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.jobs DEBUG 2023-04-26 10:42:11,187 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] job_wrapper.finish for job 3 executed (148.539 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_biom_to_tsv (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/chaillou.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chaillou.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,509 @@\n+#taxonomy\tobservation_name\tobservation_sum\tDLT0.LOT08\tDLT0.LOT05\tDLT0.LOT03\tDLT0.LOT07\tDLT0.LOT06\tDLT0.LOT01\tDLT0.LOT04\tDLT0.LOT10\tMVT0.LOT05\tMVT0.LOT01\tMVT0.LOT06\tMVT0.LOT07\tMVT0.LOT03\tMVT0.LOT09\tMVT0.LOT08\tMVT0.LOT10\tBHT0.LOT01\tBHT0.LOT07\tBHT0.LOT06\tBHT0.LOT03\tBHT0.LOT10\tBHT0.LOT05\tBHT0.LOT04\tBHT0.LOT08\tVHT0.LOT02\tVHT0.LOT10\tVHT0.LOT03\tVHT0.LOT01\tVHT0.LOT08\tVHT0.LOT06\tVHT0.LOT07\tVHT0.LOT04\tSFT0.LOT08\tSFT0.LOT07\tSFT0.LOT06\tSFT0.LOT03\tSFT0.LOT02\tSFT0.LOT05\tSFT0.LOT04\tSFT0.LOT01\tFST0.LOT07\tFST0.LOT08\tFST0.LOT05\tFST0.LOT06\tFST0.LOT01\tFST0.LOT03\tFST0.LOT10\tFST0.LOT02\tFCT0.LOT06\tFCT0.LOT10\tFCT0.LOT05\tFCT0.LOT03\tFCT0.LOT08\tFCT0.LOT02\tFCT0.LOT07\tFCT0.LOT01\tCDT0.LOT10\tCDT0.LOT08\tCDT0.LOT05\tCDT0.LOT04\tCDT0.LOT06\tCDT0.LOT09\tCDT0.LOT07\tCDT0.LOT02\n+k__Bacteria;p__Tenericutes;c__Mollicutes;o__Mycoplasmatales;f__Mycoplasmataceae;g__Candidatus Lumbricincola;s__NA\totu_01778\t200\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t98\t23\t10\t16\t19\t4\t30\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__NA\totu_01838\t444\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9\t4\t0\t0\t4\t3\t3\t0\t5\t9\t2\t371\t4\t19\t11\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Dyella;s__Ginsengisoli\totu_01386\t453\t4\t0\t0\t7\t7\t9\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t3\t3\t2\t25\t2\t10\t6\t5\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t46\t21\t27\t108\t73\t33\t49\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Planococcaceae;g__Incertae Sedis;s__NA\totu_01835\t197\t13\t118\t6\t0\t0\t8\t2\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t2\t8\t4\t4\t5\t0\t3\t5\n+k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__NA\totu_01837\t538\t9\t9\t16\t0\t7\t10\t2\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t9\t6\t0\t0\t2\t7\t6\t3\t4\t0\t0\t3\t3\t0\t13\t0\t2\t52\t19\t8\t4\t12\t41\t32\t64\t5\t5\t64\t112\n+k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__Weissella;s__NA\totu_01832\t152\t0\t0\t0\t91\t0\t0\t0\t36\t0\t0\t0\t0\t6\t0\t0\t0\t4\t0\t0\t0\t0\t2\t0\t0\t0\t9\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces;s__NA\totu_01833\t225\t0\t0\t0\t0\t3\t26\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t4\t61\t8\t3\t6\t6\t3\t59\t0\t0\t10\t0\t3\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t17\t0\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Brevibacteriaceae;g__Brevibacterium;s__Marinum\totu_00156\t229\t0\t0\t0\t0\t0\t0\t0\t3\t24\t0\t25\t20\t13\t32\t20\t7\t0\t8\t0\t0\t0\t0\t3\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t7\t0\t0\t0\t0\t15\t0\t0\t0\t3\t23\t8\n+k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;g__Neisseria;s__Perflava\totu_01719\t203\t2\t3\t4\t17\t29\t16\t23\t15\t0\t0\t10\t8\t0\t0\t0\t0\t6\t3\t4\t10\t0\t2\t0\t0\t20\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t28\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia;s__Tabacinasalis\totu_00015\t405\t0\t1\t0\t0\t4\t0\t2\t0\t4\t0\t0\t0\t0\t0\t0\t0\t15\t9\t25\t17\t9\t5\t103\t18\t14\t8\t25\t28\t44\t19\t19\t26\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\n+k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Sakei\totu_00769\t53573\t15\t9\t126\t191\t115\t208\t37\t150\t4116\t4069\t937\t1516\t395\t1818\t6200\t8784\t461\t91\t106\t270\t102\t279\t166\t156\t114\t21\t175\t90\t46\t68\t73\t63\t141\t3563\t1494\t3678\t5081\t13\t965\t138\t65\t2256\t2171\t1996\t23\t71\t30\t31\t2\t202\t49\t30\t144\t83\t123\t133\t2\t2\t38\t60\t6\t3\t4\t9\n+k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Brevis\totu_00768\t438\t0\t0\t0\t0\t4\t0\t0\t7\t0\t0\t15\t0\t13\t24\t0\t0\t4\t25\t225\t20\t3\t3\t74\t19\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__'..b'eria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Family XI Incertae Sedis;g__Gemella;s__Haemolysans\totu_01748\t187\t5\t5\t6\t6\t9\t13\t3\t15\t0\t0\t0\t0\t8\t0\t0\t0\t0\t0\t0\t0\t0\t4\t5\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t75\t6\t0\t0\t3\t7\t5\t5\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Propionibacteriales;f__Propionibacteriaceae;g__Luteococcus;s__Japonicus\totu_01747\t2123\t25\t5\t173\t66\t25\t25\t2\t19\t4\t0\t10\t0\t6\t0\t6\t0\t8\t930\t63\t35\t83\t64\t312\t147\t3\t2\t10\t4\t0\t5\t3\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t7\t0\t13\t0\t0\t0\t5\t2\t10\t0\t4\t13\t0\t0\t14\t8\t3\t3\t0\t0\n+k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Rhodocyclales;f__Rhodocyclaceae;g__Methyloversatilis;s__Universalis\totu_01744\t111\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t31\t3\t0\t0\t0\t5\t2\t0\t6\t0\t0\t0\t0\t5\t5\t0\t0\t3\t2\t4\t0\t0\t4\t0\t0\t15\t3\t2\t0\t3\t13\n+k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Family XI Incertae Sedis;g__Tissierella;s__NA\totu_01740\t506\t2\t7\t8\t0\t20\t9\t2\t0\t40\t9\t80\t85\t19\t80\t15\t49\t0\t5\t4\t0\t0\t7\t10\t16\t4\t2\t4\t5\t0\t2\t3\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\n+k__Bacteria;p__Candidate division TM7;c__NA;o__NA;f__NA;g__NA;s__NA\totu_01741\t250\t0\t0\t0\t0\t0\t0\t0\t0\t4\t6\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t7\t0\t3\t0\t12\t10\t2\t195\t0\t3\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Terrigena\totu_00695\t602\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t17\t0\t0\t0\t0\t0\t0\t7\t0\t9\t6\t0\t0\t0\t13\t116\t180\t141\t8\t4\t10\t16\t0\t0\t4\t3\t5\t16\t7\t4\t2\t0\t11\t14\t0\t3\t3\t0\n+k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Hibernum\totu_00694\t416\t3\t0\t7\t0\t44\t26\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t83\t26\t0\t4\t29\t24\t92\t16\t0\t0\t41\t11\t0\t2\t0\t0\n+k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Cheniae\totu_00693\t430\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t3\t1\t0\t2\t0\t6\t1\t0\t0\t7\t69\t166\t97\t7\t10\t22\t11\t0\t0\t0\t0\t4\t8\t0\t3\t0\t0\t3\t5\t0\t0\t0\t0\n+k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Wautersiella;s__Falsenii\totu_00519\t2807\t3\t14\t0\t9\t8\t0\t26\t16\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t37\t7\t4\t0\t0\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t570\t92\t29\t5\t4\t1908\t66\n+k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Frigidarium\totu_00690\t3053\t0\t0\t2\t0\t7\t7\t0\t0\t0\t0\t0\t0\t0\t16\t0\t0\t11\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t109\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t7\t9\t3\t4\t3\t4\t5\t3\t98\t564\t18\t206\t43\t42\t459\t1319\t0\t3\t65\t36\t0\t0\t3\t3\n+k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Arsenicoxydans\totu_01184\t87\t0\t0\t0\t0\t4\t2\t0\t0\t10\t15\t20\t0\t19\t0\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\n+k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Empedobacter;s__NA\totu_00516\t378\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t8\t3\t4\t2\t306\t51\n+k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Syringae\totu_01187\t1532\t3\t14\t10\t110\t95\t30\t479\t12\t6\t6\t65\t8\t68\t0\t0\t0\t0\t0\t3\t16\t3\t0\t3\t3\t3\t16\t4\t3\t8\t187\t3\t3\t3\t7\t2\t9\t0\t0\t5\t0\t7\t36\t41\t37\t12\t7\t15\t13\t95\t6\t0\t7\t7\t7\t36\t11\t0\t0\t3\t3\t0\t2\t0\t0\n+k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Cedrina\totu_01182\t442\t2\t1\t5\t11\t8\t18\t73\t11\t0\t15\t10\t0\t29\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t11\t3\t12\t3\t0\t0\t3\t125\t11\t2\t4\t4\t0\t42\t7\t3\t0\t0\t8\t0\t3\t4\t4\n+k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Suncheonense\totu_00698\t333\t0\t0\t0\t3\t0\t3\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t2\t9\t6\t1\t0\t2\t7\t33\t0\t20\t0\t4\t3\t3\t2\t4\t0\t2\t8\t8\t0\t3\t0\t29\t101\t41\t3\t2\t7\t20\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/cluster_filters.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster_filters.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,2162 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpy2jxg5my/galaxy-dev\n+Clonage dans \'/tmp/tmpy2jxg5my/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'ectory/000/3/working/clusterFilters_abundance.biom" ] ; then cp "/tmp/tmp4i61keb6/job_working_directory/000/3/working/clusterFilters_abundance.biom" "/tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_b5364850-68bb-461a-b125-24ecdcdf39e6.dat" ; fi; \n+if [ -f "/tmp/tmp4i61keb6/job_working_directory/000/3/working/clusterFilters_sequences.fasta" ] ; then cp "/tmp/tmp4i61keb6/job_working_directory/000/3/working/clusterFilters_sequences.fasta" "/tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_75e83388-0c36-442d-9fc7-8c8fa84cf623.dat" ; fi; \n+if [ -f "/tmp/tmp4i61keb6/job_working_directory/000/3/working/excluded.tsv" ] ; then cp "/tmp/tmp4i61keb6/job_working_directory/000/3/working/excluded.tsv" "/tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_55fc8909-8bc8-4643-8782-c6bf1d2f8aed.dat" ; fi; \n+if [ -f "/tmp/tmp4i61keb6/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmp4i61keb6/job_working_directory/000/3/working/report.html" "/tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_a3ea094e-a03b-4dbc-9e34-3a3fc2305df8.dat" ; fi; cd \'/tmp/tmp4i61keb6/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-04 14:54:58,327 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmp4i61keb6/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 14:55:04,592 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 268056\n+galaxy.jobs.runners.local DEBUG 2023-05-04 14:55:04,592 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmp4i61keb6/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-05-04 14:55:04,624 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_b5364850-68bb-461a-b125-24ecdcdf39e6.dat to /tmp/tmp4i61keb6/files/b/5/3/dataset_b5364850-68bb-461a-b125-24ecdcdf39e6.dat\n+galaxy.jobs DEBUG 2023-05-04 14:55:04,625 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_75e83388-0c36-442d-9fc7-8c8fa84cf623.dat to /tmp/tmp4i61keb6/files/7/5/e/dataset_75e83388-0c36-442d-9fc7-8c8fa84cf623.dat\n+galaxy.jobs DEBUG 2023-05-04 14:55:04,625 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_55fc8909-8bc8-4643-8782-c6bf1d2f8aed.dat to /tmp/tmp4i61keb6/files/5/5/f/dataset_55fc8909-8bc8-4643-8782-c6bf1d2f8aed.dat\n+galaxy.jobs DEBUG 2023-05-04 14:55:04,625 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_a3ea094e-a03b-4dbc-9e34-3a3fc2305df8.dat to /tmp/tmp4i61keb6/files/a/3/e/dataset_a3ea094e-a03b-4dbc-9e34-3a3fc2305df8.dat\n+galaxy.model.metadata DEBUG 2023-05-04 14:55:04,651 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.model.metadata DEBUG 2023-05-04 14:55:04,661 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.model.metadata DEBUG 2023-05-04 14:55:04,669 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 5\n+galaxy.model.metadata DEBUG 2023-05-04 14:55:04,687 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 6\n+\n+galaxy.jobs DEBUG 2023-05-04 14:55:04,800 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (182.302 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_cluster_filters (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/cluster_stats.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster_stats.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,994 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpp7deq3n5/galaxy-dev\n+Clonage dans \'/tmp/tmpp7deq3n5/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vdar'..b'e DEBUG 2023-04-26 12:35:28,108 [pN:main.1,p:216363,tN:WSGI_0] Created 1 job(s) for tool FROGS_cluster_stats request (152.333 ms)\n+\n+galaxy.jobs.mapper DEBUG 2023-04-26 12:35:28,731 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: planemo_dest\n+galaxy.jobs.handler DEBUG 2023-04-26 12:35:28,755 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner\n+galaxy.jobs DEBUG 2023-04-26 12:35:28,885 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: planemo_dest)\n+galaxy.jobs DEBUG 2023-04-26 12:35:28,915 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmpp7deq3n5/job_working_directory/000/2\n+galaxy.jobs.runners DEBUG 2023-04-26 12:35:28,960 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] Job [2] queued (204.437 ms)\n+galaxy.jobs.handler INFO 2023-04-26 12:35:28,990 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n+galaxy.jobs DEBUG 2023-04-26 12:35:29,141 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] Job wrapper for Job [2] prepared (109.168 ms)\n+galaxy.tool_util.deps DEBUG 2023-04-26 12:35:29,143 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] Using dependency frogs version 4.1.0 of type conda\n+galaxy.tool_util.deps DEBUG 2023-04-26 12:35:29,143 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] Using dependency frogs version 4.1.0 of type conda\n+galaxy.jobs.command_factory INFO 2023-04-26 12:35:29,178 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] Built script [/tmp/tmpp7deq3n5/job_working_directory/000/2/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; cluster_stats.py --input-biom \'/tmp/tmpp7deq3n5/files/2/3/c/dataset_23cfcc4a-dba9-4b62-881a-962d04f6a0e2.dat\' --output-file \'/tmp/tmpp7deq3n5/job_working_directory/000/2/outputs/galaxy_dataset_06305cb4-045f-438d-8d0b-6dc224e89466.dat\']\n+\n+galaxy.jobs.runners DEBUG 2023-04-26 12:35:29,249 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpp7deq3n5/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpp7deq3n5/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmpp7deq3n5/job_working_directory/000/2/working/summary.html" ] ; then cp "/tmp/tmpp7deq3n5/job_working_directory/000/2/working/summary.html" "/tmp/tmpp7deq3n5/job_working_directory/000/2/outputs/galaxy_dataset_06305cb4-045f-438d-8d0b-6dc224e89466.dat" ; fi; cd \'/tmp/tmpp7deq3n5/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-26 12:35:29,264 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmpp7deq3n5/job_working_directory/000/2/galaxy_2.sh\n+galaxy.web_stack DEBUG 2023-04-26 12:35:29,279 [pN:main.1,p:216424,tN:Thread-9] server_name set to: main.1\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_cluster_stats (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/databases/frogs_picrust2_db/ITS_counts.txt.gz |
| b |
| Binary file test-data/databases/frogs_picrust2_db/ITS_counts.txt.gz has changed |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/databases/frogs_picrust2_db/ec_ITS_counts.txt.gz |
| b |
| Binary file test-data/databases/frogs_picrust2_db/ec_ITS_counts.txt.gz has changed |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/databases/frogs_picrust2_default_dir.loc --- a/test-data/databases/frogs_picrust2_default_dir.loc Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/databases/frogs_picrust2_default_dir.loc Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -34,4 +34,4 @@ #-rwxrwxr-x 1 vdarbot vdarbot 600048 avril 1 2021 pro_ref.tre # # EXAMPLE FOR TEST : -picrust2_default_dir_16S 16S ${__HERE__}/frogs_picrust2_db/prokaryotic/pro_ref/ +picrust2_default_dir_16S 16S ${__HERE__}/frogs_picrust2_db/prokaryotic/pro_ref/ ${__HERE__}/frogs_picrust2_db/prokaryiotic/pro_ref/16S_counts.txt.gz sepp \ No newline at end of file |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/deseq_peepro.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deseq_peepro.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,3082 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpyujvgsy0/galaxy-dev\n+Clonage dans \'/tmp/tmpyujvgsy0/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 36% (2247/6176)\rMise \xc3\xa0 jour des fichiers: 37% (2286/6176)\rMise \xc3\xa0 jour des fichiers: 38% (2347/6176)\rMise \xc3\xa0 jour des fichiers: 39% (2409/6176)\rMise \xc3\xa0 jour des fichiers: 40% (2471/6176)\rMise \xc3\xa0 jour des fichiers: 41% (2533/6176)\rMise \xc3\xa0 jour des fichiers: 42% (2594/6176)\rMise \xc3\xa0 jour des fichiers: 43% (2656/6176)\rMise \xc3\xa0 jour des fichiers: 44% (2718/6176)\rMise \xc3\xa0 jour des fichiers: 45% (2780/6176)\rMise \xc3\xa0 jour des fichiers: 46% (2841/6176)\rMise \xc3\xa0 jour des fichiers: 47% (2903/6176)\rMise \xc3\xa0 jour des fichiers: 48% (2965/6176)\rMise \xc3\xa0 jour des fichiers: 49% (3027/6176)\rMise \xc3\xa0 jour des fichiers: 50% (3088/6176)\rMise \xc3\xa0 jour des fichiers: 51% (3150/6176)\rMise \xc3\xa0 jour des fichiers: 52% (3212/6176)\rMise \xc3\xa0 jour des fichiers: 53% (3274/6176)\rMise \xc3\xa0 jour des fichiers: 54% (3336/6176)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6176)\rMise \xc3\xa0 jour des fichiers: 56% (3459/6176)\rMise \xc3\xa0 jour des fichiers: 57% (3521/6176)\rMise \xc3\xa0 jour des fichiers: 58% (3583/6176)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6176)\rMise \xc3\xa0 jour des fichiers: 60% (3706/6176)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6176)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6176)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6176)\rMise \xc3\xa0 jour des fichiers: 64% (3953/6176)\rMise \xc3\xa0 jour des fichiers: 65% (4015/6176)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6176)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6176)\rMise \xc3\xa0 jour des fichiers: 68% (4200/6176)\rMise \xc3\xa0 jour des fichiers: 69% (4262/6176)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6176)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6176)\rMise \xc3\xa0 jour des fichiers: 72% (4447/6176)\rMise \xc3\xa0 jour des fichiers: 73% (4509/6176)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6176)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6176)\rMise \xc3\xa0 jour des fichiers: 76% (4694/6176)\rMise \xc3\xa0 jour des fichiers: 77% (4756/6176)\rMise \xc3\xa0 jour des fichiers: 78% (4818/6176)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6176)\rMise \xc3\xa0 jour des fichiers: 80% (4941/6176)\rMise \xc3\xa0 jour des fichiers: 81% (5003/6176)\rMise \xc3\xa0 jour des fichiers: 82% (5065/6176)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6176)\rMise \xc3\xa0 jour des fichiers: 84% (5188/6176)\rMise \xc3\xa0 jour des fichiers: 85% (5250/6176)\rMise \xc3\xa0 jour des fichiers: 86% (5312/6176)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6176)\rMise \xc3\xa0 jour des fichiers: 88% (5435/6176)\rMise \xc3\xa0 jour des fichiers: 89% (5497/6176)\rMise \xc3\xa0 jour des fichiers: 90% (5559/6176)\rMise \xc3\xa0 jour des fichiers: 91% (5621/6176)\rMise \xc3\xa0 jour des fichiers: 92% (5682/6176)\rMise \xc3\xa0 jour des fichiers: 93% (5744/6176)\rMise \xc3\xa0 jour des fichiers: 94% (5806/6176)\rMise \xc3\xa0 jour des fichiers: 95% (5868/6176)\rMise \xc3\xa0 jour des fichiers: 96% (5929/6176)\rMise \xc3\xa0 jour des fichiers: 97% (5991/6176)\rMise \xc3\xa0 jour des fichiers: 98% (6053/6176)\rMise \xc3\xa0 jour des fichiers: 99% (6115/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n'..b' conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; deseq2_preprocess.py --analysis \'ASV\' --data \'/tmp/tmpo3qialyz/files/4/d/0/dataset_4d055b7e-a677-4b2e-a94d-84315f492786.dat\' --out-Rdata \'/tmp/tmpo3qialyz/job_working_directory/000/2/outputs/galaxy_dataset_d6606cce-2817-40a6-b852-b36cda5f4b83.dat\' --var \'EnvType\']\n+galaxy.jobs.runners DEBUG 2023-05-08 22:41:21,914 [pN:main.1,p:15544,tN:LocalRunner.work_thread-2] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpo3qialyz/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpo3qialyz/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmpo3qialyz/job_working_directory/000/2/working/asv_dds.Rdata" ] ; then cp "/tmp/tmpo3qialyz/job_working_directory/000/2/working/asv_dds.Rdata" "/tmp/tmpo3qialyz/job_working_directory/000/2/outputs/galaxy_dataset_d6606cce-2817-40a6-b852-b36cda5f4b83.dat" ; fi; cd \'/tmp/tmpo3qialyz/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-08 22:41:21,925 [pN:main.1,p:15544,tN:LocalRunner.work_thread-2] (2) executing job script: /tmp/tmpo3qialyz/job_working_directory/000/2/galaxy_2.sh\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/deseq_visu.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deseq_visu.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,3098 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp7m6i1hb3/galaxy-dev\n+Clonage dans \'/tmp/tmp7m6i1hb3/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'OUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-be12999d9200037f8d53a21d6bb1a9a3530bc477fb4b35557938fb47596c6182\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-be12999d9200037f8d53a21d6bb1a9a3530bc477fb4b35557938fb47596c6182\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-be12999d9200037f8d53a21d6bb1a9a3530bc477fb4b35557938fb47596c6182\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; deseq2_visualisation.py --analysis \'ASV\' --abundanceData \'/tmp/tmpyx331lwu/files/8/5/1/dataset_851a201e-e1f3-4b5e-9a79-4bc7f915445a.dat\' --dds \'/tmp/tmpyx331lwu/files/d/1/7/dataset_d17130c9-7af8-48c6-b974-117aa3b44993.dat\' --var \'EnvType\' --mod1 \'BoeufHache\' --mod2 \'SaumonFume\' --padj 0.05 --html \'/tmp/tmpyx331lwu/job_working_directory/000/3/outputs/galaxy_dataset_092b5619-cb69-4cfa-b0fd-001ed2fc3e8b.dat\']\n+\n+galaxy.jobs.runners DEBUG 2023-05-08 22:38:59,172 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpyx331lwu/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpyx331lwu/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmpyx331lwu/job_working_directory/000/3/working/report.nb.html" ] ; then cp "/tmp/tmpyx331lwu/job_working_directory/000/3/working/report.nb.html" "/tmp/tmpyx331lwu/job_working_directory/000/3/outputs/galaxy_dataset_092b5619-cb69-4cfa-b0fd-001ed2fc3e8b.dat" ; fi; cd \'/tmp/tmpyx331lwu/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-08 22:38:59,183 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmpyx331lwu/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-08 22:39:22,776 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 14485\n+galaxy.jobs.runners.local DEBUG 2023-05-08 22:39:22,776 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpyx331lwu/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-05-08 22:39:22,818 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpyx331lwu/job_working_directory/000/3/outputs/galaxy_dataset_092b5619-cb69-4cfa-b0fd-001ed2fc3e8b.dat to /tmp/tmpyx331lwu/files/0/9/2/dataset_092b5619-cb69-4cfa-b0fd-001ed2fc3e8b.dat\n+galaxy.model.metadata DEBUG 2023-05-08 22:39:22,854 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.jobs DEBUG 2023-05-08 22:39:22,925 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (113.531 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGSSTAT_DESeq2_Visualisation (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/deseq_visu_2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deseq_visu_2.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,3068 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpbk65hbs9/galaxy-dev\n+Clonage dans \'/tmp/tmpbk65hbs9/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'emjm7d3ebaca4c817601cecc54647923eb4cf260b28adaacb06a74b65ed18ce0abac/__r-base@4.1.2\'\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-26 08:41:12,915 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda install -y --strict-channel-priority --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmplt0jfs0b/deps/_cache/15115056 --file /tmp/tmplt0jfs0b/tmp/jobdepsut_nemjm7d3ebaca4c817601cecc54647923eb4cf260b28adaacb06a74b65ed18ce0abac/__r-base@4.1.2\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-26 08:41:18,923 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda install -y --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmplt0jfs0b/deps/_cache/15115056 --file /tmp/tmplt0jfs0b/tmp/jobdepsut_nemjm7d3ebaca4c817601cecc54647923eb4cf260b28adaacb06a74b65ed18ce0abac/__r-base@4.1.2\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-26 08:41:25,333 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda clean --tarballs -y\n+\n+galaxy.jobs.runners ERROR 2023-04-26 08:41:26,387 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] (3) Failure preparing job\n+Traceback (most recent call last):\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 262, in prepare_job\n+ job_wrapper.runner_command_line = self.build_command_line(\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 301, in build_command_line\n+ return build_command(\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n+ __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n+ if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n+ self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n+ return self.app.toolbox.dependency_manager.dependency_shell_commands(\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n+ self.build_cache(requirements, **kwds)\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n+ self.build_environment()\n+ File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n+ raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n+galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n+galaxy.jobs DEBUG 2023-04-26 08:41:26,401 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] fail(): Moved /tmp/tmplt0jfs0b/job_working_directory/000/3/outputs/galaxy_dataset_08b8588d-8f12-440b-af76-49f93442c1fb.dat to /tmp/tmplt0jfs0b/files/0/8/b/dataset_08b8588d-8f12-440b-af76-49f93442c1fb.dat\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGSSTAT_DESeq2_Visualisation (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/filters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filters.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,74921 @@\n+#comment\tseed_id\tobservation_name\tobservation_sum\t01_subsample\t02_subsample\t03_subsample\n+no data\t01_54\tCluster_1\t1561\t512\t515\t534\n+no data\t01_92546\tCluster_2\t1556\t508\t512\t536\n+no data\t01_59\tCluster_3\t1550\t514\t502\t534\n+no data\t01_81\tCluster_4\t1564\t503\t515\t546\n+no data\t01_25\tCluster_5\t1544\t521\t550\t473\n+no data\t01_74803\tCluster_6\t1631\t512\t574\t545\n+no data\t01_38\tCluster_7\t1533\t509\t492\t532\n+no data\t01_90\tCluster_8\t1523\t526\t484\t513\n+no data\t01_97858\tCluster_9\t1571\t526\t494\t551\n+no data\t01_259\tCluster_10\t1519\t511\t529\t479\n+no data\t01_90304\tCluster_11\t1505\t469\t520\t516\n+no data\t01_22\tCluster_12\t1610\t542\t531\t537\n+no data\t01_94\tCluster_13\t1576\t527\t543\t506\n+no data\t01_76\tCluster_14\t1534\t495\t511\t528\n+no data\t01_60934\tCluster_15\t1565\t508\t527\t530\n+no data\t01_85419\tCluster_16\t1564\t535\t512\t517\n+no data\t01_54589\tCluster_17\t1502\t508\t504\t490\n+no data\t01_40\tCluster_18\t1516\t490\t531\t495\n+no data\t01_66\tCluster_19\t1465\t499\t490\t476\n+no data\t01_51488\tCluster_20\t1518\t526\t498\t494\n+no data\t01_54706\tCluster_21\t1520\t514\t507\t499\n+no data\t01_155\tCluster_22\t1523\t504\t483\t536\n+no data\t01_101\tCluster_23\t1500\t510\t472\t518\n+no data\t01_10\tCluster_24\t1530\t515\t500\t515\n+no data\t01_97506\tCluster_25\t1530\t491\t506\t533\n+no data\t01_151\tCluster_26\t1516\t494\t513\t509\n+no data\t01_108\tCluster_27\t1573\t536\t490\t547\n+no data\t01_71661\tCluster_28\t1545\t545\t507\t493\n+no data\t01_201\tCluster_29\t1537\t498\t515\t524\n+no data\t01_66997\tCluster_30\t1565\t525\t530\t510\n+no data\t01_190\tCluster_31\t1530\t511\t550\t469\n+no data\t01_96725\tCluster_32\t1546\t509\t522\t515\n+no data\t01_103\tCluster_33\t1597\t508\t544\t545\n+no data\t01_67\tCluster_34\t1499\t480\t504\t515\n+no data\t01_76743\tCluster_35\t1507\t525\t499\t483\n+no data\t01_222\tCluster_36\t1591\t536\t534\t521\n+no data\t01_19\tCluster_37\t1576\t499\t538\t539\n+no data\t01_264\tCluster_38\t1525\t473\t528\t524\n+no data\t01_91964\tCluster_39\t1512\t518\t508\t486\n+no data\t01_67210\tCluster_40\t1572\t534\t524\t514\n+no data\t01_91819\tCluster_41\t1529\t518\t517\t494\n+no data\t01_69140\tCluster_42\t1580\t540\t524\t516\n+no data\t01_65\tCluster_43\t1516\t497\t505\t514\n+no data\t01_85242\tCluster_44\t1531\t511\t518\t502\n+no data\t01_60\tCluster_45\t1584\t530\t513\t541\n+no data\t01_91485\tCluster_46\t1535\t507\t530\t498\n+no data\t01_410\tCluster_47\t1532\t499\t513\t520\n+no data\t01_86\tCluster_48\t544\t177\t203\t164\n+no data\t01_88865\tCluster_49\t245\t80\t83\t82\n+FROGS_combined\t01_71070_FROGS_combined\tCluster_50_FROGS_combined\t1597\t526\t518\t553\n+no data\t01_210\tCluster_51\t83\t22\t28\t33\n+no data\t01_1953\tCluster_52\t59\t26\t16\t17\n+no data\t01_4641\tCluster_53\t45\t17\t12\t16\n+no data\t01_3904\tCluster_54\t37\t9\t13\t15\n+no data\t01_67609\tCluster_55\t10\t2\t6\t2\n+no data\t01_97159\tCluster_56\t3\t1\t1\t1\n+FROGS_combined\t01_10004_FROGS_combined\tCluster_57_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10005_FROGS_combined\tCluster_58_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10008_FROGS_combined\tCluster_59_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10010_FROGS_combined\tCluster_60_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10018_FROGS_combined\tCluster_61_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10020_FROGS_combined\tCluster_62_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10029_FROGS_combined\tCluster_63_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10031_FROGS_combined\tCluster_64_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10032_FROGS_combined\tCluster_65_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10038_FROGS_combined\tCluster_66_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10039_FROGS_combined\tCluster_67_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_1003_FROGS_combined\tCluster_68_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10041_FROGS_combined\tCluster_69_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10043_FROGS_combined\tCluster_70_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10044_FROGS_combined\tCluster_71_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10046_FROGS_combined\tCluster_72_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10047_FROGS_combined\tCluster_73_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10051_FROGS_combined\tCluster_74_FROGS_combined\t1\t1\t0\t0\n+FROGS_combined\t01_10052_FROGS_combined\tCluster_75_FROGS_combined\t1\t1\t0\t0\n+'..b'mbined\tCluster_74870_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_98143_FROGS_combined\tCluster_74871_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_98144_FROGS_combined\tCluster_74872_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_98146_FROGS_combined\tCluster_74873_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_98148_FROGS_combined\tCluster_74874_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9814_FROGS_combined\tCluster_74875_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_98159_FROGS_combined\tCluster_74876_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_98161_FROGS_combined\tCluster_74877_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9820_FROGS_combined\tCluster_74878_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9823_FROGS_combined\tCluster_74879_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9824_FROGS_combined\tCluster_74880_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9826_FROGS_combined\tCluster_74881_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9830_FROGS_combined\tCluster_74882_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9834_FROGS_combined\tCluster_74883_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9835_FROGS_combined\tCluster_74884_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9841_FROGS_combined\tCluster_74885_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9848_FROGS_combined\tCluster_74886_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9862_FROGS_combined\tCluster_74887_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9866_FROGS_combined\tCluster_74888_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9872_FROGS_combined\tCluster_74889_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9874_FROGS_combined\tCluster_74890_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9880_FROGS_combined\tCluster_74891_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9882_FROGS_combined\tCluster_74892_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9885_FROGS_combined\tCluster_74893_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9886_FROGS_combined\tCluster_74894_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9895_FROGS_combined\tCluster_74895_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9900_FROGS_combined\tCluster_74896_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9904_FROGS_combined\tCluster_74897_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9911_FROGS_combined\tCluster_74898_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9913_FROGS_combined\tCluster_74899_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9917_FROGS_combined\tCluster_74900_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9923_FROGS_combined\tCluster_74901_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9925_FROGS_combined\tCluster_74902_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9927_FROGS_combined\tCluster_74903_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_992_FROGS_combined\tCluster_74904_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9930_FROGS_combined\tCluster_74905_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9935_FROGS_combined\tCluster_74906_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9939_FROGS_combined\tCluster_74907_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_994_FROGS_combined\tCluster_74908_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9950_FROGS_combined\tCluster_74909_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9955_FROGS_combined\tCluster_74910_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9958_FROGS_combined\tCluster_74911_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9960_FROGS_combined\tCluster_74912_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9968_FROGS_combined\tCluster_74913_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9973_FROGS_combined\tCluster_74914_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9974_FROGS_combined\tCluster_74915_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9975_FROGS_combined\tCluster_74916_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9978_FROGS_combined\tCluster_74917_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9981_FROGS_combined\tCluster_74918_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9985_FROGS_combined\tCluster_74919_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9986_FROGS_combined\tCluster_74920_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_9999_FROGS_combined\tCluster_74921_FROGS_combined\t1\t0\t0\t1\n+FROGS_combined\t03_999_FROGS_combined\tCluster_74922_FROGS_combined\t1\t0\t0\t1\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfun --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfun Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' +git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true +git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc.tsv Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,11 @@ +#blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length seed_id observation_name observation_sum 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 +Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Oscillibacter;unknown species HQ785790.1.1449 100.0 100.0 0.0 403 M02944:219:000000000-B6TML:1:1102:9099:12653 Cluster_1 243473 233 1305 1338 1495 598 348 395 2874 7160 25 6914 9935 15 5834 3173 2776 3139 3049 7358 3516 4819 89 768 158 205 63 204 72 4631 496 2803 1551 6231 1344 9366 7343 4415 1522 7335 5823 3464 5127 225 1457 465 425 578 445 271 3593 3408 11535 45 12854 4777 5248 8442 12633 5259 13924 9587 10678 8315 +Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Multi-affiliation multi-subject 100.0 100.0 0.0 426 M02944:219:000000000-B6TML:1:1102:5178:4304 Cluster_2 217042 398 1359 2720 3700 2166 548 2786 713 2851 3309 3405 2875 1547 4031 9781 4123 1986 1190 1897 3920 5053 719 2183 280 986 970 1069 165 5551 3806 9913 7876 3738 11421 5678 2313 3986 9454 1609 2163 1639 756 1408 3566 1938 1035 2739 3614 1705 4964 5597 3497 6844 6126 3565 3108 896 4885 3192 8005 4534 5326 3865 +Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;Eisenbergiella;unknown species multi-subject 99.75 100.0 0.0 401 M02944:219:000000000-B6TML:1:1102:25966:6564 Cluster_3 185228 842 1141 1162 1488 659 566 1822 1699 2709 2202 2769 1114 1806 2064 6555 5217 5265 20805 2725 6685 7949 4948 88 1572 3705 1466 1032 723 1617 1202 1266 2912 2020 842 2817 1706 4674 1892 1659 937 1226 2938 160 89 824 87 186 326 1490 2422 756 1769 1907 2959 1271 1191 5254 7123 12594 4108 7510 8390 6326 +Bacteria;Firmicutes;Clostridia;Clostridia vadinBB60 group;unknown family;unknown genus;unknown species GQ175436.1.1437 99.5 100.0 0.0 404 M02944:219:000000000-B6TML:1:1102:23486:4021 Cluster_4 113087 2280 676 1035 2733 1837 698 1118 17 30 7 28 10 7 5 2944 1092 1795 590 3034 913 1707 1311 1733 600 1012 393 1199 2003 5 1 4 41 6 9 18 6823 329 2262 7796 12328 7331 7710 2401 1809 1770 1331 8170 1071 845 9 10 10 30 18 12 17 3928 3449 1847 4401 2077 2536 1876 +Bacteria;Firmicutes;Clostridia;Clostridia vadinBB60 group;unknown family;unknown genus;gut metagenome CDZB01072114.19608.21101 99.01 100.0 0.0 404 M02944:219:000000000-B6TML:1:1114:7531:19741 Cluster_5 104097 14 16 18 11 49 60 44 227 7500 22187 17526 19048 11102 20612 0 0 94 77 0 2 39 1 1 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 2 1 5369 1 3 2 33 2 2 3 27 8 10 +Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species DQ456366.1.1454 100.0 100.0 0.0 401 M02944:219:000000000-B6TML:1:1102:12645:4964 Cluster_6 102648 3028 7155 7405 9799 4656 1759 2455 51 39 37 78 47 13 19 2668 2347 288 558 432 900 5393 1507 2756 3386 3607 2661 4604 2104 5 7 3 4 4 2 11 108 5 4 21 13 87 16 5819 610 1198 5003 6177 2239 5907 38 596 27 86 18 35 18 224 1154 2566 389 83 163 256 +Bacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Multi-affiliation multi-subject 100.0 100.0 0.0 402 M02944:219:000000000-B6TML:1:1102:25163:5970 Cluster_7 100935 1148 1468 1044 1396 552 612 1846 13 13 15 35 9 24 21 2666 728 4407 3321 9514 1597 2373 969 372 97 697 42 836 399 1 2 6 8 6 7 4 5184 1406 2379 1471 4165 2616 473 1876 1757 3013 1270 2225 1771 3610 41 20 32 76 34 22 11 15266 4545 2580 2981 1403 638 3822 +Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp. multi-subject 99.5 100.0 0.0 404 M02944:219:000000000-B6TML:1:2118:16716:22396 Cluster_10 52413 2 4 7 19 4 7 7 290 369 3062 948 1596 231 1769 824 152 165 190 350 57 344 1 0 1 9 0 0 0 1634 963 3978 1161 398 15 1884 278 2075 333 629 1036 1579 4682 26 0 0 0 1 0 1 717 1213 4106 167 1136 1806 513 58 995 5041 610 160 3817 993 +Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species multi-subject 99.75 100.0 0.0 401 M02944:219:000000000-B6TML:1:1102:10609:2758 Cluster_11 49142 762 2421 812 1403 859 973 2543 107 152 233 186 639 85 364 177 222 525 249 311 947 411 355 114 736 720 257 940 314 358 720 41 22 727 348 205 49 18 176 152 31 48 376 1781 6486 2989 4222 3170 3299 2726 167 434 198 453 281 304 295 266 269 274 179 61 134 66 +Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Multi-affiliation multi-subject 100.0 100.0 0.0 404 M02944:219:000000000-B6TML:1:1102:14141:20035 Cluster_12 53185 175 168 505 260 140 338 316 1055 491 4500 1006 448 1647 1191 323 682 771 510 839 1232 708 11 198 26 224 32 50 11 559 263 281 2647 71 526 875 1022 612 103 269 371 382 271 358 869 296 348 586 368 627 1384 1800 613 3138 1499 978 3175 1861 1951 1888 1655 1355 911 1416 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_function.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_function.biom Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +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": "2018-10-04T16:37:49", "rows": [{"id": "Cluster_1", "metadata": {"blast_taxonomy": ["Bacteria", "Firmicutes", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Oscillibacter", "unknown species"], "seed_id": "M02944:219:000000000-B6TML:1:1102:9099:12653", "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Bacteria", "Firmicutes", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Oscillibacter", "unknown species"], "evalue": "0.0", "aln_length": 403, "perc_query_coverage": 100.0, "subject": "HQ785790.1.1449"}], "NSTI": "0.033280000000000004", "picrust2_affiliations": "Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;Oscillibacter_sp.", "blast_picrust_ref_perc_identity": "99.26", "blast_picrust_ref_perc_query_coverage": "100.0"}}, {"id": "Cluster_2", "metadata": {"blast_taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Multi-affiliation"], "seed_id": "M02944:219:000000000-B6TML:1:1102:5178:4304", "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "LXJJ02000010.3161.4631"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli S88"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CU928161.4443202.4444743"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CU651637.2709763.2711303"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli O157:H7"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP033605.4932246.4933797"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Shigella flexneri"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP033510.2312050.2313603"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli O32:H37 str. P4"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "AJQW01000057.1.1280"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP032515.4680373.4681924"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP032265.2506313.2507866"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli DEC8C"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "AIGH01000069.160053.161583"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "unknown species"], "eval'..b' [5, 23, 3386], [5, 24, 3607], [5, 25, 2661], [5, 26, 4604], [5, 27, 2104], [5, 28, 5], [5, 29, 7], [5, 30, 3], [5, 31, 4], [5, 32, 4], [5, 33, 2], [5, 34, 11], [5, 35, 108], [5, 36, 5], [5, 37, 4], [5, 38, 21], [5, 39, 13], [5, 40, 87], [5, 41, 16], [5, 42, 5819], [5, 43, 610], [5, 44, 1198], [5, 45, 5003], [5, 46, 6177], [5, 47, 2239], [5, 48, 5907], [5, 49, 38], [5, 50, 596], [5, 51, 27], [5, 52, 86], [5, 53, 18], [5, 54, 35], [5, 55, 18], [5, 56, 224], [5, 57, 1154], [5, 58, 2566], [5, 59, 389], [5, 60, 83], [5, 61, 163], [5, 62, 256], [6, 0, 1148], [6, 1, 1468], [6, 2, 1044], [6, 3, 1396], [6, 4, 552], [6, 5, 612], [6, 6, 1846], [6, 7, 13], [6, 8, 13], [6, 9, 15], [6, 10, 35], [6, 11, 9], [6, 12, 24], [6, 13, 21], [6, 14, 2666], [6, 15, 728], [6, 16, 4407], [6, 17, 3321], [6, 18, 9514], [6, 19, 1597], [6, 20, 2373], [6, 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[9, 57, 1951], [9, 58, 1888], [9, 59, 1655], [9, 60, 1355], [9, 61, 911], [9, 62, 1416]], "shape": [10, 63], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_function.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_function.fasta Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,20 @@ +>Cluster_1 +TGGGGAATATTGGGCAATGGACGCAAGTCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCAGGGAACAGTAGAAGAGGGTACCTGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGCCGGCAAGTCAGATGTGAAATCTGGAGGCTTAACCTCCAAACTGCATTTGAAACTGTTGGTCTTGAGTACCGGAGAGGTTATCGGAATTCCTTGTGTAGCGGTGAAATGCGTAGATATAAGGAAGAACACCAGTGGCGAAGGCGGATAACTGGACGGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAAC +>Cluster_2 +TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAAC +>Cluster_3 +TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGTGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGAGTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAAGCAAGTCTGGAGTGAAAACCCGGGGCTTAACCCCGGGATTGCTTTGGAAACTGTTTAACTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC +>Cluster_4 +TGGGGAATATTGGGCAATGGAGGCAACTCTGACCCAGCAACGCCGCGTGAATGATGAAGGTCTTCGGATTGTAAAGTTCTGTGACGGGGGACGAACACAATGACGGTACCCCGATAGCAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTAGCAAGTTGGCAGCGTAATTCCGGGGCTCAACTCCGGCGCTACTGCCAAAACTGTTGAACTTGAGTGCAGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACATCGGTGGCGAAGGCGACTTACTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAAC +>Cluster_5 +TGGGGAATATTGGGCAATGGAGGGAACTCTGACCCAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATTGTAAAACTCTTTAAGCGGGGACGAAGAAAGTGACTGTACCCGCAGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTGCCAAGTTGGCAGCGTAATTCCGTGGCTTAACCGCGGAACTACTGCCAAAACTGGTAGGCTTGAGTGCGGCAGGGGTATGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAAGCGACATACTGGGCCGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAAC +>Cluster_6 +TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAACTGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGTGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTAGATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC +>Cluster_7 +TAGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGGAGGATGACACTTTTCGGAGCGTAAACTCCTTTTCTTAGGGAAGAATTCTGACGGTACCTAAGGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGATTATCAAGTCTCTTGTGAAATCTAATGGCTTAACCATTAAACTGCTTGGGAAACTGATAGTCTAGAGTGAGGGAGAGGCAGATGGAATTGGTGGTGTAGGGGTAAAATCCGTAGATATCACCAAGAATACCCATTGCGAAGGCGATCTGCTGGAACTCAACTGACGCTAAGGCGCGAAAGCGTGGGGAGCAAAC +>Cluster_10 +TGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGATGAAGGCTTTCGGGTTGTAAACTTCTTTTATTCGGGACGAAGCAAGTGACGGTACCGAATGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGACTGCAAGTCAGATGTGAAAACTATGGGCTCAACCCATAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCATAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC +>Cluster_11 +TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATAGGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTTTATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC +>Cluster_12 +TGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCGGGGACGAAACAAATGACGGTACCCGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_function.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_function.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1162 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp4273t1nv/galaxy-dev\n+Clonage dans \'/tmp/tmp4273t1nv/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n+\n+[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n+[notice] To update, run: pip install --upgrade pip\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) ('..b'b_working_directory/000/5/galaxy_5.sh\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,325 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_db725e94-3a7d-41ec-adaa-1244567389ce.dat to /tmp/tmp4273t1nv/files/d/b/7/dataset_db725e94-3a7d-41ec-adaa-1244567389ce.dat\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,330 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_2122339b-71c0-4022-b021-90db95a8c0e1.dat to /tmp/tmp4273t1nv/files/2/1/2/dataset_2122339b-71c0-4022-b021-90db95a8c0e1.dat\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,332 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_6336af35-9eb4-4d0c-8d57-8003aadbd4bf.dat to /tmp/tmp4273t1nv/files/6/3/3/dataset_6336af35-9eb4-4d0c-8d57-8003aadbd4bf.dat\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,334 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_9caba39b-ecaa-41a8-9a90-0a0cb84b1f98.dat to /tmp/tmp4273t1nv/files/9/c/a/dataset_9caba39b-ecaa-41a8-9a90-0a0cb84b1f98.dat\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,336 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_74c9f54d-b000-4304-afa4-acbb8875462d.dat to /tmp/tmp4273t1nv/files/7/4/c/dataset_74c9f54d-b000-4304-afa4-acbb8875462d.dat\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,340 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_7fc1784c-aa05-4115-a182-e6d08ac9cd05.dat to /tmp/tmp4273t1nv/files/7/f/c/dataset_7fc1784c-aa05-4115-a182-e6d08ac9cd05.dat\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,344 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_5777a52e-e1f9-483b-bcdc-b52d82e4ef3a.dat to /tmp/tmp4273t1nv/files/5/7/7/dataset_5777a52e-e1f9-483b-bcdc-b52d82e4ef3a.dat\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,347 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_c0387e32-e757-49fd-a2bf-56cfaf491599.dat to /tmp/tmp4273t1nv/files/c/0/3/dataset_c0387e32-e757-49fd-a2bf-56cfaf491599.dat\n+galaxy.model.metadata DEBUG 2023-05-19 16:19:37,417 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 5\n+galaxy.model.metadata DEBUG 2023-05-19 16:19:37,430 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 6\n+galaxy.model.metadata DEBUG 2023-05-19 16:19:37,442 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 7\n+galaxy.model.metadata DEBUG 2023-05-19 16:19:37,453 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 8\n+galaxy.model.metadata DEBUG 2023-05-19 16:19:37,469 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 9\n+galaxy.model.metadata DEBUG 2023-05-19 16:19:37,483 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 10\n+galaxy.model.metadata DEBUG 2023-05-19 16:19:37,496 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 11\n+galaxy.model.metadata DEBUG 2023-05-19 16:19:37,513 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 12\n+galaxy.jobs DEBUG 2023-05-19 16:19:37,721 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 5 executed (422.874 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGSFUNC_step3_functions (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_pathways_predictions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_pathways_predictions.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,11 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t0.0\t0.0\t1.018181818181818\t0.0\t0.0\t1.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t1.5\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0909090909090908\t1.0909090909090908\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0909090909090908\t1.024390243902439\t0.0\t0.0\t1.0\t1.1428571428571428\n+Cluster_6\t1.0769230769230769\t0.0\t0.0\t1.1612903225806452\t0.0\t0.0\t1.180327868852459\t1.2000000000000002\t1.1666666666666667\t0.0\t0.0\t0.0\t1.1764705882352942\t1.0909090909090908\t1.0\t1.0\t0.0\t1.2307692307692308\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.3333333333333333\t1.1764705882352942\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0769230769230769\t1.0\t1.2\t1.2307692307692308\t0.0\t0.0\t1.0769230769230769\t0.0\t0.0\t0.0\t1.105263157894737\t1.3333333333333333\t0.0\t0.0\t0.0\t0.0\t0.0\t1.3333333333333333\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t1.0588235294117647\t0.0\t1.0\t1.25\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.1428571428571428\t0.0\t0.0\t1.0769230769230769\t1.0\t1.3333333333333333\t1.1764705882352942\t1.1764705882352942\t1.0645161290322582\t0.0\t0.0\t0.0\t1.0769230769230769\t0.0\t0.0\t0.0\t0.0\t0.0\t1.3333333333333333\t0.0\t0.0\t1.2413793103448276\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.153846153846154\t0.0\t0.0\t1.1111111111111112\t1.1428571428571428\t1.0\t0.0\t1.3333333333333333\t0.0\t1.0\t1.0\t1.1111111111111112\t0.0\t0.0\t1.1428571428571428\t0.0\t1.0\t0.0\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.2\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.4545454545454546\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.2307692307692308\t0.0\t1.4545454545454546\t1.2\t1.1428571428571428\t1.2\t0.0\t1.411764705882353\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1748251748251748\t0.0\t1.0\t1.105263157894737\t1.2000000000000002\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t1.3333333333333333\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.2\t1.2\t1.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0909090909090908\t1.05\t1.1111111111111112\t0.0\t0.0\t1.2307692307692308\n+Cluster_7\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.0\t0.0\t1.1764705882352942\t1.0\t1.0\t0.0\t0.0\t1.0666666666666667\t1.0588235294117647\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.3333333333333333\t0.0\t1.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.3333333333333333\t0.0\t0.0\t1.0\t1.0\t0.0\t1.0\t1.25\t0.0\t1.0\t0.0\t0.0\t1.0\t0.0\t1.0909090909090908\t1.0526315789473684\t1.2903225806451613\t0.0\t1.0769230769230769\t1.0\t1.25\t1.1111111111111112\t1.1111111111111112\t0.0\t0.0\t1.0909090909090908\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t1.2\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t1.1538461538461537\t1.2\t1.0909090909090908\t1.0769230769230769\t1.3124999999999998\t1.0\t1.0\t1.1428571428571428\t1.0\t0.0\t0.0\t1.2\t0.0\t0.0\t0.0\t1.0\t1.0\t1.0\t1.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.0\t0.0\t1.0\t1.0\t1.0\t1.2\t1.2\t0.0\t0.0\t1.0\t1.1428571428571428\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t1.0\t0.0\t1.4117647058823528\t1.2\t1.0\t1.2\t1.0909090909090908\t1.3846153846153844\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.0\t0.0\t1.1428571428571428\t1.0\t1.0\t0.0\t1.1785714285714286\t0.0\t1.1111111111111112\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t1.125\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t1.0909090909090908\t1.0909090909090908\t0.0\t0.0\t0.0\t1.12\t0.0\t1.0169491525423728\t0.0\t1.0\t0.0\t0.0\t1.0909090909090908\t0.0\t1.2\t1.0\t0.0\t1.1111111111111112\t0.0\t1.0\t1.1428571428571428\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_pathways_strat.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_pathways_strat.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,53629 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|
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_pathways_summary.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_pathways_summary.html Tue May 23 07:59:04 2023 +0000 |
| [ |
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If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<html>\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="4.1.0">\n+\t\t<!-- CSS -->\n+\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n+\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n+\t\t<style type="text/css">\n+\t\t\t/*\n+\t\t\t * jDistrib 0.1.0 - CSS jDistrib Library\t\n+\t\t\t *\t\t \n+\t\t\t * Copyright (c) 2015 Escudie Frederic\n+\t\t\t * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.\n+\t\t\t */\n+\t\t\t#sunburst-graph{margin-left:auto;margin-right:auto}.jDistrib-walk-rank{height:100%;margin-right:2px;padding:8px;float:left;border-top-right-radius:7px;border-bottom-right-radius:7px;cursor:pointer;box-shadow:1px 1px 1px #555}.jDistrib-walk-rank-size{margin-left:5px;padding:4px;background-color:#FFF;color:#648a89;border-radius:9px;text-align:center;font-size:10px;font-family:sans-serif}.jDistrib-root-label{font-weight:700;cursor:pointer}.jDistrib-arc-label{cursor:pointer}.jDistrib-arc{cursor:pointer;stroke:#fff;fill-rule:evenodd}.jDistrib-tooltip{position:absolute;padding:10px;font:12px sans-serif;background:#8EADAC;border:0;border-radius:8px;pointer-events:none}.jDistrib-empty-details{color:#fff;background-color:#8EADAC;padding:15px;margin-bottom:20px;border:1px solid transparent;border-radius:4px}.jDistrib-table-details>tbody>tr:nth-of-type(2n+1){background-color:#F5F5F5}.jDistrib-table-details{border:1px solid #DDD;border-radius:8px;border-spacing:1px;border-collapse:separate}.jDistrib-table-details td,th{padding:2px 8px}.jDistrib-table-details .number{text-align:right}.jDistrib-export-toggle{height:30px;width:30px;padding:1px}.jDistrib-export-toggle div{background-color:#636363;border-radius:2px;height:3px;margin-top:2px;margin-bottom:2px}\n+\t\t</style>\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t\t\t\theight: 0px;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tfloat: none !important;\n+\t\t\t}\n+\t\t\t.page-item.active .page-link {\n+\t\t\t\tz-index: 1;\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t\tborder-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn {\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#8EADAC;\n+\t\t\t\tbackground-color: #8EADAC;\n+\t\t\t}\n+\t\t\t.btn:focus, .btn:active {\n+\t\t\t\toutline: none !important;\n+\t\t\t\tbox-shadow: none !important;\n+\t\t\t}\n+\t\t\t.btn:hover{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tborder:#648a89;\n+\t\t\t\tbackground-color: #648a89;\n+\t\t\t}\n+\t\t\t.pb-2, .py-2 {\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 4rem !important;\n+\t\t\t}\n+\t\t\t.pb-2-first{\n+\t\t\t\tpadding-bottom: 1.5rem !important;\n+\t\t\t\tmargin-bottom: 2rem !important;\n+\t\t\t\tmargin-top: 1rem !important;\n+\t\t\t}\n+\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n+\t\t\t\tcolor: #fff;\n+\t\t\t\tbackground-color: #8EADAF;\n+\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n+\t\t\t}\n+\t\t\ta {\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\ta:hover{\n+\t\t\t\tcolor:#648a89;\n+\t\t\t}\n+\t\t\t.page-link{\n+\t\t\t\tcolor: #8EAEAF;\n+\t\t\t}\n+\t\t\t'..b'15\\": 3287, \\"16\\": 1792, \\"17\\": 1121, \\"18\\": 1784, \\"19\\": 3247, \\"20\\": 4247, \\"21\\": 647, \\"22\\": 1722, \\"23\\": 261, \\"24\\": 865, \\"25\\": 751, \\"26\\": 924, \\"27\\": 161, \\"28\\": 4061, \\"29\\": 2381, \\"30\\": 6260, \\"31\\": 5173, \\"32\\": 2984, \\"33\\": 5284, \\"34\\": 4602, \\"35\\": 2155, \\"36\\": 3294, \\"37\\": 5859, \\"38\\": 1523, \\"39\\": 2040, \\"40\\": 1535, \\"41\\": 738, \\"42\\": 1256, \\"43\\": 2884, \\"44\\": 1631, \\"45\\": 932, \\"46\\": 2475, \\"47\\": 2650, \\"48\\": 1450, \\"49\\": 3650, \\"50\\": 4028, \\"51\\": 3113, \\"52\\": 5048, \\"53\\": 5083, \\"54\\": 2877, \\"55\\": 2619, \\"56\\": 876, \\"57\\": 4394, \\"58\\": 2946, \\"59\\": 6745, \\"60\\": 3954, \\"61\\": 4686, \\"62\\": 3434})\\"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+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\n+\t\t\t\t// Load active tab\n+\t\t\t\ttaxBySample_load( "tax-distrib" );\n+\t\t\t\t\n+\t\t\t\t$(\'#filter-log\').append( table("Chimera detection by sample", table_categories, table_series) );\n+\t\t\t\t$(\'#filter-log table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#filter-log table\').DataTable({\n+\t\t\t\t\tdom: \t"<\'#details-csv-export\'><\'row\'<\'col-sm-5\'l><\'col-sm-7\'f>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-12\'tr>>" +\n+\t\t\t\t\t\t\t"<\'row\'<\'col-sm-5\'i><\'col-sm-7\'p>>",\n+\t\t\t\t\t\'lengthMenu\': [[10, 25, 50, 100, -1], [10, 25, 50, 100, "All"]],\n+\t\t\t\t});\n+\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n+\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n+\t\t\t\t$(\'#details-csv-export\').datatableExport({\n+\t\t\t\t\t\'table_id\': "details-table"\n+\t\t\t\t});\n+\t\t\t});\n+\t\t</script>\n+\t</head>\n+\t<body>\n+\t\t<!-- Alert -->\n+\t\t<p id="js-alert" class="alert alert-warning">\n+\t\t\tjavascript is needed to display data.<br />\n+\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+\t\t<!-- Content -->\n+\t\t<div id="content" class="hidden">\n+\n+\t\t\t<div id="tab-content" class="tab-content">\n+\t\t\t\t<div id="tax-distrib" role="tabpanel" class="tab-pane active">\n+\t \t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Pathway abundances per sample\n+\n+\t\t\t\t\t</h2>\n+\t\t\t\t\t<button id="display-global-sunburst" class="btn d-block mx-auto" data-toggle="modal" data-target="#sunburst-modal">\n+\t\t\t\t\t\t<span class="fa fa-pie-chart" aria-hidden="true"> Display global distribution</span>\n+\t\t\t\t\t</button>\n+\t\t\t\t\t<table id="taxBySample-table" class="table table-striped">\n+\t\t\t\t\t\t<thead>\n+\t\t\t\t\t\t</thead>\n+\t\t\t\t\t\t<tbody></tbody>\n+\t\t\t\t\t\t<tfoot>\n+\t\t\t\t\t\t\t<tr>\n+\t\t\t\t\t\t\t\t<th>\n+\t\t\t\t\t\t\t\t\t<button id="display-spl-sunburst" class="btn table-action" disabled data-toggle="modal" data-target="#sunburst-modal"><span class="fa fa-pie-chart" aria-hidden="true"> Display distribution</span></button>\n+\t\t\t\t\t\t\t\t</th>\n+\t\t\t\t\t\t\t</tr>\n+\t\t\t\t\t\t</tfoot>\n+\t\t\t\t\t</table>\n+\t\t\t\t</div>\n+\t\t\t<div class="modal" id="sunburst-modal" tabindex="-1" role="dialog" aria-hidden="true">\n+\t\t\t\t<div class="modal-dialog modal-lg">\n+\t\t\t\t\t<div class="modal-content">\n+\t\t\t\t\t\t<div class="modal-header">\n+\t\t\t\t\t\t\t<h6 class="modal-title">Pathways distribution</h6>\n+\t\t\t\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+\t\t\t\t\t\t</div>\n+\t\t\t\t\t\t<div class="modal-body">\n+\t\t\t\t\t\t\t<div id="sunburst-walktrace"></div>\n+\t\t\t\t\t\t\t<div id="sunburst-graph"></div>\n+\t\t\t\t\t\t\t<div>\n+\t\t\t\t\t\t\t\t</br><h6>Detail on selected:</h6>\n+\t\t\t\t\t\t\t\t<div id="sunburst-detail"></div>\n+\t\t\t\t\t\t\t</div>\n+\t\t\t\t\t\t</div>\n+\t\t\t\t\t\t<div class="modal-footer">\n+\t\t\t\t\t\t\t<span id="sunburst-menu"></span>\n+\t\t\t\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n+\t\t\t\t\t\t</div>\n+\t\t\t\t\t</div>\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t</div>\n+\t</body>\n+</html>\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_pathways_unstrat.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_pathways_unstrat.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,251 @@\n+classification\tdb_link\tobservation_name\tobservation_sum\tSC1703-104_TTGCCC-B6TML_L001_R\tSC1703-105_CAGTCT-B6TML_L001_R\tSC1703-106_TTAAAT-B6TML_L001_R\tSC1703-107_AATTGC-B6TML_L001_R\tSC1703-108_ACTCGA-B6TML_L001_R\tSC1703-109_GTTACC-B6TML_L001_R\tSC1703-110_CAGATG-B6TML_L001_R\tSC1703-125_TCGCGC-B6TML_L001_R\tSC1703-126_TAACTT-B6TML_L001_R\tSC1703-127_CTGTAA-B6TML_L001_R\tSC1703-128_CCATTG-B6TML_L001_R\tSC1703-129_TAGGCT-B6TML_L001_R\tSC1703-130_TTCTTG-B6TML_L001_R\tSC1703-131_CCGACC-B6TML_L001_R\tSC1703-132_TTAGCT-B6TML_L001_R\tSC1703-133_CAGAGC-B6TML_L001_R\tSC1703-134_AATATG-B6TML_L001_R\tSC1703-135_TGAGCA-B6TML_L001_R\tSC1703-136_AATCAC-B6TML_L001_R\tSC1703-137_GGTAGC-B6TML_L001_R\tSC1703-138_CTCTCG-B6TML_L001_R\tSC1703-145_AGCGAC-B6TML_L001_R\tSC1703-146_GCCAAG-B6TML_L001_R\tSC1703-147_AGGTTC-B6TML_L001_R\tSC1703-148_TTTTTC-B6TML_L001_R\tSC1703-149_GTCGTG-B6TML_L001_R\tSC1703-150_GCTATC-B6TML_L001_R\tSC1703-151_TATGCG-B6TML_L001_R\tSC1703-41_TCGTTC-B6TML_L001_R\tSC1703-42_GCGATG-B6TML_L001_R\tSC1703-43_ATATAA-B6TML_L001_R\tSC1703-44_ATACTG-B6TML_L001_R\tSC1703-45_GGAGAG-B6TML_L001_R\tSC1703-46_ACGAGA-B6TML_L001_R\tSC1703-47_ATTACA-B6TML_L001_R\tSC1703-48_TGATTT-B6TML_L001_R\tSC1703-49_GGGGTG-B6TML_L001_R\tSC1703-50_ACAAAA-B6TML_L001_R\tSC1703-51_CTCCAG-B6TML_L001_R\tSC1703-52_GGTGTT-B6TML_L001_R\tSC1703-53_CGGGAG-B6TML_L001_R\tSC1703-54_TGGTAG-B6TML_L001_R\tSC1703-62_TGCGGG-B6TML_L001_R\tSC1703-63_TCTATG-B6TML_L001_R\tSC1703-64_GGACGG-B6TML_L001_R\tSC1703-65_AGAGGG-B6TML_L001_R\tSC1703-66_ATGAAC-B6TML_L001_R\tSC1703-67_TACCTG-B6TML_L001_R\tSC1703-68_CTAGAG-B6TML_L001_R\tSC1703-83_CTTGCA-B6TML_L001_R\tSC1703-84_CATGTT-B6TML_L001_R\tSC1703-85_TGGATT-B6TML_L001_R\tSC1703-86_AACGCA-B6TML_L001_R\tSC1703-87_TTCGAG-B6TML_L001_R\tSC1703-88_AAGCTA-B6TML_L001_R\tSC1703-89_AGTTTG-B6TML_L001_R\tSC1703-90_TCCCCA-B6TML_L001_R\tSC1703-91_AACTAG-B6TML_L001_R\tSC1703-92_GTTCGC-B6TML_L001_R\tSC1703-93_TGCCTT-B6TML_L001_R\tSC1703-94_ATAAGA-B6TML_L001_R\tSC1703-95_CACACT-B6TML_L001_R\tSC1703-96_ACAGTT-B6TML_L001_R\n+Biosynthesis;Cofactor, Carrier, and Vitamin Biosynthesis;Carrier Biosynthesis;N10-formyl-tetrahydrofolate biosynthesis\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=1CMET2-PWY\t1CMET2-PWY\t927684.2471538748\t7771.848912803767\t14550.56118405238\t14189.010237139522\t19077.458595669184\t9601.022946604224\t5311.386445901301\t11110.576523303067\t6664.964283662128\t14870.437120519862\t23097.332579307542\t22031.236621795193\t23827.99465527487\t9806.627134895085\t23287.689938012827\t20429.965908030503\t14208.47891180511\t13781.717425098926\t27606.834603576273\t17210.526504232716\t16427.235674515236\t23681.543722473263\t8963.109791113597\t6184.111397445648\t6790.477955072719\t10434.626225582524\t5393.202105875216\t9062.985496500736\t4987.458116492045\t10426.069717385071\t5348.034776031318\t12388.318766690787\t12553.994229110722\t8232.398602010442\t7350.539029337016\t15310.744578228532\t16218.83884638255\t13935.99538740025\t9833.506810497332\t14817.531730158298\t15756.233557755957\t12009.111512405387\t18686.54504903672\t12512.194841079527\t13580.436537937787\t10058.849993394497\t12981.905680714932\t18708.86682059204\t10421.082233341867\t15643.757631411429\t10571.49725246205\t11118.016933906272\t17418.575398581615\t13156.490904856253\t17754.89241763858\t10505.979240405686\t12691.14745334794\t23526.30875474508\t28152.38824654989\t32493.719641021587\t25014.136835338017\t20562.932374517255\t27109.439631553272\t20473.344721293648\n+Superpathways;Superpathways;unknow;superpathway of chorismate metabolism\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALL-CHORISMATE-PWY\tALL-CHORISMATE-PWY\t128140.7736287208\t320.9624175662686\t1008.2326990168227\t1770.9521088501856\t2409.985071960181\t1345.601504456415\t407.66948995230473\t1908.8945131820672\t386.6749672439121\t1510.7554024493686\t1742.1455656412725\t1823.574154404105\t1536.0729727867051\t824.0986751052706\t2140.3696695686417\t5894.59745908816\t2441.2962721364174\t1552.6774585477083\t958.4391811784636\t1554.421221739443\t2556.0138835679836\t3365.594269807512\t546.2193167293985\t1282.3103049666245\t186.222034596'..b'hesis (prokaryotic)\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=UBISYN-PWY\tUBISYN-PWY\t103858.1690088619\t283.8557548849694\t857.2970795672918\t1428.00671147494\t1933.5822973879115\t1055.6951674553789\t346.749906089441\t1604.9103272494349\t288.8943839261784\t1126.66296374311\t1250.0138278055124\t1352.6763149912217\t1138.2839079962312\t593.9631676031337\t1581.6698246873405\t4825.763957611481\t1918.211339708544\t1382.0521688734486\t849.0363208807887\t1416.6368513351201\t2091.8218480785467\t2766.4464531937388\t466.43374616245313\t1003.4002142043897\t144.56418551839175\t575.2255768716637\t387.8366722833915\t634.7686239480747\t115.54607556217086\t2143.0988381466377\t1438.7567516062481\t3772.72656113961\t2988.7500590323143\t1462.1963680616043\t4315.248308940894\t2217.7692399998714\t1616.2497725244123\t2079.7587226048186\t4583.913939648795\t1001.5227466875572\t1485.0154897292168\t1098.2365486353374\t443.93982932279005\t912.0770189625796\t1955.0142471356696\t1284.2867465943698\t663.3965325002138\t1637.7059942990818\t1969.172271496301\t1175.1063134585977\t1934.8767195491605\t2161.112299112384\t1395.894751669367\t2610.512427071326\t2418.3526042781864\t1399.0607103275108\t1219.447198492738\t701.250471758203\t3033.57279225788\t1929.7858215173665\t4239.384401677083\t2333.6501232288256\t2398.108049124061\t2419.2126691765907\n+Biosynthesis;Carbohydrate Biosynthesis;Sugar Biosynthesis;UDP-N-acetyl-D-glucosamine biosynthesis I\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=UDPNAGSYN-PWY\tUDPNAGSYN-PWY\t1048419.8001489481\t6766.185504471118\t8771.17856639686\t9838.869975430502\t13387.17483264015\t6965.613267497504\t4397.794425088211\t9144.41725220489\t7477.300760558702\t19856.18115016376\t38374.19163107772\t31552.329788421004\t34059.51260873622\t16946.075180330918\t34303.54705421636\t21739.28604694809\t14231.415431810892\t17678.16551755997\t30022.701373987325\t25860.874850954104\t17784.583873423988\t23562.17541791721\t8599.742818061677\t5452.131224175115\t4082.621368259923\t8474.65398358582\t3524.1465071684306\t5816.773924486878\t4396.328960374379\t11122.803115062992\t4908.896250726809\t11953.232802538503\t13198.701938812888\t10488.359217140394\t7324.001590255255\t17871.0743178017\t24240.136117777864\t15450.707038969818\t11872.529130435525\t20099.625689764853\t25782.92211487701\t17627.573699931796\t22009.10519394557\t8906.80965864585\t11264.633918349735\t9390.241208928634\t7104.597745127698\t17685.71369297843\t7963.064399862438\t11717.510669022933\t11235.358051195046\t11479.819870446734\t20009.349064343263\t16491.475983324548\t22200.452754216003\t11238.31905161429\t14997.63516144053\t37319.08720243839\t35322.406310496364\t34107.61845531864\t32391.292498843413\t25042.047369969645\t29879.379754193083\t25657.345814203323\n+Biosynthesis;Amino Acid Biosynthesis;Proteinogenic Amino Acid Biosynthesis;L-valine biosynthesis\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=VALSYN-PWY\tVALSYN-PWY\t1406181.5843505547\t10684.910156546483\t18976.923220449982\t18486.72420752998\t25290.373468875503\t12754.883404746864\t7156.599891624007\t14503.12004036198\t9094.285963847777\t25263.90262908061\t42551.78579183445\t38994.781352656624\t42285.80108355911\t19323.601876318047\t42002.79842228746\t29780.60846116226\t19703.198069940474\t22569.62039674206\t38989.61304862352\t32321.6757306435\t23335.073155163114\t33985.00912983194\t11694.978163174403\t8725.043001031105\t8335.694826572677\t13240.178673554536\t6538.382510741776\t11449.85685041585\t6930.363655053134\t14771.985665406823\t6743.192044422416\t16300.418836600396\t15653.732328803198\t14525.717183788292\t9593.72614590039\t23116.77181643358\t29660.906969471704\t20400.915099286296\t15414.24681153891\t25132.915122548573\t31632.994179303143\t21894.346102294094\t28386.107283144374\t16308.361958728472\t18609.91639148099\t14007.367568843936\t16395.507761486464\t27202.814905682022\t13608.517957005228\t20151.97585989198\t14143.581942644538\t14234.935612270985\t24860.894194913755\t18259.296360388158\t27745.870286889243\t14227.588190474917\t15995.258460700343\t45778.78628939491\t45322.76509773363\t44965.837757481444\t41081.327973799685\t32515.946190633553\t39655.429651332626\t32911.841167466635\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_pathways_unstrat_per_seq.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_pathways_unstrat_per_seq.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,248 @@\n+pathway\tSC1703-104_TTGCCC-B6TML_L001_R\tSC1703-105_CAGTCT-B6TML_L001_R\tSC1703-106_TTAAAT-B6TML_L001_R\tSC1703-107_AATTGC-B6TML_L001_R\tSC1703-108_ACTCGA-B6TML_L001_R\tSC1703-109_GTTACC-B6TML_L001_R\tSC1703-110_CAGATG-B6TML_L001_R\tSC1703-125_TCGCGC-B6TML_L001_R\tSC1703-126_TAACTT-B6TML_L001_R\tSC1703-127_CTGTAA-B6TML_L001_R\tSC1703-128_CCATTG-B6TML_L001_R\tSC1703-129_TAGGCT-B6TML_L001_R\tSC1703-130_TTCTTG-B6TML_L001_R\tSC1703-131_CCGACC-B6TML_L001_R\tSC1703-132_TTAGCT-B6TML_L001_R\tSC1703-133_CAGAGC-B6TML_L001_R\tSC1703-134_AATATG-B6TML_L001_R\tSC1703-135_TGAGCA-B6TML_L001_R\tSC1703-136_AATCAC-B6TML_L001_R\tSC1703-137_GGTAGC-B6TML_L001_R\tSC1703-138_CTCTCG-B6TML_L001_R\tSC1703-145_AGCGAC-B6TML_L001_R\tSC1703-146_GCCAAG-B6TML_L001_R\tSC1703-147_AGGTTC-B6TML_L001_R\tSC1703-148_TTTTTC-B6TML_L001_R\tSC1703-149_GTCGTG-B6TML_L001_R\tSC1703-150_GCTATC-B6TML_L001_R\tSC1703-151_TATGCG-B6TML_L001_R\tSC1703-41_TCGTTC-B6TML_L001_R\tSC1703-42_GCGATG-B6TML_L001_R\tSC1703-43_ATATAA-B6TML_L001_R\tSC1703-44_ATACTG-B6TML_L001_R\tSC1703-45_GGAGAG-B6TML_L001_R\tSC1703-46_ACGAGA-B6TML_L001_R\tSC1703-47_ATTACA-B6TML_L001_R\tSC1703-48_TGATTT-B6TML_L001_R\tSC1703-49_GGGGTG-B6TML_L001_R\tSC1703-50_ACAAAA-B6TML_L001_R\tSC1703-51_CTCCAG-B6TML_L001_R\tSC1703-52_GGTGTT-B6TML_L001_R\tSC1703-53_CGGGAG-B6TML_L001_R\tSC1703-54_TGGTAG-B6TML_L001_R\tSC1703-62_TGCGGG-B6TML_L001_R\tSC1703-63_TCTATG-B6TML_L001_R\tSC1703-64_GGACGG-B6TML_L001_R\tSC1703-65_AGAGGG-B6TML_L001_R\tSC1703-66_ATGAAC-B6TML_L001_R\tSC1703-67_TACCTG-B6TML_L001_R\tSC1703-68_CTAGAG-B6TML_L001_R\tSC1703-83_CTTGCA-B6TML_L001_R\tSC1703-84_CATGTT-B6TML_L001_R\tSC1703-85_TGGATT-B6TML_L001_R\tSC1703-86_AACGCA-B6TML_L001_R\tSC1703-87_TTCGAG-B6TML_L001_R\tSC1703-88_AAGCTA-B6TML_L001_R\tSC1703-89_AGTTTG-B6TML_L001_R\tSC1703-90_TCCCCA-B6TML_L001_R\tSC1703-91_AACTAG-B6TML_L001_R\tSC1703-92_GTTCGC-B6TML_L001_R\tSC1703-93_TGCCTT-B6TML_L001_R\tSC1703-94_ATAAGA-B6TML_L001_R\tSC1703-95_CACACT-B6TML_L001_R\tSC1703-96_ACAGTT-B6TML_L001_R\n+1CMET2-PWY\t7523.245840080972\t12668.56882591093\t12655.536831983805\t17900.17344129555\t9354.903846153846\t4783.831113360324\t9575.02089068826\t3815.298471659919\t4996.802236842105\t12669.20141700405\t6589.848684210527\t5056.822226720648\t4874.638552631579\t7270.75798582996\t17400.690900809717\t11624.659777327935\t9803.775556680162\t23542.722813765184\t8685.309321862349\t12632.444979757085\t19009.724048582993\t8517.258997975709\t5967.141842105263\t6692.740748987853\t9987.728380566801\t5381.057044534413\t8588.617267206477\t5381.073127530364\t6398.173694331984\t4640.9401720647775\t9313.197479757086\t10516.17571862348\t4625.653087044535\t6114.265688259109\t8176.182074898787\t11165.840587044533\t9373.164615384616\t8285.544139676113\t11204.46367408907\t15629.832236842105\t11382.90572874494\t16357.444585020243\t11623.22354251012\t11495.278734817814\t7975.653846153846\t11865.911943319838\t19957.38410931174\t8921.708137651822\t12874.476325910931\t7001.268866396761\t7479.402469635628\t8205.011528340081\t9289.710384615384\t8637.769483805669\t6027.73467611336\t7347.624746963562\t12519.90221659919\t17439.18988866397\t26173.384615384617\t14838.317419028339\t13346.239483805668\t18210.432803643725\t12819.135991902835\n+ALL-CHORISMATE-PWY\t153.30755555555552\t523.4666666666666\t1047.7075555555555\t1425.1813333333332\t834.311111111111\t211.0853333333333\t1073.1297777777777\t274.64088888888887\t1098.159111111111\t1274.5777777777776\t1311.5555555555554\t1107.4035555555554\t595.8853333333333\t1552.6853333333333\t3767.492444444444\t1588.1146666666664\t764.9777777777778\t458.3742222222222\t730.6924444444444\t1509.9297777777776\t1946.3368888888886\t276.95199999999994\t840.863111111111\t107.84799999999998\t379.79644444444443\t373.6257777777777\t411.75911111111105\t63.55555555555555\t2138.1591111111106\t1466.0186666666666\t3818.3368888888886\t3033.7146666666663\t1439.822222222222\t4399.2\t2187.0853333333334\t890.9333333333333\t1535.3519999999999\t3641.5368888888884\t619.7591111111111\t833.1555555555555\t631.3146666666667\t291.2\t542.3368888888888\t1373.5742222222223\t746.4888888888888\t398.66666666666663\t1055.0222222222221\t1392.063111111111\t656.7368'..b'77777777\t8622.966666666667\t10960.366666666669\t12928.144444444446\t20216.666666666668\t13171.477777777778\t13072.222222222223\t13895.922222222223\t13266.300000000001\t11600.0\t13620.0\t23156.666666666668\t11011.855555555556\t16829.25555555556\t4812.966666666668\t4090.7444444444445\t3557.4111111111115\t5370.366666666667\t5946.666666666666\t3147.0333333333333\t2853.3333333333335\t28040.744444444448\t20187.033333333333\t23250.000000000004\t16362.58888888889\t14050.366666666667\t15151.477777777778\t15149.25555555556\n+UBISYN-PWY\t149.25374999999997\t509.6249999999999\t1020.0037499999997\t1387.4962499999997\t812.2499999999999\t205.50374999999994\t1044.7537499999999\t267.3787499999999\t1069.12125\t1240.8749999999998\t1276.8749999999998\t1078.12125\t580.1287499999999\t1511.6287499999999\t3667.8712499999992\t1546.1212499999997\t744.7499999999999\t446.2537499999999\t711.3712499999999\t1470.0037499999999\t1894.8712499999995\t269.6287499999999\t818.6287499999997\t104.99624999999997\t369.75374999999997\t363.7462499999999\t400.8712499999999\t61.874999999999986\t2081.6212499999997\t1427.2537499999999\t3717.3712499999992\t2953.4962499999992\t1401.7499999999998\t4282.874999999999\t2129.25375\t867.3749999999998\t1494.7537499999999\t3545.2462499999992\t603.3712499999999\t811.1249999999999\t614.6212499999999\t283.49999999999994\t527.9962499999999\t1337.2537499999999\t726.7499999999999\t388.12499999999994\t1027.1249999999998\t1355.2537499999999\t639.3712499999999\t1861.5037499999996\t2098.87875\t1311.3787499999999\t2566.4962499999992\t2297.2499999999995\t1336.8712499999997\t1165.4999999999998\t336.00374999999997\t1831.8712499999995\t1196.9999999999998\t3001.8712499999992\t1700.2462499999997\t1997.2462499999995\t1449.3712499999997\n+UDPNAGSYN-PWY\t5070.257264957265\t5501.025641025641\t6776.795726495726\t9112.366666666667\t4824.2991452991455\t3273.9666666666667\t6993.086324786325\t7818.693162393162\t19969.999145299145\t39108.17094017094\t31802.64957264957\t33810.65726495726\t17558.735897435898\t34546.428205128206\t20529.973504273505\t13065.879487179487\t17379.786324786324\t29649.667521367523\t25619.742735042735\t17064.93247863248\t20736.323931623934\t7610.684615384615\t4227.445299145299\t2591.7\t6510.111965811966\t2397.1017094017093\t3782.3068376068377\t3284.4957264957266\t11233.922222222223\t4681.55641025641\t12376.939316239317\t14698.494871794872\t10209.290598290598\t7660.846153846154\t18212.197435897437\t24549.128205128203\t15787.607692307693\t12127.170085470085\t20106.69145299145\t25946.264957264957\t17704.571794871794\t21835.384615384617\t6035.631623931624\t8438.12905982906\t7472.854700854701\t4300.410256410257\t13527.752136752137\t5800.752991452991\t8295.400854700856\t11815.368376068376\t11635.812820512821\t20162.804273504273\t17370.349572649575\t22730.11965811966\t11468.289743589745\t15460.03418803419\t37607.47094017094\t35058.56324786325\t32862.1452991453\t32811.04188034188\t25570.178632478634\t30141.89658119658\t26041.170085470087\n+VALSYN-PWY\t10493.26008097166\t18114.42975708502\t17538.427807981494\t24299.95206477733\t12347.22252747253\t6839.5179757085025\t14060.156842105265\t8301.335066512434\t23226.683325621747\t40408.800520532095\t36295.74080393291\t39797.066061307116\t18526.1242799306\t39299.75418160787\t27699.511029496818\t18102.76886639676\t20842.452834008098\t36749.61233661076\t30152.256257952577\t21340.393713128975\t31280.365396182766\t11585.735558126084\t8285.955511856564\t8216.809207634471\t12975.998918449972\t6475.501457489879\t11277.514239444767\t6912.8665413533845\t13219.19795835743\t6179.359097744361\t14503.301515326779\t14307.172249855408\t13086.19034123771\t8731.172874493926\t21075.620722961245\t28098.55078079815\t18320.630989010988\t14391.169126662811\t23980.13925390399\t30508.917611336034\t20848.853799884328\t26587.21029496819\t16010.884048582997\t17576.966356275305\t13568.65934065934\t15980.157056101792\t26811.59392712551\t13140.38842105263\t19612.266350491616\t12698.77870445344\t12888.994031231925\t23825.35108733372\t17154.210219780216\t25779.172267206475\t12972.169849624059\t14909.354106419894\t42739.30033545401\t41358.059323308276\t41096.249450549454\t37838.15397339503\t29334.287981492194\t35754.99243493348\t29885.954320416426\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/frogsfunc_placeseq.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frogsfunc_placeseq.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1944 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpr6jvdj77/galaxy-dev\n+Clonage dans \'/tmp/tmpr6jvdj77/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n+\n+[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n+[notice] To update, run: pip install --upgrade pip\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) ('..b'ctory.py", line 81, in build_command\n+ __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n+ File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n+ if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n+ File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n+ self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n+ File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n+ return self.app.toolbox.dependency_manager.dependency_shell_commands(\n+ File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n+ self.build_cache(requirements, **kwds)\n+ File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n+ self.build_environment()\n+ File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n+ raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n+galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n+galaxy.jobs DEBUG 2023-05-19 15:50:36,663 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_4d1ced49-69cd-4696-8d92-ce4a5967c293.dat to /tmp/tmpr6jvdj77/files/4/d/1/dataset_4d1ced49-69cd-4696-8d92-ce4a5967c293.dat\n+galaxy.jobs DEBUG 2023-05-19 15:50:36,664 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_642e9579-12ff-44c4-8eb5-e82b7de244a3.dat to /tmp/tmpr6jvdj77/files/6/4/2/dataset_642e9579-12ff-44c4-8eb5-e82b7de244a3.dat\n+galaxy.jobs DEBUG 2023-05-19 15:50:36,665 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_80f0d648-c925-4e66-b028-316c06951a95.dat to /tmp/tmpr6jvdj77/files/8/0/f/dataset_80f0d648-c925-4e66-b028-316c06951a95.dat\n+galaxy.jobs DEBUG 2023-05-19 15:50:36,666 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_ed4e7d62-8117-490e-8d85-a0b9b41fcbba.dat to /tmp/tmpr6jvdj77/files/e/d/4/dataset_ed4e7d62-8117-490e-8d85-a0b9b41fcbba.dat\n+galaxy.jobs DEBUG 2023-05-19 15:50:36,667 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_bcfc1b01-ff11-44b0-9338-5d13e4068d08.dat to /tmp/tmpr6jvdj77/files/b/c/f/dataset_bcfc1b01-ff11-44b0-9338-5d13e4068d08.dat\n+galaxy.jobs DEBUG 2023-05-19 15:50:36,669 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_c69b2d6d-7eee-4ced-9efe-5c87cb3bf3e4.dat to /tmp/tmpr6jvdj77/files/c/6/9/dataset_c69b2d6d-7eee-4ced-9efe-5c87cb3bf3e4.dat\n+galaxy.jobs DEBUG 2023-05-19 15:50:36,670 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_d4a40bbb-8eee-4697-b354-8e592d6be533.dat to /tmp/tmpr6jvdj77/files/d/4/a/dataset_d4a40bbb-8eee-4697-b354-8e592d6be533.dat\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGSFUNC_step1_placeseqs (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/input/frogsfunc.biom --- a/test-data/input/frogsfunc.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/input/frogsfunc.biom Tue May 23 07:59:04 2023 +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": "2018-10-04T16:37:49", "rows": [{"id": "Cluster_1", "metadata": {"blast_taxonomy": ["Bacteria", "Firmicutes", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Oscillibacter", "unknown species"], "seed_id": "M02944:219:000000000-B6TML:1:1102:9099:12653", "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Bacteria", "Firmicutes", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Oscillibacter", "unknown species"], "evalue": "0.0", "aln_length": 403, "perc_query_coverage": 100.0, "subject": "HQ785790.1.1449"}]}}, {"id": "Cluster_2", "metadata": {"blast_taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Multi-affiliation"], "seed_id": "M02944:219:000000000-B6TML:1:1102:5178:4304", "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "LXJJ02000010.3161.4631"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli S88"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CU928161.4443202.4444743"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CU651637.2709763.2711303"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli O157:H7"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP033605.4932246.4933797"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Shigella flexneri"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP033510.2312050.2313603"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli O32:H37 str. P4"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "AJQW01000057.1.1280"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP032515.4680373.4681924"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP032265.2506313.2507866"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli DEC8C"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "AIGH01000069.160053.161583"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "unknown species"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "JX984110.1.1220"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella",'..b'5, 21, 1507], [5, 22, 2756], [5, 23, 3386], [5, 24, 3607], [5, 25, 2661], [5, 26, 4604], [5, 27, 2104], [5, 28, 5], [5, 29, 7], [5, 30, 3], [5, 31, 4], [5, 32, 4], [5, 33, 2], [5, 34, 11], [5, 35, 108], [5, 36, 5], [5, 37, 4], [5, 38, 21], [5, 39, 13], [5, 40, 87], [5, 41, 16], [5, 42, 5819], [5, 43, 610], [5, 44, 1198], [5, 45, 5003], [5, 46, 6177], [5, 47, 2239], [5, 48, 5907], [5, 49, 38], [5, 50, 596], [5, 51, 27], [5, 52, 86], [5, 53, 18], [5, 54, 35], [5, 55, 18], [5, 56, 224], [5, 57, 1154], [5, 58, 2566], [5, 59, 389], [5, 60, 83], [5, 61, 163], [5, 62, 256], [6, 0, 1148], [6, 1, 1468], [6, 2, 1044], [6, 3, 1396], [6, 4, 552], [6, 5, 612], [6, 6, 1846], [6, 7, 13], [6, 8, 13], [6, 9, 15], [6, 10, 35], [6, 11, 9], [6, 12, 24], [6, 13, 21], [6, 14, 2666], [6, 15, 728], [6, 16, 4407], [6, 17, 3321], [6, 18, 9514], [6, 19, 1597], [6, 20, 2373], [6, 21, 969], [6, 22, 372], [6, 23, 97], [6, 24, 697], [6, 25, 42], [6, 26, 836], [6, 27, 399], [6, 28, 1], [6, 29, 2], [6, 30, 6], [6, 31, 8], [6, 32, 6], [6, 33, 7], [6, 34, 4], [6, 35, 5184], [6, 36, 1406], [6, 37, 2379], [6, 38, 1471], [6, 39, 4165], [6, 40, 2616], [6, 41, 473], [6, 42, 1876], [6, 43, 1757], [6, 44, 3013], [6, 45, 1270], [6, 46, 2225], [6, 47, 1771], [6, 48, 3610], [6, 49, 41], [6, 50, 20], [6, 51, 32], [6, 52, 76], [6, 53, 34], [6, 54, 22], [6, 55, 11], [6, 56, 15266], [6, 57, 4545], [6, 58, 2580], [6, 59, 2981], [6, 60, 1403], [6, 61, 638], [6, 62, 3822], [7, 0, 2], [7, 1, 4], [7, 2, 7], [7, 3, 19], [7, 4, 4], [7, 5, 7], [7, 6, 7], [7, 7, 290], [7, 8, 369], [7, 9, 3062], [7, 10, 948], [7, 11, 1596], [7, 12, 231], [7, 13, 1769], [7, 14, 824], [7, 15, 152], [7, 16, 165], [7, 17, 190], [7, 18, 350], [7, 19, 57], [7, 20, 344], [7, 21, 1], [7, 23, 1], [7, 24, 9], [7, 28, 1634], [7, 29, 963], [7, 30, 3978], [7, 31, 1161], [7, 32, 398], [7, 33, 15], [7, 34, 1884], [7, 35, 278], [7, 36, 2075], [7, 37, 333], [7, 38, 629], [7, 39, 1036], [7, 40, 1579], [7, 41, 4682], [7, 42, 26], [7, 46, 1], [7, 48, 1], [7, 49, 717], [7, 50, 1213], [7, 51, 4106], [7, 52, 167], [7, 53, 1136], [7, 54, 1806], [7, 55, 513], [7, 56, 58], [7, 57, 995], [7, 58, 5041], [7, 59, 610], [7, 60, 160], [7, 61, 3817], [7, 62, 993], [8, 0, 762], [8, 1, 2421], [8, 2, 812], [8, 3, 1403], [8, 4, 859], [8, 5, 973], [8, 6, 2543], [8, 7, 107], [8, 8, 152], [8, 9, 233], [8, 10, 186], [8, 11, 639], [8, 12, 85], [8, 13, 364], [8, 14, 177], [8, 15, 222], [8, 16, 525], [8, 17, 249], [8, 18, 311], [8, 19, 947], [8, 20, 411], [8, 21, 355], [8, 22, 114], [8, 23, 736], [8, 24, 720], [8, 25, 257], [8, 26, 940], [8, 27, 314], [8, 28, 358], [8, 29, 720], [8, 30, 41], [8, 31, 22], [8, 32, 727], [8, 33, 348], [8, 34, 205], [8, 35, 49], [8, 36, 18], [8, 37, 176], [8, 38, 152], [8, 39, 31], [8, 40, 48], [8, 41, 376], [8, 42, 1781], [8, 43, 6486], [8, 44, 2989], [8, 45, 4222], [8, 46, 3170], [8, 47, 3299], [8, 48, 2726], [8, 49, 167], [8, 50, 434], [8, 51, 198], [8, 52, 453], [8, 53, 281], [8, 54, 304], [8, 55, 295], [8, 56, 266], [8, 57, 269], [8, 58, 274], [8, 59, 179], [8, 60, 61], [8, 61, 134], [8, 62, 66], [9, 0, 175], [9, 1, 168], [9, 2, 505], [9, 3, 260], [9, 4, 140], [9, 5, 338], [9, 6, 316], [9, 7, 1055], [9, 8, 491], [9, 9, 4500], [9, 10, 1006], [9, 11, 448], [9, 12, 1647], [9, 13, 1191], [9, 14, 323], [9, 15, 682], [9, 16, 771], [9, 17, 510], [9, 18, 839], [9, 19, 1232], [9, 20, 708], [9, 21, 11], [9, 22, 198], [9, 23, 26], [9, 24, 224], [9, 25, 32], [9, 26, 50], [9, 27, 11], [9, 28, 559], [9, 29, 263], [9, 30, 281], [9, 31, 2647], [9, 32, 71], [9, 33, 526], [9, 34, 875], [9, 35, 1022], [9, 36, 612], [9, 37, 103], [9, 38, 269], [9, 39, 371], [9, 40, 382], [9, 41, 271], [9, 42, 358], [9, 43, 869], [9, 44, 296], [9, 45, 348], [9, 46, 586], [9, 47, 368], [9, 48, 627], [9, 49, 1384], [9, 50, 1800], [9, 51, 613], [9, 52, 3138], [9, 53, 1499], [9, 54, 978], [9, 55, 3175], [9, 56, 1861], [9, 57, 1951], [9, 58, 1888], [9, 59, 1655], [9, 60, 1355], [9, 61, 911], [9, 62, 1416]], "shape": [10, 63], "matrix_type": "sparse"}\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/log_chimera.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_chimera.txt Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1091 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpo_r_z575/galaxy-dev\n+Clonage dans \'/tmp/tmpo_r_z575/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 44% (2768/6175)\rMise \xc3\xa0 jour des fichiers: 45% (2779/6175)\rMise \xc3\xa0 jour des fichiers: 46% (2841/6175)\rMise \xc3\xa0 jour des fichiers: 47% (2903/6175)\rMise \xc3\xa0 jour des fichiers: 48% (2964/6175)\rMise \xc3\xa0 jour des fichiers: 49% (3026/6175)\rMise \xc3\xa0 jour des fichiers: 50% (3088/6175)\rMise \xc3\xa0 jour des fichiers: 51% (3150/6175)\rMise \xc3\xa0 jour des fichiers: 52% (3211/6175)\rMise \xc3\xa0 jour des fichiers: 53% (3273/6175)\rMise \xc3\xa0 jour des fichiers: 54% (3335/6175)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6175)\rMise \xc3\xa0 jour des fichiers: 56% (3458/6175)\rMise \xc3\xa0 jour des fichiers: 57% (3520/6175)\rMise \xc3\xa0 jour des fichiers: 58% (3582/6175)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6175)\rMise \xc3\xa0 jour des fichiers: 60% (3705/6175)\rMise \xc3\xa0 jour des fichiers: 60% (3759/6175)\rMise \xc3\xa0 jour des fichiers: 61% (3767/6175)\rMise \xc3\xa0 jour des fichiers: 62% (3829/6175)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6175)\rMise \xc3\xa0 jour des fichiers: 64% (3952/6175)\rMise \xc3\xa0 jour des fichiers: 65% (4014/6175)\rMise \xc3\xa0 jour des fichiers: 66% (4076/6175)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6175)\rMise \xc3\xa0 jour des fichiers: 68% (4199/6175)\rMise \xc3\xa0 jour des fichiers: 69% (4261/6175)\rMise \xc3\xa0 jour des fichiers: 70% (4323/6175)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6175)\rMise \xc3\xa0 jour des fichiers: 72% (4446/6175)\rMise \xc3\xa0 jour des fichiers: 73% (4508/6175)\rMise \xc3\xa0 jour des fichiers: 74% (4570/6175)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6175)\rMise \xc3\xa0 jour des fichiers: 76% (4693/6175)\rMise \xc3\xa0 jour des fichiers: 77% (4755/6175)\rMise \xc3\xa0 jour des fichiers: 78% (4817/6175)\rMise \xc3\xa0 jour des fichiers: 79% (4879/6175)\rMise \xc3\xa0 jour des fichiers: 80% (4940/6175)\rMise \xc3\xa0 jour des fichiers: 81% (5002/6175)\rMise \xc3\xa0 jour des fichiers: 82% (5064/6175)\rMise \xc3\xa0 jour des fichiers: 83% (5126/6175)\rMise \xc3\xa0 jour des fichiers: 84% (5187/6175)\rMise \xc3\xa0 jour des fichiers: 85% (5249/6175)\rMise \xc3\xa0 jour des fichiers: 86% (5311/6175)\rMise \xc3\xa0 jour des fichiers: 87% (5373/6175)\rMise \xc3\xa0 jour des fichiers: 88% (5434/6175)\rMise \xc3\xa0 jour des fichiers: 89% (5496/6175)\rMise \xc3\xa0 jour des fichiers: 90% (5558/6175)\rMise \xc3\xa0 jour des fichiers: 91% (5620/6175)\rMise \xc3\xa0 jour des fichiers: 92% (5681/6175)\rMise \xc3\xa0 jour des fichiers: 93% (5743/6175)\rMise \xc3\xa0 jour des fichiers: 94% (5805/6175)\rMise \xc3\xa0 jour des fichiers: 95% (5867/6175)\rMise \xc3\xa0 jour des fichiers: 96% (5928/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual'..b'dat\' --out-abundance \'/tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_d8aea5cb-a5bf-45e6-80f9-c8a9c9c3c28b.dat\']\n+galaxy.jobs.runners DEBUG 2023-04-14 08:58:09,384 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpo_r_z575/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpo_r_z575/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmpo_r_z575/job_working_directory/000/3/working/non_chimera.fasta" ] ; then cp "/tmp/tmpo_r_z575/job_working_directory/000/3/working/non_chimera.fasta" "/tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_aea36576-9657-4334-90f0-9dce5336d078.dat" ; fi; \n+if [ -f "/tmp/tmpo_r_z575/job_working_directory/000/3/working/non_chimera_abundance.biom" ] ; then cp "/tmp/tmpo_r_z575/job_working_directory/000/3/working/non_chimera_abundance.biom" "/tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_d8aea5cb-a5bf-45e6-80f9-c8a9c9c3c28b.dat" ; fi; \n+if [ -f "/tmp/tmpo_r_z575/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmpo_r_z575/job_working_directory/000/3/working/report.html" "/tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_89d82b28-b154-4b39-9e19-48b26e4e974f.dat" ; fi; cd \'/tmp/tmpo_r_z575/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-14 08:58:09,418 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmpo_r_z575/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-14 08:59:50,043 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 62985\n+galaxy.jobs.runners.local DEBUG 2023-04-14 08:59:50,044 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpo_r_z575/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-04-14 08:59:50,130 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_aea36576-9657-4334-90f0-9dce5336d078.dat to /tmp/tmpo_r_z575/files/a/e/a/dataset_aea36576-9657-4334-90f0-9dce5336d078.dat\n+galaxy.jobs DEBUG 2023-04-14 08:59:50,132 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_d8aea5cb-a5bf-45e6-80f9-c8a9c9c3c28b.dat to /tmp/tmpo_r_z575/files/d/8/a/dataset_d8aea5cb-a5bf-45e6-80f9-c8a9c9c3c28b.dat\n+galaxy.jobs DEBUG 2023-04-14 08:59:50,133 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_89d82b28-b154-4b39-9e19-48b26e4e974f.dat to /tmp/tmpo_r_z575/files/8/9/d/dataset_89d82b28-b154-4b39-9e19-48b26e4e974f.dat\n+\n+galaxy.model.metadata DEBUG 2023-04-14 08:59:50,280 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.model.metadata DEBUG 2023-04-14 08:59:50,300 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.model.metadata DEBUG 2023-04-14 08:59:50,317 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 5\n+galaxy.jobs DEBUG 2023-04-14 08:59:50,491 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (377.147 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_remove_chimera (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/log_cluster_filter.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_cluster_filter.txt Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,4407 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpt04nlgwt/galaxy-dev\n+Clonage dans \'/tmp/tmpt04nlgwt/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 87% (5412/6175)\rMise \xc3\xa0 jour des fichiers: 88% (5434/6175)\rMise \xc3\xa0 jour des fichiers: 89% (5496/6175)\rMise \xc3\xa0 jour des fichiers: 90% (5558/6175)\rMise \xc3\xa0 jour des fichiers: 91% (5620/6175)\rMise \xc3\xa0 jour des fichiers: 92% (5681/6175)\rMise \xc3\xa0 jour des fichiers: 93% (5743/6175)\rMise \xc3\xa0 jour des fichiers: 94% (5805/6175)\rMise \xc3\xa0 jour des fichiers: 95% (5867/6175)\rMise \xc3\xa0 jour des fichiers: 96% (5928/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.0.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already s'..b'-unknown --offline --prefix /tmp/tmp0e0byafl/deps/_cache/7aceb47c --file /tmp/tmp0e0byafl/tmp/jobdepsi9acpvk650a80fe6225de7a3ec39e762f65eff821399f3b512517273aa2912df4da17ac1/__blast@2.10\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-24 12:41:23,375 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] Executing command: /home/vdarbot/miniconda3/bin/conda clean --tarballs -y\n+galaxy.jobs.runners ERROR 2023-04-24 12:41:23,872 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] (4) Failure preparing job\n+Traceback (most recent call last):\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 262, in prepare_job\n+ job_wrapper.runner_command_line = self.build_command_line(\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 301, in build_command_line\n+ return build_command(\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n+ __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n+ if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n+ self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n+ return self.app.toolbox.dependency_manager.dependency_shell_commands(\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n+ self.build_cache(requirements, **kwds)\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n+ self.build_environment()\n+ File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n+ raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n+galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n+galaxy.jobs DEBUG 2023-04-24 12:41:23,881 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0e0byafl/job_working_directory/000/4/outputs/galaxy_dataset_97aceb5f-017c-4369-ba43-dc82c1c7e195.dat to /tmp/tmp0e0byafl/files/9/7/a/dataset_97aceb5f-017c-4369-ba43-dc82c1c7e195.dat\n+galaxy.jobs DEBUG 2023-04-24 12:41:23,881 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0e0byafl/job_working_directory/000/4/outputs/galaxy_dataset_02f9b27d-ebb1-4278-b358-f3d9b48741ed.dat to /tmp/tmp0e0byafl/files/0/2/f/dataset_02f9b27d-ebb1-4278-b358-f3d9b48741ed.dat\n+galaxy.jobs DEBUG 2023-04-24 12:41:23,881 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0e0byafl/job_working_directory/000/4/outputs/galaxy_dataset_5313f1d9-9886-4cc9-92eb-867a98549f44.dat to /tmp/tmp0e0byafl/files/5/3/1/dataset_5313f1d9-9886-4cc9-92eb-867a98549f44.dat\n+galaxy.jobs DEBUG 2023-04-24 12:41:23,881 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0e0byafl/job_working_directory/000/4/outputs/galaxy_dataset_44eb313c-90b3-4a63-bc8c-cb0ebd3cafd8.dat to /tmp/tmp0e0byafl/files/4/4/e/dataset_44eb313c-90b3-4a63-bc8c-cb0ebd3cafd8.dat\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_cluster_filters (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/log_clustering.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_clustering.txt Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,3398 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpte1clwq8/galaxy-dev\n+Clonage dans \'/tmp/tmpte1clwq8/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.0.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'4603-8a03-9f6d64d86a2d.dat\' --distance 1 --fastidious]\n+galaxy.jobs.runners DEBUG 2023-04-14 08:50:10,389 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] (6) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpcq21inwm/job_working_directory/000/6/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpcq21inwm/job_working_directory/000/6/galaxy_6.ec; \n+if [ -f "/tmp/tmpcq21inwm/job_working_directory/000/6/working/seeds.fasta" ] ; then cp "/tmp/tmpcq21inwm/job_working_directory/000/6/working/seeds.fasta" "/tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_14ba7874-54ce-43a5-87a6-b7a1c47d6283.dat" ; fi; \n+if [ -f "/tmp/tmpcq21inwm/job_working_directory/000/6/working/abundance.biom" ] ; then cp "/tmp/tmpcq21inwm/job_working_directory/000/6/working/abundance.biom" "/tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_3096e670-1508-4844-87c0-41e9f0aa6534.dat" ; fi; \n+if [ -f "/tmp/tmpcq21inwm/job_working_directory/000/6/working/swarms.tsv" ] ; then cp "/tmp/tmpcq21inwm/job_working_directory/000/6/working/swarms.tsv" "/tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_257d6537-09d0-4603-8a03-9f6d64d86a2d.dat" ; fi; cd \'/tmp/tmpcq21inwm/job_working_directory/000/6\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-14 08:50:10,406 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] (6) executing job script: /tmp/tmpcq21inwm/job_working_directory/000/6/galaxy_6.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-14 08:50:51,797 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 60087\n+galaxy.jobs.runners.local DEBUG 2023-04-14 08:50:51,798 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmpcq21inwm/job_working_directory/000/6/galaxy_6.sh\n+galaxy.jobs DEBUG 2023-04-14 08:50:51,850 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_14ba7874-54ce-43a5-87a6-b7a1c47d6283.dat to /tmp/tmpcq21inwm/files/1/4/b/dataset_14ba7874-54ce-43a5-87a6-b7a1c47d6283.dat\n+galaxy.jobs DEBUG 2023-04-14 08:50:51,850 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_3096e670-1508-4844-87c0-41e9f0aa6534.dat to /tmp/tmpcq21inwm/files/3/0/9/dataset_3096e670-1508-4844-87c0-41e9f0aa6534.dat\n+galaxy.jobs DEBUG 2023-04-14 08:50:51,850 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_257d6537-09d0-4603-8a03-9f6d64d86a2d.dat to /tmp/tmpcq21inwm/files/2/5/7/dataset_257d6537-09d0-4603-8a03-9f6d64d86a2d.dat\n+galaxy.model.metadata DEBUG 2023-04-14 08:50:51,887 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 8\n+galaxy.model.metadata DEBUG 2023-04-14 08:50:51,910 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 9\n+\n+galaxy.model.metadata DEBUG 2023-04-14 08:50:51,950 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 10\n+galaxy.jobs DEBUG 2023-04-14 08:50:52,161 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] job_wrapper.finish for job 6 executed (321.489 ms)\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 2 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_clustering (Test #1): failed\n+FROGS_clustering (Test #2): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/log_itsx.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_itsx.txt Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,2969 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpwwu6f1vn/galaxy-dev\n+Clonage dans \'/tmp/tmpwwu6f1vn/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.0.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' defaults --unknown --offline --prefix /tmp/tmpd3p5ubjb/deps/_cache/9f25569a --file /tmp/tmpd3p5ubjb/tmp/jobdepsgq21duab6e7112901d5dd6e96453a8b7da7ce67279ca30759431991ef0a96736574ad7cc/__itsx@1.1.2\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-14 09:34:12,729 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] Executing command: /home/vdarbot/miniconda3/bin/conda clean --tarballs -y\n+galaxy.jobs.runners ERROR 2023-04-14 09:34:13,259 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] (3) Failure preparing job\n+Traceback (most recent call last):\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 262, in prepare_job\n+ job_wrapper.runner_command_line = self.build_command_line(\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 301, in build_command_line\n+ return build_command(\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n+ __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n+ if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n+ self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n+ return self.app.toolbox.dependency_manager.dependency_shell_commands(\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n+ self.build_cache(requirements, **kwds)\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n+ self.build_environment()\n+ File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n+ raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n+galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n+galaxy.jobs DEBUG 2023-04-14 09:34:13,270 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] fail(): Moved /tmp/tmpd3p5ubjb/job_working_directory/000/3/outputs/galaxy_dataset_eb210f71-b7d0-4eed-baab-fa570cba8b2b.dat to /tmp/tmpd3p5ubjb/files/e/b/2/dataset_eb210f71-b7d0-4eed-baab-fa570cba8b2b.dat\n+galaxy.jobs DEBUG 2023-04-14 09:34:13,271 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] fail(): Moved /tmp/tmpd3p5ubjb/job_working_directory/000/3/outputs/galaxy_dataset_d893a6fe-8b40-46f5-938e-7342b0c55609.dat to /tmp/tmpd3p5ubjb/files/d/8/9/dataset_d893a6fe-8b40-46f5-938e-7342b0c55609.dat\n+galaxy.jobs DEBUG 2023-04-14 09:34:13,271 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] fail(): Moved /tmp/tmpd3p5ubjb/job_working_directory/000/3/outputs/galaxy_dataset_6adbd5e6-23b2-454a-b3fe-00b90d1e5175.dat to /tmp/tmpd3p5ubjb/files/6/a/d/dataset_6adbd5e6-23b2-454a-b3fe-00b90d1e5175.dat\n+galaxy.jobs DEBUG 2023-04-14 09:34:13,271 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] fail(): Moved /tmp/tmpd3p5ubjb/job_working_directory/000/3/outputs/galaxy_dataset_711d0d72-2bfc-461c-825e-2f5d09ec28ed.dat to /tmp/tmpd3p5ubjb/files/7/1/1/dataset_711d0d72-2bfc-461c-825e-2f5d09ec28ed.dat\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_itsx (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/log_itsx_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_itsx_2.txt Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,2123 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmplk5ol3bv/galaxy-dev\n+Clonage dans \'/tmp/tmplk5ol3bv/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'utputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpdsj8fglo/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpdsj8fglo/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/out_removed.fasta" ] ; then cp "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/out_removed.fasta" "/tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_0b3c0f65-0f64-4b9d-bb19-88848296bee2.dat" ; fi; \n+if [ -f "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/itsx.fasta" ] ; then cp "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/itsx.fasta" "/tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_272b90f4-455c-4b37-acca-d2ba900832bf.dat" ; fi; \n+if [ -f "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/itsx.biom" ] ; then cp "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/itsx.biom" "/tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_785a7a4c-b2d5-472c-b215-60167be9b383.dat" ; fi; \n+if [ -f "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/report.html" "/tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_f732cc6d-108e-4666-82ec-c76136a23aa5.dat" ; fi; cd \'/tmp/tmpdsj8fglo/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-24 12:30:42,301 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] (3) executing job script: /tmp/tmpdsj8fglo/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-24 12:30:51,283 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 94333\n+galaxy.jobs.runners.local DEBUG 2023-04-24 12:30:51,283 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpdsj8fglo/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-04-24 12:30:51,326 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_0b3c0f65-0f64-4b9d-bb19-88848296bee2.dat to /tmp/tmpdsj8fglo/files/0/b/3/dataset_0b3c0f65-0f64-4b9d-bb19-88848296bee2.dat\n+galaxy.jobs DEBUG 2023-04-24 12:30:51,327 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_272b90f4-455c-4b37-acca-d2ba900832bf.dat to /tmp/tmpdsj8fglo/files/2/7/2/dataset_272b90f4-455c-4b37-acca-d2ba900832bf.dat\n+galaxy.jobs DEBUG 2023-04-24 12:30:51,327 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_785a7a4c-b2d5-472c-b215-60167be9b383.dat to /tmp/tmpdsj8fglo/files/7/8/5/dataset_785a7a4c-b2d5-472c-b215-60167be9b383.dat\n+galaxy.jobs DEBUG 2023-04-24 12:30:51,327 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_f732cc6d-108e-4666-82ec-c76136a23aa5.dat to /tmp/tmpdsj8fglo/files/f/7/3/dataset_f732cc6d-108e-4666-82ec-c76136a23aa5.dat\n+galaxy.model.metadata DEBUG 2023-04-24 12:30:51,408 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.model.metadata DEBUG 2023-04-24 12:30:51,442 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.model.metadata DEBUG 2023-04-24 12:30:51,451 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 5\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_itsx (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/log_preprocess.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_preprocess.txt Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1951 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp9rmcpqjk/galaxy-dev\n+Clonage dans \'/tmp/tmp9rmcpqjk/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.0.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'hread] Calling on_field_end with no data\n+multipart.multipart DEBUG 2023-04-13 21:16:08,633 [pN:main.1,p:45312,tN:MainThread] Calling on_end with no data\n+\n+galaxy.tools INFO 2023-04-13 21:16:09,139 [pN:main.1,p:45312,tN:WSGI_0] Validated and populated state for tool request (16.082 ms)\n+galaxy.tools.actions.upload DEBUG 2023-04-13 21:16:09,148 [pN:main.1,p:45312,tN:WSGI_0] Persisted uploads (0.129 ms)\n+galaxy.tools.actions.upload DEBUG 2023-04-13 21:16:09,339 [pN:main.1,p:45312,tN:WSGI_0] Checked uploads (191.181 ms)\n+galaxy.tools.actions.upload DEBUG 2023-04-13 21:16:09,343 [pN:main.1,p:45312,tN:WSGI_0] Created upload job (3.659 ms)\n+galaxy.tools.execute DEBUG 2023-04-13 21:16:09,343 [pN:main.1,p:45312,tN:WSGI_0] Tool upload1 created job None (195.550 ms)\n+galaxy.web_stack.handlers INFO 2023-04-13 21:16:09,388 [pN:main.1,p:45312,tN:WSGI_0] (Job[id=2,tool_id=upload1]) Handler \'_default_\' assigned using \'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED\' assignment method\n+galaxy.tools.execute DEBUG 2023-04-13 21:16:09,416 [pN:main.1,p:45312,tN:WSGI_0] Created 1 job(s) for tool upload1 request (277.313 ms)\n+\n+galaxy.jobs.mapper DEBUG 2023-04-13 21:16:09,914 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: upload_dest\n+galaxy.jobs.handler DEBUG 2023-04-13 21:16:09,922 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner\n+galaxy.jobs DEBUG 2023-04-13 21:16:09,993 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: upload_dest)\n+galaxy.jobs DEBUG 2023-04-13 21:16:10,010 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmp9rmcpqjk/job_working_directory/000/2\n+galaxy.jobs.runners DEBUG 2023-04-13 21:16:10,044 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] Job [2] queued (121.464 ms)\n+galaxy.jobs.handler INFO 2023-04-13 21:16:10,060 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n+galaxy.jobs DEBUG 2023-04-13 21:16:10,221 [pN:main.1,p:45312,tN:LocalRunner.work_thread-2] Job wrapper for Job [2] prepared (131.529 ms)\n+galaxy.jobs.command_factory INFO 2023-04-13 21:16:10,240 [pN:main.1,p:45312,tN:LocalRunner.work_thread-2] Built script [/tmp/tmp9rmcpqjk/job_working_directory/000/2/tool_script.sh] for tool command [python \'/tmp/tmp9rmcpqjk/galaxy-dev/tools/data_source/upload.py\' \'/tmp/tmp9rmcpqjk/galaxy-dev\' \'/tmp/tmp9rmcpqjk/job_working_directory/000/2/registry.xml\' \'/tmp/tmp9rmcpqjk/tmp/upload_params_smi_3ore\' \'2:/tmp/tmp9rmcpqjk/job_working_directory/000/2/working/dataset_1c6df421-4c92-4641-a2a3-3d1a72a61e9d_files:/tmp/tmp9rmcpqjk/job_working_directory/000/2/outputs/galaxy_dataset_1c6df421-4c92-4641-a2a3-3d1a72a61e9d.dat\']\n+galaxy.jobs.runners DEBUG 2023-04-13 21:16:10,303 [pN:main.1,p:45312,tN:LocalRunner.work_thread-2] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmp9rmcpqjk/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp9rmcpqjk/job_working_directory/000/2/galaxy_2.ec; cd \'/tmp/tmp9rmcpqjk/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-13 21:16:10,320 [pN:main.1,p:45312,tN:LocalRunner.work_thread-2] (2) executing job script: /tmp/tmp9rmcpqjk/job_working_directory/000/2/galaxy_2.sh\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 2 test(s) - out of 2 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_preprocess (Test #1): failed\n+FROGS_preprocess (Test #2): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/multihits.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multihits.tsv Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,865 @@\n+#observation_name\tblast_taxonomy\t blast_subject\tblast_perc_identity\tblast_perc_query_coverage\tblast_evalue\tblast_aln_length\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tLXJJ02000010.3161.4631\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli S88\tCU928161.4443202.4444743\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCU651637.2709763.2711303\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli O157:H7\tCP033605.4932246.4933797\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Shigella flexneri\tCP033510.2312050.2313603\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli O32:H37 str. P4\tAJQW01000057.1.1280\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP032515.4680373.4681924\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP032265.2506313.2507866\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli DEC8C\tAIGH01000069.160053.161583\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;unknown species\tJX984110.1.1220\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCU651637.3470321.3471862\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli O157:H7\tCP033605.5076505.5078058\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Shigella flexneri\tCP033510.2451439.2452992\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP031134.1449423.1450976\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP030919.3931874.3933427\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia albertii\tCP030783.4472057.4473578\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli S88\tCU928161.4403031.4404573\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli 55989\tCU928145.3776861.3778402\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCU651637.227496.229042\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP032515.4721466.4723017\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP032265.3415857.3417410\t100.0\t100.0\t0.0\t426\n+Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli O157:H7\tCP033605.4835899.4837452'..b'bacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tAL111168.39249.40761\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tAL111168.696424.697936\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tZ29326.264.1776\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tCP013116.654878.656395\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tCP013116.351319.352836\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tJX912519.1.1435\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tCP013034.1173635.1175152\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tCP013034.894477.895994\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tCP013034.1570901.1572418\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tAF550626.1.1417\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tAF550622.1.1417\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tAF550621.1.1417\t100.0\t100.0\t0.0\t402\n+Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tAF550620.1.1417\t100.0\t100.0\t0.0\t402\n+Cluster_10\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp.\tGU128175.1.1435\t99.5\t100.0\t0.0\t404\n+Cluster_10\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp.\tJN874874.1.1444\t99.5\t100.0\t0.0\t404\n+Cluster_11\tBacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species\tEF025229.1.1453\t99.75\t100.0\t0.0\t401\n+Cluster_11\tBacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species\tGQ175509.1.1455\t99.75\t100.0\t0.0\t401\n+Cluster_11\tBacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species\tFJ440057.1.1453\t99.75\t100.0\t0.0\t401\n+Cluster_11\tBacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species\tJQ248111.1.1514\t99.75\t100.0\t0.0\t401\n+Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\tEU763264.1.1364\t100.0\t100.0\t0.0\t404\n+Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\tEU767001.1.1361\t100.0\t100.0\t0.0\t404\n+Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\tEU767866.1.1364\t100.0\t100.0\t0.0\t404\n+Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\tEU767539.1.1358\t100.0\t100.0\t0.0\t404\n+Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Flavonifractor plautii\tCP015406.84360.85899\t100.0\t100.0\t0.0\t404\n+Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Flavonifractor plautii\tAY724678.1.1465\t100.0\t100.0\t0.0\t404\n+Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Flavonifractor plautii\tY18187.1.1550\t100.0\t100.0\t0.0\t404\n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/phyloseq_alpha_diversity.nb.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phyloseq_alpha_diversity.nb.html Tue May 23 07:59:04 2023 +0000 |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/phyloseq_alpha_diversity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phyloseq_alpha_diversity.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,65 @@ + Observed Chao1 se.chao1 Shannon +DLT0.LOT08 210 210 0 2.01603767724795 +DLT0.LOT05 221 254.785714285714 13.3895041926063 1.79800937304124 +DLT0.LOT03 226 226 0 3.45528429286049 +DLT0.LOT07 221 221 0 2.98216090690738 +DLT0.LOT06 278 278 0 3.20952140178085 +DLT0.LOT01 281 281 0 4.10685205650844 +DLT0.LOT04 247 247 0 2.47304361554073 +DLT0.LOT10 236 236 0 3.55173827807196 +MVT0.LOT05 158 158 0 2.34503849832531 +MVT0.LOT01 128 128 0 2.28541492757583 +MVT0.LOT06 157 157 0 3.92479836105885 +MVT0.LOT07 157 157 0 3.75898496293381 +MVT0.LOT03 160 160 0 3.34027078029461 +MVT0.LOT09 122 122 0 3.95221379962838 +MVT0.LOT08 124 124 0 2.30012425431142 +MVT0.LOT10 95 95 0 1.25959560361526 +BHT0.LOT01 103 103 0 2.53131370126125 +BHT0.LOT07 144 144 0 3.15166550279444 +BHT0.LOT06 155 155 0 2.92765820448176 +BHT0.LOT03 153 153 0 2.95001637842565 +BHT0.LOT10 159 159 0 2.7790079222459 +BHT0.LOT05 183 183 0 2.53671816912042 +BHT0.LOT04 209 209 0 3.47635995384084 +BHT0.LOT08 178 178 0 3.09192502544742 +VHT0.LOT02 132 132 0 1.4154609826759 +VHT0.LOT10 134 134 0 1.87555746873306 +VHT0.LOT03 206 206 0 3.51078572003616 +VHT0.LOT01 235 235 0 2.67402666784541 +VHT0.LOT08 157 157 0 3.31989163716182 +VHT0.LOT06 182 182 0 1.88583439498533 +VHT0.LOT07 156 156 0 1.41904291231118 +VHT0.LOT04 193 193 0 2.64373071960283 +SFT0.LOT08 111 165.473684210526 21.5900554349517 1.13874307530455 +SFT0.LOT07 110 110 0 2.96744303252776 +SFT0.LOT06 126 126 0 2.49355558700118 +SFT0.LOT03 119 119 0 2.92356922933234 +SFT0.LOT02 104 104 0 2.47818417340797 +SFT0.LOT05 75 210.125 60.9771168818602 1.33504649810823 +SFT0.LOT04 70 70 0 1.4778600596069 +SFT0.LOT01 117 117 0 1.98786858579725 +FST0.LOT07 150 150 0 2.99751683958306 +FST0.LOT08 152 152 0 3.4863921810005 +FST0.LOT05 156 156 0 3.37246744717753 +FST0.LOT06 165 165 0 3.40841441699795 +FST0.LOT01 149 149 0 2.43179269800015 +FST0.LOT03 168 168 0 2.92905427377967 +FST0.LOT10 186 186 0 3.03616027233611 +FST0.LOT02 179 179 0 3.18742279060019 +FCT0.LOT06 140 140 0 3.08227430433618 +FCT0.LOT10 172 172 0 3.89564247946871 +FCT0.LOT05 166 166 0 1.99860208269453 +FCT0.LOT03 197 197 0 2.70414675332528 +FCT0.LOT08 218 218 0 3.88853679266027 +FCT0.LOT02 195 195 0 2.55307056135657 +FCT0.LOT07 199 199 0 3.50534515553006 +FCT0.LOT01 200 200 0 3.88749477420522 +CDT0.LOT10 125 125 0 1.04948460066206 +CDT0.LOT08 175 175 0 3.25853898017873 +CDT0.LOT05 264 264 0 4.2074225334087 +CDT0.LOT04 269 269 0 4.45683686305649 +CDT0.LOT06 119 119 0 1.23721179294724 +CDT0.LOT09 177 177 0 1.91666097264414 +CDT0.LOT07 161 161 0 3.09013417675057 +CDT0.LOT02 174 174 0 2.42745280040353 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/phyloseq_beta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phyloseq_beta Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1019 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp0r1_03t5/galaxy-dev\n+Clonage dans \'/tmp/tmp0r1_03t5/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' > \'/tmp/tmp0r1_03t5/tmp/jobdeps4kqb1j_rae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\'\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-05-04 11:01:15,333 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --strict-channel-priority --override-channels --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmp0r1_03t5/deps/_cache/49469f18 --file /tmp/tmp0r1_03t5/tmp/jobdeps4kqb1j_rae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-05-04 11:01:48,691 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmp0r1_03t5/deps/_cache/49469f18 --file /tmp/tmp0r1_03t5/tmp/jobdeps4kqb1j_rae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-05-04 11:02:00,522 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] Executing command: /home/vdarbot/miniconda3/bin/conda clean --tarballs -y\n+galaxy.jobs.runners ERROR 2023-05-04 11:02:01,265 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] (2) Failure preparing job\n+Traceback (most recent call last):\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 262, in prepare_job\n+ job_wrapper.runner_command_line = self.build_command_line(\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 301, in build_command_line\n+ return build_command(\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n+ __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n+ if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n+ self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n+ return self.app.toolbox.dependency_manager.dependency_shell_commands(\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n+ self.build_cache(requirements, **kwds)\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n+ self.build_environment()\n+ File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n+ raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n+galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n+galaxy.jobs DEBUG 2023-05-04 11:02:01,293 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0r1_03t5/job_working_directory/000/2/outputs/galaxy_dataset_65844486-b9e0-448d-a4e7-c957aa6072f2.dat to /tmp/tmp0r1_03t5/files/6/5/8/dataset_65844486-b9e0-448d-a4e7-c957aa6072f2.dat\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/phyloseq_beta.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phyloseq_beta.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1933 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpad8ioi4m/galaxy-dev\n+Clonage dans \'/tmp/tmpad8ioi4m/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'q $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-9dee567f8c5699ef583dd7c0b3a5ebc0a1f72d2a74b08bf3a782619c50641ad7\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-9dee567f8c5699ef583dd7c0b3a5ebc0a1f72d2a74b08bf3a782619c50641ad7\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-9dee567f8c5699ef583dd7c0b3a5ebc0a1f72d2a74b08bf3a782619c50641ad7\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-9dee567f8c5699ef583dd7c0b3a5ebc0a1f72d2a74b08bf3a782619c50641ad7\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; phyloseq_beta_diversity.py --rdata \'/tmp/tmpad8ioi4m/files/7/7/d/dataset_77d86ccc-5832-4281-891a-9cc9d46b5a13.dat\' --varExp \'EnvType\' --distance-methods \'cc,unifrac\' --matrix-outdir \'BetaMatrix\' --html \'/tmp/tmpad8ioi4m/job_working_directory/000/2/outputs/galaxy_dataset_988dd726-32cd-49ca-95ac-0092e604cda6.dat\']\n+galaxy.jobs.runners DEBUG 2023-05-09 09:01:51,694 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpad8ioi4m/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpad8ioi4m/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmpad8ioi4m/job_working_directory/000/2/working/beta_diversity.nb.html" ] ; then cp "/tmp/tmpad8ioi4m/job_working_directory/000/2/working/beta_diversity.nb.html" "/tmp/tmpad8ioi4m/job_working_directory/000/2/outputs/galaxy_dataset_988dd726-32cd-49ca-95ac-0092e604cda6.dat" ; fi; cd \'/tmp/tmpad8ioi4m/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-09 09:01:51,720 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmpad8ioi4m/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 09:02:22,742 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 31392\n+galaxy.jobs.runners.local DEBUG 2023-05-09 09:02:22,745 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpad8ioi4m/job_working_directory/000/2/galaxy_2.sh\n+galaxy.jobs DEBUG 2023-05-09 09:02:22,864 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpad8ioi4m/job_working_directory/000/2/outputs/galaxy_dataset_988dd726-32cd-49ca-95ac-0092e604cda6.dat to /tmp/tmpad8ioi4m/files/9/8/8/dataset_988dd726-32cd-49ca-95ac-0092e604cda6.dat\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/phyloseq_import.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phyloseq_import.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,4772 @@\n+Traceback (most recent call last):\n+ File "/home/vdarbot/.local/bin/planemo", line 5, in <module>\n+ from planemo.cli import planemo\n+ModuleNotFoundError: No module named \'planemo\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpf4wcyew3/galaxy-dev\n+Clonage dans \'/tmp/tmpf4wcyew3/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: ale'..b'? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; phyloseq_import_data.py --biomfile \'/tmp/tmpxabawrwn/files/4/3/4/dataset_434a7334-afaf-49b1-ba0f-31e716f2d862.dat\' --samplefile \'/tmp/tmpxabawrwn/files/2/1/c/dataset_21ca4a43-514c-4a2f-bb48-192e0d7f8eae.dat\' --treefile \'/tmp/tmpxabawrwn/files/a/3/b/dataset_a3bbbfdb-4632-46c5-b438-98b059b1dae2.dat\' --ranks Kingdom Phylum Class Order Family Genus Species --html \'/tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_50731ca5-13e1-4fed-9fbc-202ba6a8e124.dat\' --rdata \'/tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_316c9e1c-9c8f-4b9e-93d3-9154ca0b0020.dat\']\n+galaxy.jobs.runners DEBUG 2023-05-04 10:48:35,016 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] (4) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpxabawrwn/job_working_directory/000/4/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpxabawrwn/job_working_directory/000/4/galaxy_4.ec; \n+if [ -f "/tmp/tmpxabawrwn/job_working_directory/000/4/working/asv_data.Rdata" ] ; then cp "/tmp/tmpxabawrwn/job_working_directory/000/4/working/asv_data.Rdata" "/tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_316c9e1c-9c8f-4b9e-93d3-9154ca0b0020.dat" ; fi; \n+if [ -f "/tmp/tmpxabawrwn/job_working_directory/000/4/working/report.nb.html" ] ; then cp "/tmp/tmpxabawrwn/job_working_directory/000/4/working/report.nb.html" "/tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_50731ca5-13e1-4fed-9fbc-202ba6a8e124.dat" ; fi; cd \'/tmp/tmpxabawrwn/job_working_directory/000/4\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-04 10:48:35,034 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] (4) executing job script: /tmp/tmpxabawrwn/job_working_directory/000/4/galaxy_4.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 10:48:49,807 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 147064\n+galaxy.jobs.runners.local DEBUG 2023-05-04 10:48:49,807 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmpxabawrwn/job_working_directory/000/4/galaxy_4.sh\n+galaxy.jobs DEBUG 2023-05-04 10:48:49,866 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_316c9e1c-9c8f-4b9e-93d3-9154ca0b0020.dat to /tmp/tmpxabawrwn/files/3/1/6/dataset_316c9e1c-9c8f-4b9e-93d3-9154ca0b0020.dat\n+galaxy.jobs DEBUG 2023-05-04 10:48:49,866 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_50731ca5-13e1-4fed-9fbc-202ba6a8e124.dat to /tmp/tmpxabawrwn/files/5/0/7/dataset_50731ca5-13e1-4fed-9fbc-202ba6a8e124.dat\n+galaxy.model.metadata DEBUG 2023-05-04 10:48:49,894 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.model.metadata DEBUG 2023-05-04 10:48:49,902 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 5\n+galaxy.jobs DEBUG 2023-05-04 10:48:49,998 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] job_wrapper.finish for job 4 executed (138.053 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGSSTAT_Phyloseq_Import_Data (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/phyloseq_manova.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phyloseq_manova.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1943 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpcmrjfx4c/galaxy-dev\n+Clonage dans \'/tmp/tmpcmrjfx4c/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 96% (5977/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-p'..b'd15031\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-dbbdef0a126c47fedd769f0626029b80e8d70048c298b953c5df12ebc3d15031\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-dbbdef0a126c47fedd769f0626029b80e8d70048c298b953c5df12ebc3d15031\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-dbbdef0a126c47fedd769f0626029b80e8d70048c298b953c5df12ebc3d15031\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; phyloseq_manova.py --rdata \'/tmp/tmpcmrjfx4c/files/e/b/9/dataset_eb9da6fd-a90e-43f2-97f0-6ae9c961e49d.dat\' --varExp \'EnvType\' --distance-matrix \'/tmp/tmpcmrjfx4c/files/e/2/4/dataset_e249ce0e-97c6-4f34-a568-0e388a7121c8.dat\' --html \'/tmp/tmpcmrjfx4c/job_working_directory/000/3/outputs/galaxy_dataset_022f0c6b-6cec-45d2-aae8-251561944899.dat\']\n+galaxy.jobs.runners DEBUG 2023-05-04 11:02:16,249 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpcmrjfx4c/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpcmrjfx4c/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmpcmrjfx4c/job_working_directory/000/3/working/manova.nb.html" ] ; then cp "/tmp/tmpcmrjfx4c/job_working_directory/000/3/working/manova.nb.html" "/tmp/tmpcmrjfx4c/job_working_directory/000/3/outputs/galaxy_dataset_022f0c6b-6cec-45d2-aae8-251561944899.dat" ; fi; cd \'/tmp/tmpcmrjfx4c/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-04 11:02:16,263 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmpcmrjfx4c/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 11:02:33,355 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 178722\n+galaxy.jobs.runners.local DEBUG 2023-05-04 11:02:33,355 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpcmrjfx4c/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-05-04 11:02:33,388 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpcmrjfx4c/job_working_directory/000/3/outputs/galaxy_dataset_022f0c6b-6cec-45d2-aae8-251561944899.dat to /tmp/tmpcmrjfx4c/files/0/2/2/dataset_022f0c6b-6cec-45d2-aae8-251561944899.dat\n+galaxy.model.metadata DEBUG 2023-05-04 11:02:33,456 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.jobs DEBUG 2023-05-04 11:02:33,558 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (176.376 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/phyloseq_manova.nb.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phyloseq_manova.nb.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1910 @@\n+<!DOCTYPE html>\n+\n+<html>\n+\n+<head>\n+\n+<meta charset="utf-8" />\n+<meta name="generator" content="pandoc" />\n+<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />\n+\n+\n+\n+\n+<title>FROGS Phyloseq: Multivariate Analysis of Variance (version 4.1.0)</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+document.addEventListener(\'DOMContentLoaded\', function(e) {\n+ var hs = document.querySelectorAll("div.section[class*=\'level\'] > :first-child");\n+ var i, h, a;\n+ for (i = 0; i < hs.length; i++) {\n+ h = hs[i];\n+ if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6\n+ a = h.attributes;\n+ while (a.length > 0) h.removeAttribute(a[0].name);\n+ }\n+});\n+</script>\n+<script>/*! jQuery v3.6.0 | (c) OpenJS Foundation and other contributors | jquery.org/license */\n+!function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],r=Object.getPrototypeOf,s=t.slice,g=t.flat?function(e){return t.flat.call(e)}:function(e){return 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add bootstrap table styles to pandoc tables\n+function bootstrapStylePandocTables() {\n+ $(\'tr.odd\').parent(\'tbody\').parent(\'table\').addClass(\'table table-condensed\');\n+}\n+$(document).ready(function () {\n+ bootstrapStylePandocTables();\n+});\n+\n+$(document).ready(function () {\n+ $(\'.knitsql-table\').addClass(\'kable-table\');\n+ var container = $(\'.kable-table\');\n+ container.each(function() {\n+\n+ // move the caption out of the table\n+ var table = $(this).children(\'table\');\n+ var caption = table.children(\'caption\').detach();\n+ caption.insertBefore($(this)).css(\'display\', \'inherit\');\n+ });\n+});\n+\n+</script>\n+\n+<!-- tabsets -->\n+\n+<script>\n+$(document).ready(function () {\n+ window.buildTabsets("TOC");\n+});\n+\n+$(document).ready(function () {\n+ $(\'.tabset-dropdown > .nav-tabs > li\').click(function () {\n+ $(this).parent().toggleClass(\'nav-tabs-open\');\n+ });\n+});\n+</script>\n+\n+<!-- code folding -->\n+<script>\n+$(document).ready(function () {\n+ window.initializeSourceEmbed("phyloseq_manova.Rmd");\n+ window.initializeCodeFolding("hide" === "show");\n+});\n+</script>\n+\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\n+<script>\n+ (function () {\n+ var script = document.createElement("script");\n+ script.type = "text/javascript";\n+ script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";\n+ document.getElementsByTagName("head")[0].appendChild(script);\n+ })();\n+</script>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,18230 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpjctq_t9e/galaxy-dev\n+Clonage dans \'/tmp/tmpjctq_t9e/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vd'..b'py", line 1900, in _execute_context\n+ self.dialect.do_execute(\n+ File "/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 736, in do_execute\n+ cursor.execute(statement, parameters)\n+sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked\n+[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id \n+FROM history_dataset_collection_association, job_to_output_dataset_collection \n+WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.metadata, history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata_deferred, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id \n+FROM history_dataset_association, job_to_output_dataset \n+WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 \n+FROM job \n+WHERE job.state IN (?, ?, ?) AND job.handler = ?]\n+[parameters: (<states.DELETED_NEW: \'deleted_new\'>, <states.DELETING: \'deleting\'>, <states.STOPPING: \'stop\'>, \'main.1\')]\n+(Background on this error at: https://sqlalche.me/e/14/e3q8)\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 7 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_affiliation_filters (Test #1): passed\n+FROGS_affiliation_filters (Test #2): passed\n+FROGS_affiliation_postprocess (Test #1): passed\n+FROGS_affiliation_stats (Test #1): passed\n+FROGS_biom_to_stdBiom (Test #1): passed\n+FROGS_biom_to_tsv (Test #1): passed\n+FROGS_cluster_filters (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test.sh Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,42 @@ +#!/bin/sh +WRAPPER_DIR=~/Bureau/FROGS-wrappers/tools/frogs/ +DIR=planemo_test_4.1.0_vincentdarbot/ +mkdir -p $DIR + +# cd +# . planemo/bin/activate +# cd ~/Bureau/FROGS-wrappers/tools/frogs/test-data + +####################################################################################################### +# TEST LA STRUCTURE +for i in $WRAPPER_DIR/*.xml +do + echo $i + planemo lint $i > $DIR/`basename $i |sed 's/\.xml//'`.lint.log 2>&1 +done + +grep Failed $DIR/*.lint.log + +####################################################################################################### +# VALIDE L'EXECUTION +for i in `ls $WRAPPER_DIR/*.xml | grep -v frogsfunc` +do + echo $i + planemo test --no_cleanup --conda_channels vincentdarbot,conda-forge,bioconda,defaults $i > $DIR/$(basename $i | sed 's/\.xml//').test.log 2>&1 +done + +# si erreur sur github action alors tester +# planemo test --no_cleanup --docker $i > ~/workspace/toolshed_doc/planemo_test_3.2.3_galaxy3/$(basename $i | sed 's/\.xml//').dockertest.log 2>&1 + +grep FAILED $DIR/*test.log + + +grep "test(s) executed passed" $DIR/*test.log + +####################################################################################################### +# TEST SOUS GALAXY + +####################################################################################################### +# SOUMISSION AU TOOLSHED + + |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_2.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,3399 @@\n+planemo couldn\'t find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data.\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpm9gahpt0/galaxy-dev\n+Clonage dans \'/tmp/tmpm9gahpt0/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 81% (5022/6175)\rMise \xc3\xa0 jour des fichiers: 82% (5064/6175)\rMise \xc3\xa0 jour des fichiers: 83% (5126/6175)\rMise \xc3\xa0 jour des fichiers: 84% (5187/6175)\rMise \xc3\xa0 jour des fichiers: 85% (5249/6175)\rMise \xc3\xa0 jour des fichiers: 86% (5311/6175)\rMise \xc3\xa0 jour des fichiers: 87% (5373/6175)\rMise \xc3\xa0 jour des fichiers: 88% (5434/6175)\rMise \xc3\xa0 jour des fichiers: 89% (5496/6175)\rMise \xc3\xa0 jour des fichiers: 90% (5558/6175)\rMise \xc3\xa0 jour des fichiers: 91% (5620/6175)\rMise \xc3\xa0 jour des fichiers: 92% (5681/6175)\rMise \xc3\xa0 jour des fichiers: 93% (5743/6175)\rMise \xc3\xa0 jour des fichiers: 94% (5805/6175)\rMise \xc3\xa0 jour des fichiers: 95% (5867/6175)\rMise \xc3\xa0 jour des fichiers: 96% (5928/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and p'..b'r(\n+bioblend.ConnectionError: Unexpected HTTP status code: 500: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0, "traceback": "Traceback (most recent call last):\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1900, in _execute_context\\n self.dialect.do_execute(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/default.py\\", line 736, in do_execute\\n cursor.execute(statement, parameters)\\nsqlite3.OperationalError: database is locked\\n\\nThe above exception was the direct cause of the following exception:\\n\\nTraceback (most recent call last):\\n File \\"/tmp/tmpt2afa7q5/galaxy-dev/lib/galaxy/web/framework/decorators.py\\", line 337, in decorator\\n rval = func(self, trans, *args, **kwargs)\\n File \\"/tmp/tmpt2afa7q5/galaxy-dev/lib/galaxy/webapps/galaxy/api/users.py\\", line 325, in create\\n user = trans.get_or_create_remote_user(remote_user_email=payload[\\"remote_user_email\\"])\\n File \\"/tmp/tmpt2afa7q5/galaxy-dev/lib/galaxy/webapps/base/webapp.py\\", line 740, in get_or_create_remote_user\\n self.sa_session.query(self.app.model.User)\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 2824, in first\\n return self.limit(1)._iter().first()\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 2916, in _iter\\n result = self.session.execute(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/orm/session.py\\", line 1714, in execute\\n result = conn._execute_20(statement, params or {}, execution_options)\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1705, in _execute_20\\n return meth(self, args_10style, kwargs_10style, execution_options)\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/sql/elements.py\\", line 334, in _execute_on_connection\\n return connection._execute_clauseelement(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1572, in _execute_clauseelement\\n ret = self._execute_context(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1943, in _execute_context\\n self._handle_dbapi_exception(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 2124, in _handle_dbapi_exception\\n util.raise_(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/util/compat.py\\", line 211, in raise_\\n raise exception\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1900, in _execute_context\\n self.dialect.do_execute(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/default.py\\", line 736, in do_execute\\n cursor.execute(statement, parameters)\\nsqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked\\n[SQL: SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.username AS galaxy_user_username, galaxy_user.password AS galaxy_user_password, galaxy_user.last_password_change AS galaxy_user_last_password_change, galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS galaxy_user_activation_token \\nFROM galaxy_user \\nWHERE galaxy_user.email = ?\\n LIMIT ? OFFSET ?]\\n[parameters: (\'planemo@galaxyproject.org\', 1, 0)]\\n(Background on this error at: https://sqlalche.me/e/14/e3q8)\\n"}\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_3.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_3.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,17850 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp1lnw8o38/galaxy-dev\n+Clonage dans \'/tmp/tmp1lnw8o38/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 44% (2755/6175)\rMise \xc3\xa0 jour des fichiers: 45% (2779/6175)\rMise \xc3\xa0 jour des fichiers: 46% (2841/6175)\rMise \xc3\xa0 jour des fichiers: 47% (2903/6175)\rMise \xc3\xa0 jour des fichiers: 48% (2964/6175)\rMise \xc3\xa0 jour des fichiers: 49% (3026/6175)\rMise \xc3\xa0 jour des fichiers: 50% (3088/6175)\rMise \xc3\xa0 jour des fichiers: 51% (3150/6175)\rMise \xc3\xa0 jour des fichiers: 52% (3211/6175)\rMise \xc3\xa0 jour des fichiers: 53% (3273/6175)\rMise \xc3\xa0 jour des fichiers: 54% (3335/6175)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6175)\rMise \xc3\xa0 jour des fichiers: 56% (3458/6175)\rMise \xc3\xa0 jour des fichiers: 57% (3520/6175)\rMise \xc3\xa0 jour des fichiers: 58% (3582/6175)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6175)\rMise \xc3\xa0 jour des fichiers: 60% (3705/6175)\rMise \xc3\xa0 jour des fichiers: 61% (3767/6175)\rMise \xc3\xa0 jour des fichiers: 62% (3829/6175)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6175)\rMise \xc3\xa0 jour des fichiers: 64% (3952/6175)\rMise \xc3\xa0 jour des fichiers: 65% (4014/6175)\rMise \xc3\xa0 jour des fichiers: 66% (4076/6175)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6175)\rMise \xc3\xa0 jour des fichiers: 68% (4199/6175)\rMise \xc3\xa0 jour des fichiers: 69% (4261/6175)\rMise \xc3\xa0 jour des fichiers: 70% (4323/6175)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6175)\rMise \xc3\xa0 jour des fichiers: 72% (4446/6175)\rMise \xc3\xa0 jour des fichiers: 73% (4508/6175)\rMise \xc3\xa0 jour des fichiers: 74% (4570/6175)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6175)\rMise \xc3\xa0 jour des fichiers: 76% (4693/6175)\rMise \xc3\xa0 jour des fichiers: 77% (4755/6175)\rMise \xc3\xa0 jour des fichiers: 78% (4817/6175)\rMise \xc3\xa0 jour des fichiers: 79% (4879/6175)\rMise \xc3\xa0 jour des fichiers: 80% (4940/6175)\rMise \xc3\xa0 jour des fichiers: 81% (5002/6175)\rMise \xc3\xa0 jour des fichiers: 82% (5064/6175)\rMise \xc3\xa0 jour des fichiers: 83% (5126/6175)\rMise \xc3\xa0 jour des fichiers: 84% (5187/6175)\rMise \xc3\xa0 jour des fichiers: 85% (5249/6175)\rMise \xc3\xa0 jour des fichiers: 86% (5311/6175)\rMise \xc3\xa0 jour des fichiers: 87% (5373/6175)\rMise \xc3\xa0 jour des fichiers: 88% (5434/6175)\rMise \xc3\xa0 jour des fichiers: 89% (5496/6175)\rMise \xc3\xa0 jour des fichiers: 90% (5558/6175)\rMise \xc3\xa0 jour des fichiers: 91% (5620/6175)\rMise \xc3\xa0 jour des fichiers: 92% (5681/6175)\rMise \xc3\xa0 jour des fichiers: 93% (5743/6175)\rMise \xc3\xa0 jour des fichiers: 94% (5805/6175)\rMise \xc3\xa0 jour des fichiers: 95% (5867/6175)\rMise \xc3\xa0 jour des fichiers: 96% (5928/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+'..b'runners DEBUG 2023-05-03 18:26:52,562 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] (61) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmp1lnw8o38/job_working_directory/000/61/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp1lnw8o38/job_working_directory/000/61/galaxy_61.ec; \n+if [ -f "/tmp/tmp1lnw8o38/job_working_directory/000/61/working/abundance.biom" ] ; then cp "/tmp/tmp1lnw8o38/job_working_directory/000/61/working/abundance.biom" "/tmp/tmp1lnw8o38/job_working_directory/000/61/outputs/galaxy_dataset_b71cc5e6-174b-4877-ab2f-50c9e54ced3d.dat" ; fi; \n+if [ -f "/tmp/tmp1lnw8o38/job_working_directory/000/61/working/seed.fasta" ] ; then cp "/tmp/tmp1lnw8o38/job_working_directory/000/61/working/seed.fasta" "/tmp/tmp1lnw8o38/job_working_directory/000/61/outputs/galaxy_dataset_c6200c47-8aae-4f25-9108-d5de09303397.dat" ; fi; cd \'/tmp/tmp1lnw8o38/job_working_directory/000/61\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-03 18:26:52,583 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] (61) executing job script: /tmp/tmp1lnw8o38/job_working_directory/000/61/galaxy_61.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-03 18:26:56,881 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 132858\n+galaxy.jobs.runners.local DEBUG 2023-05-03 18:26:56,881 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmp1lnw8o38/job_working_directory/000/61/galaxy_61.sh\n+galaxy.jobs DEBUG 2023-05-03 18:26:56,960 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp1lnw8o38/job_working_directory/000/61/outputs/galaxy_dataset_b71cc5e6-174b-4877-ab2f-50c9e54ced3d.dat to /tmp/tmp1lnw8o38/files/b/7/1/dataset_b71cc5e6-174b-4877-ab2f-50c9e54ced3d.dat\n+galaxy.jobs DEBUG 2023-05-03 18:26:56,960 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp1lnw8o38/job_working_directory/000/61/outputs/galaxy_dataset_c6200c47-8aae-4f25-9108-d5de09303397.dat to /tmp/tmp1lnw8o38/files/c/6/2/dataset_c6200c47-8aae-4f25-9108-d5de09303397.dat\n+galaxy.model.metadata DEBUG 2023-05-03 18:26:57,048 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 84\n+galaxy.model.metadata DEBUG 2023-05-03 18:26:57,069 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 85\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 10 test(s) - out of 22 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_affiliation_filters (Test #1): passed\n+FROGS_affiliation_filters (Test #2): passed\n+FROGS_affiliation_postprocess (Test #1): passed\n+FROGS_affiliation_stats (Test #1): passed\n+FROGS_biom_to_stdBiom (Test #1): passed\n+FROGS_biom_to_tsv (Test #1): passed\n+FROGS_cluster_filters (Test #1): failed\n+FROGS_clustering (Test #1): failed\n+FROGS_demultiplex (Test #1): passed\n+FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n+FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): failed\n+FROGSSTAT_Phyloseq_Sample_Clustering (Test #1): failed\n+FROGSSTAT_Phyloseq_Composition_Visualisation (Test #1): passed\n+FROGSSTAT_Phyloseq_Import_Data (Test #1): passed\n+FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance (Test #1): failed\n+FROGSSTAT_Phyloseq_Structure_Visualisation (Test #1): passed\n+FROGS_preprocess (Test #1): failed\n+FROGS_preprocess (Test #2): failed\n+FROGS_remove_chimera (Test #1): passed\n+FROGS_taxonomic_affiliation (Test #1): failed\n+FROGS_Tree (Test #1): failed\n+FROGS_tsv_to_biom (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/affiliation_filters.xml +Applying linter tests... CHECK +.. CHECK: 2 test(s) found. +Applying linter output... CHECK +.. INFO: 5 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 13 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS Affiliation Filters]. +.. CHECK: Tool defines an id [FROGS_affiliation_filters]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.test.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,2139 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp9qcmzckb/galaxy-dev\n+Clonage dans \'/tmp/tmp9qcmzckb/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'y/000/6/outputs/galaxy_dataset_c1e7acbe-eaaa-4955-b77c-2c777fe2f343.dat" ; fi; \n+if [ -f "/tmp/tmp9qcmzckb/job_working_directory/000/6/working/report.html" ] ; then cp "/tmp/tmp9qcmzckb/job_working_directory/000/6/working/report.html" "/tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_2019c937-3bcb-4b7a-a326-b14c4ce97e2d.dat" ; fi; cd \'/tmp/tmp9qcmzckb/job_working_directory/000/6\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:07:35,439 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] (6) executing job script: /tmp/tmp9qcmzckb/job_working_directory/000/6/galaxy_6.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-25 10:07:39,758 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 126528\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:07:39,758 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmp9qcmzckb/job_working_directory/000/6/galaxy_6.sh\n+galaxy.jobs DEBUG 2023-04-25 10:07:39,815 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_595edf96-87d7-45f4-ae55-5e2a8f60c7d8.dat to /tmp/tmp9qcmzckb/files/5/9/5/dataset_595edf96-87d7-45f4-ae55-5e2a8f60c7d8.dat\n+galaxy.jobs DEBUG 2023-04-25 10:07:39,815 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_02e54cad-416c-40a5-b04f-1c9a2e7fe716.dat to /tmp/tmp9qcmzckb/files/0/2/e/dataset_02e54cad-416c-40a5-b04f-1c9a2e7fe716.dat\n+galaxy.jobs DEBUG 2023-04-25 10:07:39,817 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_6035da0d-daec-46e8-a9ac-65b28363051f.dat to /tmp/tmp9qcmzckb/files/6/0/3/dataset_6035da0d-daec-46e8-a9ac-65b28363051f.dat\n+galaxy.jobs DEBUG 2023-04-25 10:07:39,817 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_c1e7acbe-eaaa-4955-b77c-2c777fe2f343.dat to /tmp/tmp9qcmzckb/files/c/1/e/dataset_c1e7acbe-eaaa-4955-b77c-2c777fe2f343.dat\n+galaxy.jobs DEBUG 2023-04-25 10:07:39,820 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_2019c937-3bcb-4b7a-a326-b14c4ce97e2d.dat to /tmp/tmp9qcmzckb/files/2/0/1/dataset_2019c937-3bcb-4b7a-a326-b14c4ce97e2d.dat\n+galaxy.model.metadata DEBUG 2023-04-25 10:07:39,864 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 9\n+galaxy.model.metadata DEBUG 2023-04-25 10:07:39,873 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 10\n+galaxy.model.metadata DEBUG 2023-04-25 10:07:39,882 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 11\n+galaxy.model.metadata DEBUG 2023-04-25 10:07:39,891 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 12\n+galaxy.model.metadata DEBUG 2023-04-25 10:07:39,900 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 13\n+galaxy.jobs DEBUG 2023-04-25 10:07:39,983 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 6 executed (175.968 ms)\n+\n+galaxy.tool_util.verify INFO: ## files diff on \'/tmp/tmp7b94ceug07-affiliation_deleted.html\' and \'/tmp/tmpya0eqxsh07-affiliation_deleted.html\': lines_diff = 0, found diff = 22\n+Shut down\n+supervisord has terminated\n+There were problems with 2 test(s) - out of 2 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_affiliation_filters (Test #1): failed\n+FROGS_affiliation_filters (Test #2): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/affiliation_postprocess.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 3 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 6 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS Affiliation postprocess]. +.. CHECK: Tool defines an id [FROGS_affiliation_postprocess]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.test.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1889 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmppi6b2sqi/galaxy-dev\n+Clonage dans \'/tmp/tmppi6b2sqi/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'or was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; affiliation_postprocess.py --identity 99.0 --coverage 99.0 --input-biom \'/tmp/tmppi6b2sqi/files/6/9/b/dataset_69bad65a-6880-44a6-a703-46cd3ec77d1a.dat\' --input-fasta \'/tmp/tmppi6b2sqi/files/9/6/a/dataset_96ab65c6-95ab-49c2-ba7b-e40554eefe31.dat\' --output-biom \'/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_dc3db348-241c-4e43-bab5-082edcccca7e.dat\' --output-fasta \'/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_f6a5f1c0-aa78-46d7-b45f-d5b2070860d4.dat\' --output-compo \'/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_27919559-054e-4612-9447-e22347219a85.dat\']\n+galaxy.jobs.runners DEBUG 2023-04-25 10:08:39,296 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmppi6b2sqi/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmppi6b2sqi/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/affiliation.biom" ] ; then cp "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/affiliation.biom" "/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_dc3db348-241c-4e43-bab5-082edcccca7e.dat" ; fi; \n+if [ -f "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/sequences.fasta" ] ; then cp "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/sequences.fasta" "/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_f6a5f1c0-aa78-46d7-b45f-d5b2070860d4.dat" ; fi; \n+if [ -f "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/aggregation_composition.txt" ] ; then cp "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/aggregation_composition.txt" "/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_27919559-054e-4612-9447-e22347219a85.dat" ; fi; cd \'/tmp/tmppi6b2sqi/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:08:39,310 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] (3) executing job script: /tmp/tmppi6b2sqi/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-25 10:08:44,022 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 127528\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:08:44,022 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmppi6b2sqi/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-04-25 10:08:44,080 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_dc3db348-241c-4e43-bab5-082edcccca7e.dat to /tmp/tmppi6b2sqi/files/d/c/3/dataset_dc3db348-241c-4e43-bab5-082edcccca7e.dat\n+galaxy.jobs DEBUG 2023-04-25 10:08:44,080 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_f6a5f1c0-aa78-46d7-b45f-d5b2070860d4.dat to /tmp/tmppi6b2sqi/files/f/6/a/dataset_f6a5f1c0-aa78-46d7-b45f-d5b2070860d4.dat\n+galaxy.jobs DEBUG 2023-04-25 10:08:44,081 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_27919559-054e-4612-9447-e22347219a85.dat to /tmp/tmppi6b2sqi/files/2/7/9/dataset_27919559-054e-4612-9447-e22347219a85.dat\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_affiliation_postprocess (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/affiliation_stats.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 1 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 8 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS_6_Affiliation_Stat]. +.. CHECK: Tool defines an id [FROGS_affiliation_stats]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.test.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,992 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp6sl3s_05/galaxy-dev\n+Clonage dans \'/tmp/tmp6sl3s_05/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vdar'..b'patching to planemo_runner runner\n+galaxy.jobs DEBUG 2023-04-25 10:09:43,253 [pN:main.1,p:128442,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: planemo_dest)\n+galaxy.jobs DEBUG 2023-04-25 10:09:43,259 [pN:main.1,p:128442,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmp6sl3s_05/job_working_directory/000/2\n+galaxy.jobs.runners DEBUG 2023-04-25 10:09:43,276 [pN:main.1,p:128442,tN:JobHandlerQueue.monitor_thread] Job [2] queued (72.382 ms)\n+galaxy.jobs.handler INFO 2023-04-25 10:09:43,286 [pN:main.1,p:128442,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n+galaxy.jobs DEBUG 2023-04-25 10:09:43,374 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] Job wrapper for Job [2] prepared (82.886 ms)\n+galaxy.tool_util.deps DEBUG 2023-04-25 10:09:43,375 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] Using dependency frogs version 4.1.0 of type conda\n+galaxy.tool_util.deps DEBUG 2023-04-25 10:09:43,375 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] Using dependency frogs version 4.1.0 of type conda\n+galaxy.jobs.command_factory INFO 2023-04-25 10:09:43,392 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] Built script [/tmp/tmp6sl3s_05/job_working_directory/000/2/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; affiliation_stats.py --input-biom \'/tmp/tmp6sl3s_05/files/0/8/c/dataset_08cb8a17-6762-4e50-b5de-4602c2fef700.dat\' --output-file \'/tmp/tmp6sl3s_05/job_working_directory/000/2/outputs/galaxy_dataset_1a79590c-5959-4e26-a94c-eb1d3d789546.dat\' --taxonomic-ranks Domain Phylum Class Order Family Genus Species --rarefaction-ranks Family Genus Species --multiple-tag \'blast_affiliations\' --tax-consensus-tag \'blast_taxonomy\' --identity-tag \'perc_identity\' --coverage-tag \'perc_query_coverage\']\n+galaxy.jobs.runners DEBUG 2023-04-25 10:09:43,464 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmp6sl3s_05/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp6sl3s_05/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmp6sl3s_05/job_working_directory/000/2/working/summary.html" ] ; then cp "/tmp/tmp6sl3s_05/job_working_directory/000/2/working/summary.html" "/tmp/tmp6sl3s_05/job_working_directory/000/2/outputs/galaxy_dataset_1a79590c-5959-4e26-a94c-eb1d3d789546.dat" ; fi; cd \'/tmp/tmp6sl3s_05/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:09:43,479 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmp6sl3s_05/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.tool_util.verify INFO: ## files diff on \'/tmp/tmp_oyu80z611-affiliationsStat.html\' and \'/tmp/tmp1flu7_ok11-affiliationsStat.html\': lines_diff = 2, found diff = 24\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_affiliation_stats (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/biom_to_stdBiom.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 2 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 1 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS BIOM to std BIOM]. +.. CHECK: Tool defines an id [FROGS_biom_to_stdBiom]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.test.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1003 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp2vc8jplr/galaxy-dev\n+Clonage dans \'/tmp/tmp2vc8jplr/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; biom_to_stdBiom.py --input-biom \'/tmp/tmp2vc8jplr/files/b/e/1/dataset_be142786-3b8d-42d8-a52e-e159f016b5aa.dat\' --output-biom \'/tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_9b56e9ef-f202-48bb-a0e4-572245eae18f.dat\' --output-metadata \'/tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_2a18acad-24f5-46f0-9fd8-9bcd0550af07.dat\']\n+galaxy.jobs.runners DEBUG 2023-04-25 10:10:41,741 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmp2vc8jplr/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp2vc8jplr/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmp2vc8jplr/job_working_directory/000/2/working/abundance.biom" ] ; then cp "/tmp/tmp2vc8jplr/job_working_directory/000/2/working/abundance.biom" "/tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_9b56e9ef-f202-48bb-a0e4-572245eae18f.dat" ; fi; \n+if [ -f "/tmp/tmp2vc8jplr/job_working_directory/000/2/working/blast_details.tsv" ] ; then cp "/tmp/tmp2vc8jplr/job_working_directory/000/2/working/blast_details.tsv" "/tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_2a18acad-24f5-46f0-9fd8-9bcd0550af07.dat" ; fi; cd \'/tmp/tmp2vc8jplr/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:10:41,757 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmp2vc8jplr/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-25 10:10:45,694 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 129418\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:10:45,695 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmp2vc8jplr/job_working_directory/000/2/galaxy_2.sh\n+galaxy.jobs DEBUG 2023-04-25 10:10:45,742 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_9b56e9ef-f202-48bb-a0e4-572245eae18f.dat to /tmp/tmp2vc8jplr/files/9/b/5/dataset_9b56e9ef-f202-48bb-a0e4-572245eae18f.dat\n+galaxy.jobs DEBUG 2023-04-25 10:10:45,742 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_2a18acad-24f5-46f0-9fd8-9bcd0550af07.dat to /tmp/tmp2vc8jplr/files/2/a/1/dataset_2a18acad-24f5-46f0-9fd8-9bcd0550af07.dat\n+galaxy.model.metadata DEBUG 2023-04-25 10:10:45,779 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 2\n+galaxy.model.metadata DEBUG 2023-04-25 10:10:45,787 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.jobs DEBUG 2023-04-25 10:10:45,862 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 2 executed (125.434 ms)\n+\n+galaxy.tool_util.verify INFO: ## files diff on \'/tmp/tmp7mjnslv513-affiliation_multihit.tsv\' and \'/tmp/tmp9q6ya5ku13-affiliation_multihit.tsv\': lines_diff = 0, found diff = 97\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_biom_to_stdBiom (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/biom_to_tsv.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 2 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 3 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS BIOM to TSV]. +.. CHECK: Tool defines an id [FROGS_biom_to_tsv]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.test.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1825 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpe5j6sxz0/galaxy-dev\n+Clonage dans \'/tmp/tmpe5j6sxz0/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'ers.local DEBUG 2023-04-25 10:11:33,704 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] (1) executing job script: /tmp/tmpe5j6sxz0/job_working_directory/000/1/galaxy_1.sh\n+galaxy.jobs.mapper DEBUG 2023-04-25 10:11:34,350 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: upload_dest\n+galaxy.jobs.handler DEBUG 2023-04-25 10:11:34,357 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner\n+galaxy.jobs DEBUG 2023-04-25 10:11:34,488 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: upload_dest)\n+galaxy.jobs DEBUG 2023-04-25 10:11:34,497 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmpe5j6sxz0/job_working_directory/000/2\n+galaxy.jobs.runners DEBUG 2023-04-25 10:11:34,513 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] Job [2] queued (155.352 ms)\n+galaxy.jobs.handler INFO 2023-04-25 10:11:34,523 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n+galaxy.jobs DEBUG 2023-04-25 10:11:34,647 [pN:main.1,p:130255,tN:LocalRunner.work_thread-1] Job wrapper for Job [2] prepared (109.936 ms)\n+galaxy.jobs.command_factory INFO 2023-04-25 10:11:34,663 [pN:main.1,p:130255,tN:LocalRunner.work_thread-1] Built script [/tmp/tmpe5j6sxz0/job_working_directory/000/2/tool_script.sh] for tool command [python \'/tmp/tmpe5j6sxz0/galaxy-dev/tools/data_source/upload.py\' \'/tmp/tmpe5j6sxz0/galaxy-dev\' \'/tmp/tmpe5j6sxz0/job_working_directory/000/2/registry.xml\' \'/tmp/tmpe5j6sxz0/tmp/upload_params_4dov0ik0\' \'2:/tmp/tmpe5j6sxz0/job_working_directory/000/2/working/dataset_30175cbd-5fac-4cdb-b7e6-37e4713ed524_files:/tmp/tmpe5j6sxz0/job_working_directory/000/2/outputs/galaxy_dataset_30175cbd-5fac-4cdb-b7e6-37e4713ed524.dat\']\n+\n+galaxy.jobs.runners DEBUG 2023-04-25 10:11:34,709 [pN:main.1,p:130255,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpe5j6sxz0/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpe5j6sxz0/job_working_directory/000/2/galaxy_2.ec; cd \'/tmp/tmpe5j6sxz0/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:11:34,726 [pN:main.1,p:130255,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmpe5j6sxz0/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-25 10:11:37,539 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 130274\n+galaxy.jobs.runners.local DEBUG 2023-04-25 10:11:37,539 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpe5j6sxz0/job_working_directory/000/1/galaxy_1.sh\n+galaxy.jobs DEBUG 2023-04-25 10:11:37,638 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpe5j6sxz0/job_working_directory/000/1/outputs/galaxy_dataset_8be40f4f-af9e-4fc5-a44a-5745106653c7.dat to /tmp/tmpe5j6sxz0/files/8/b/e/dataset_8be40f4f-af9e-4fc5-a44a-5745106653c7.dat\n+\n+galaxy.model.metadata DEBUG 2023-04-25 10:11:37,703 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1\n+galaxy.jobs DEBUG 2023-04-25 10:11:37,785 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 1 executed (187.283 ms)\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_biom_to_tsv (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/cluster_filters.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 4 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 13 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS_4 Cluster filters]. +.. CHECK: Tool defines an id [FROGS_cluster_filters]. +.. CHECK: Tool targets 16.01 Galaxy profile. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.test.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1049 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpwby5bixe/galaxy-dev\n+Clonage dans \'/tmp/tmpwby5bixe/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b"23-04-25 10:12:47,421 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --strict-channel-priority --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-2e551f2af3517c80384199d3fff6b06c5fa3d12c3c5277abd509d92437d55a28 frogs=4.1.0 blast=2.10\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:09,029 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-2e551f2af3517c80384199d3fff6b06c5fa3d12c3c5277abd509d92437d55a28 frogs=4.1.0 blast=2.10\n+\n+galaxy.tool_util.deps.resolvers.conda DEBUG 2023-04-25 10:13:13,057 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Removing failed conda install of [CondaTarget[frogs,version=4.1.0], CondaTarget[blast,version=2.10]]\n+galaxy.tool_util.deps DEBUG 2023-04-25 10:13:13,057 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Using dependency frogs version 4.1.0 of type conda\n+galaxy.tool_util.deps DEBUG 2023-04-25 10:13:13,057 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Using dependency blast version 2.10 of type conda\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:13,058 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --strict-channel-priority --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-2e551f2af3517c80384199d3fff6b06c5fa3d12c3c5277abd509d92437d55a28 frogs=4.1.0 blast=2.10\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:22,977 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-2e551f2af3517c80384199d3fff6b06c5fa3d12c3c5277abd509d92437d55a28 frogs=4.1.0 blast=2.10\n+\n+galaxy.tool_util.deps.resolvers.conda DEBUG 2023-04-25 10:13:31,937 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Removing failed conda install of [CondaTarget[frogs,version=4.1.0], CondaTarget[blast,version=2.10]]\n+galaxy.tool_util.deps DEBUG 2023-04-25 10:13:31,937 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Using dependency frogs version 4.1.0 of type conda\n+galaxy.tool_util.deps DEBUG 2023-04-25 10:13:31,937 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Using dependency blast version 2.10 of type conda\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:31,937 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda list --name __frogs@4.1.0 --export > '/tmp/tmpwby5bixe/tmp/jobdeps72lihs9lae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0'\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:36,783 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --strict-channel-priority --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmpwby5bixe/deps/_cache/7aceb47c --file /tmp/tmpwby5bixe/tmp/jobdeps72lihs9lae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\n+\n+galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:18:09,666 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmpwby5bixe/deps/_cache/7aceb47c --file /tmp/tmpwby5bixe/tmp/jobdeps72lihs9lae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\n+\n+\n+Aborted!\n+Shut down\n+\n+Aborted!\n" |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/cluster_stats.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/cluster_stats.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/cluster_stats.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 1 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 1 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS_Cluster_Stat]. +.. CHECK: Tool defines an id [FROGS_cluster_stats]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/clustering.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/clustering.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/clustering.xml +Applying linter tests... CHECK +.. CHECK: 2 test(s) found. +Applying linter output... CHECK +.. INFO: 3 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 7 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS_2 Clustering swarm]. +.. CHECK: Tool defines an id [FROGS_clustering]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/clustering.test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/clustering.test.log Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,12 @@ +Traceback (most recent call last): + File "/home/vdarbot/miniconda3/bin/planemo", line 5, in <module> + from planemo.cli import planemo + File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/planemo/cli.py", line 24, in <module> + from planemo.galaxy import profiles + File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/planemo/galaxy/__init__.py", line 4, in <module> + File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/planemo/galaxy/config.py", line 29, in <module> + File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/galaxy/tool_util/deps/__init__.py", line 17, in <module> + File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/galaxy/util/__init__.py", line 63, in <module> + File "src/lxml/etree.pyx", line 96, in init lxml.etree + File "/home/vdarbot/miniconda3/lib/python3.9/abc.py", line 107, in __new__ +KeyboardInterrupt |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/demultiplex.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/demultiplex.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/demultiplex.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 3 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 7 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS_0 Demultiplex reads]. +.. CHECK: Tool defines an id [FROGS_demultiplex]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/deseq2_preprocess.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/deseq2_preprocess.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,23 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/deseq2_preprocess.xml +Failed linting +Applying linter tests... FAIL +.. ERROR: Test 1: Found output tag with unknown name [dds], valid names ['dds_asv', 'dds_function', 'phyloseq'] +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 3 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 8 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT DESeq2 Preprocess]. +.. CHECK: Tool defines an id [FROGSSTAT_DESeq2_Preprocess]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... FAIL +.. ERROR: Invalid XML found in file: deseq2_preprocess.xml. Errors [/tmp/tmpjg7yzk7o:30:0:ERROR:SCHEMASV:SCHEMAV_CVC_COMPLEX_TYPE_2_3: Element 'inputs': Character content other than whitespace is not allowed because the content type is 'element-only'.] |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/deseq2_visualisation.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/deseq2_visualisation.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/deseq2_visualisation.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 3 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 8 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT DESeq2 Visualisation]. +.. CHECK: Tool defines an id [FROGSSTAT_DESeq2_Visualisation]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_functions.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_functions.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,28 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/frogsfunc_functions.xml +Failed linting +Applying linter tests... FAIL +.. ERROR: Test 1: Test param function not found in the inputs +.. ERROR: Test 1: Test param marker not found in the inputs +.. ERROR: Test 1: Test param min_reads not found in the inputs +.. ERROR: Test 1: Test param min_samples not found in the inputs +.. ERROR: Test 1: Test param strat not found in the inputs +.. ERROR: Test 1: Found output tag with unknown name [output_function_abund], valid names ['summary_file', 'output_biom', 'output_fasta', 'output_otu_norm', 'output_weighted', 'output_excluded', 'output_copy_ec_abund', 'output_copy_ko_abund', 'output_copy_cog_abund', 'output_copy_pfam_abund', 'output_copy_tigrfam_abund', 'output_copy_pheno_abund', 'output_function_ec_abund', 'output_function_ko_abund', 'output_function_cog_abund', 'output_function_pfam_abund', 'output_function_tigrfam_abund', 'output_function_pheno_abund'] +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 18 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 10 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSFUNC_2_functions]. +.. CHECK: Tool defines an id [FROGSFUNC_step3_functions]. +.. CHECK: Tool targets 16.01 Galaxy profile. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_pathways.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_pathways.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/frogsfunc_pathways.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 2 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 4 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSFUNC_3_pathways]. +.. CHECK: Tool defines an id [FROGSFUNC_step4_pathways]. +.. CHECK: Tool targets 16.01 Galaxy profile. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_placeseqs.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_placeseqs.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/frogsfunc_placeseqs.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 7 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 5 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSFUNC_1_placeseqs_and_copynumbers]. +.. CHECK: Tool defines an id [FROGSFUNC_step1_placeseqs]. +.. CHECK: Tool targets 16.01 Galaxy profile. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/itsx.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/itsx.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,23 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/itsx.xml +Failed linting +Applying linter tests... FAIL +.. ERROR: Test 1: Test param trim_sequence not found in the inputs +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 4 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 5 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS ITSx]. +.. CHECK: Tool defines an id [FROGS_itsx]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/normalisation.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/normalisation.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/normalisation.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 3 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 5 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS Abundance normalisation]. +.. CHECK: Tool defines an id [FROGS_normalisation]. +.. CHECK: Tool targets 16.01 Galaxy profile. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_alpha_diversity.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_alpha_diversity.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_alpha_diversity.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 2 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 3 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Alpha Diversity]. +.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Alpha_Diversity]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_beta_diversity.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_beta_diversity.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_beta_diversity.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 1 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 4 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Beta Diversity]. +.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Beta_Diversity]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_clustering.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_clustering.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_clustering.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 1 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 3 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Sample Clustering]. +.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Sample_Clustering]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_composition.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_composition.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_composition.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 1 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 6 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Composition Visualisation]. +.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Composition_Visualisation]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_import_data.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_import_data.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_import_data.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 2 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 5 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Import Data]. +.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Import_Data]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_manova.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_manova.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_manova.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 1 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 3 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Multivariate Analysis Of Variance]. +.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_structure.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_structure.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_structure.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 1 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 4 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Structure Visualisation]. +.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Structure_Visualisation]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/preprocess.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/preprocess.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/preprocess.xml +Applying linter tests... CHECK +.. CHECK: 2 test(s) found. +Applying linter output... CHECK +.. INFO: 3 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 44 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS_1 Pre-process]. +.. CHECK: Tool defines an id [FROGS_preprocess]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/remove_chimera.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/remove_chimera.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/remove_chimera.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 4 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 4 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS_3 Remove chimera]. +.. CHECK: Tool defines an id [FROGS_remove_chimera]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/taxonomic_affiliation.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/taxonomic_affiliation.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/taxonomic_affiliation.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 2 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 5 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS_5 Taxonomic affiliation]. +.. CHECK: Tool defines an id [FROGS_taxonomic_affiliation]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/tree.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/tree.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/tree.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 2 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 2 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS Tree]. +.. CHECK: Tool defines an id [FROGS_Tree]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.1.0_vincentdarbot/tsv_to_biom.lint.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.1.0_vincentdarbot/tsv_to_biom.lint.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -0,0 +1,21 @@ +Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/tsv_to_biom.xml +Applying linter tests... CHECK +.. CHECK: 1 test(s) found. +Applying linter output... CHECK +.. INFO: 2 outputs found. +Applying linter inputs... CHECK +.. INFO: Found 3 input parameters. +Applying linter help... CHECK +.. CHECK: Tool contains help section. +.. CHECK: Help contains valid reStructuredText. +Applying linter general... CHECK +.. CHECK: Tool defines a version [4.1.0+galaxy1]. +.. CHECK: Tool defines a name [FROGS TSV_to_BIOM]. +.. CHECK: Tool defines an id [FROGS_tsv_to_biom]. +.. CHECK: Tool specifies profile version [20.05]. +Applying linter command... CHECK +.. INFO: Tool contains a command. +Applying linter citations... CHECK +.. CHECK: Found 2 likely valid citations. +Applying linter tool_xsd... CHECK +.. INFO: File validates against XML schema. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_4.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_4.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,6086 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpvrixslsg/galaxy-dev\n+Clonage dans \'/tmp/tmpvrixslsg/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'er.work_thread-0] (83) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpvrixslsg/job_working_directory/000/83/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpvrixslsg/job_working_directory/000/83/galaxy_83.ec; \n+if [ -f "/tmp/tmpvrixslsg/job_working_directory/000/83/working/abundance.biom" ] ; then cp "/tmp/tmpvrixslsg/job_working_directory/000/83/working/abundance.biom" "/tmp/tmpvrixslsg/job_working_directory/000/83/outputs/galaxy_dataset_5a468301-746c-42ad-bcf0-7ddd00ea53e5.dat" ; fi; \n+if [ -f "/tmp/tmpvrixslsg/job_working_directory/000/83/working/seed.fasta" ] ; then cp "/tmp/tmpvrixslsg/job_working_directory/000/83/working/seed.fasta" "/tmp/tmpvrixslsg/job_working_directory/000/83/outputs/galaxy_dataset_5049f307-1911-43a7-a62f-fcba4c73ff64.dat" ; fi; cd \'/tmp/tmpvrixslsg/job_working_directory/000/83\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-04 14:20:47,839 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] (83) executing job script: /tmp/tmpvrixslsg/job_working_directory/000/83/galaxy_83.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 14:20:50,912 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 267154\n+galaxy.jobs.runners.local DEBUG 2023-05-04 14:20:50,913 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpvrixslsg/job_working_directory/000/83/galaxy_83.sh\n+galaxy.jobs DEBUG 2023-05-04 14:20:50,948 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpvrixslsg/job_working_directory/000/83/outputs/galaxy_dataset_5a468301-746c-42ad-bcf0-7ddd00ea53e5.dat to /tmp/tmpvrixslsg/files/5/a/4/dataset_5a468301-746c-42ad-bcf0-7ddd00ea53e5.dat\n+galaxy.jobs DEBUG 2023-05-04 14:20:50,948 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpvrixslsg/job_working_directory/000/83/outputs/galaxy_dataset_5049f307-1911-43a7-a62f-fcba4c73ff64.dat to /tmp/tmpvrixslsg/files/5/0/4/dataset_5049f307-1911-43a7-a62f-fcba4c73ff64.dat\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 10 test(s) - out of 31 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_affiliation_filters (Test #1): passed\n+FROGS_affiliation_filters (Test #2): passed\n+FROGS_affiliation_postprocess (Test #1): passed\n+FROGS_affiliation_stats (Test #1): passed\n+FROGS_biom_to_stdBiom (Test #1): passed\n+FROGS_biom_to_tsv (Test #1): passed\n+FROGS_cluster_filters (Test #1): failed\n+FROGS_clustering (Test #1): passed\n+FROGS_clustering (Test #2): passed\n+FROGS_cluster_stats (Test #1): passed\n+FROGS_demultiplex (Test #1): passed\n+FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n+FROGSSTAT_DESeq2_Visualisation (Test #1): failed\n+FROGSFUNC_step3_functions (Test #1): failed\n+FROGSFUNC_step4_pathways (Test #1): failed\n+FROGSFUNC_step1_placeseqs (Test #1): failed\n+FROGS_itsx (Test #1): passed\n+FROGS_normalisation (Test #1): passed\n+FROGSSTAT_Phyloseq_Alpha_Diversity (Test #1): passed\n+FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): failed\n+FROGSSTAT_Phyloseq_Sample_Clustering (Test #1): passed\n+FROGSSTAT_Phyloseq_Composition_Visualisation (Test #1): passed\n+FROGSSTAT_Phyloseq_Import_Data (Test #1): passed\n+FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance (Test #1): passed\n+FROGSSTAT_Phyloseq_Structure_Visualisation (Test #1): passed\n+FROGS_preprocess (Test #1): failed\n+FROGS_preprocess (Test #2): failed\n+FROGS_remove_chimera (Test #1): passed\n+FROGS_taxonomic_affiliation (Test #1): failed\n+FROGS_Tree (Test #1): passed\n+FROGS_tsv_to_biom (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_5.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_5.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,17841 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpu_fgppyy/galaxy-dev\n+Clonage dans \'/tmp/tmpu_fgppyy/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vd'..b", job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id \n+FROM history_dataset_collection_association, job_to_output_dataset_collection \n+WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.metadata, history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata_deferred, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id \n+FROM history_dataset_association, job_to_output_dataset \n+WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 \n+FROM job \n+WHERE job.state IN (?, ?, ?) AND job.handler = ?]\n+[parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main.1')]\n+(Background on this error at: https://sqlalche.me/e/14/e3q8)\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 3 test(s) - out of 16 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_affiliation_filters (Test #1): passed\n+FROGS_affiliation_filters (Test #2): passed\n+FROGS_affiliation_postprocess (Test #1): passed\n+FROGS_affiliation_stats (Test #1): passed\n+FROGS_biom_to_stdBiom (Test #1): passed\n+FROGS_biom_to_tsv (Test #1): passed\n+FROGS_cluster_filters (Test #1): passed\n+FROGS_clustering (Test #1): passed\n+FROGS_clustering (Test #2): passed\n+FROGS_cluster_stats (Test #1): passed\n+FROGS_demultiplex (Test #1): passed\n+FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n+FROGSSTAT_DESeq2_Visualisation (Test #1): passed\n+FROGSFUNC_step3_functions (Test #1): passed\n+FROGSFUNC_step4_pathways (Test #1): failed\n+FROGSFUNC_step1_placeseqs (Test #1): failed\n" |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/planemo_test_6.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/planemo_test_6.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,6602 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmppgarrkg4/galaxy-dev\n+Clonage dans \'/tmp/tmppgarrkg4/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'tmp/tmppgarrkg4/job_working_directory/000/88/galaxy_88.ec; \n+if [ -f "/tmp/tmppgarrkg4/job_working_directory/000/88/working/abundance.biom" ] ; then cp "/tmp/tmppgarrkg4/job_working_directory/000/88/working/abundance.biom" "/tmp/tmppgarrkg4/job_working_directory/000/88/outputs/galaxy_dataset_4e1c8324-7bde-462f-9fc0-01789f3287a0.dat" ; fi; \n+if [ -f "/tmp/tmppgarrkg4/job_working_directory/000/88/working/seed.fasta" ] ; then cp "/tmp/tmppgarrkg4/job_working_directory/000/88/working/seed.fasta" "/tmp/tmppgarrkg4/job_working_directory/000/88/outputs/galaxy_dataset_bc63d7f9-f46a-4cb9-85c8-261c177d796f.dat" ; fi; cd \'/tmp/tmppgarrkg4/job_working_directory/000/88\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-09 13:02:49,951 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] (88) executing job script: /tmp/tmppgarrkg4/job_working_directory/000/88/galaxy_88.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 13:02:54,169 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 159506\n+galaxy.jobs.runners.local DEBUG 2023-05-09 13:02:54,169 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmppgarrkg4/job_working_directory/000/88/galaxy_88.sh\n+galaxy.jobs DEBUG 2023-05-09 13:02:54,213 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppgarrkg4/job_working_directory/000/88/outputs/galaxy_dataset_4e1c8324-7bde-462f-9fc0-01789f3287a0.dat to /tmp/tmppgarrkg4/files/4/e/1/dataset_4e1c8324-7bde-462f-9fc0-01789f3287a0.dat\n+galaxy.jobs DEBUG 2023-05-09 13:02:54,213 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppgarrkg4/job_working_directory/000/88/outputs/galaxy_dataset_bc63d7f9-f46a-4cb9-85c8-261c177d796f.dat to /tmp/tmppgarrkg4/files/b/c/6/dataset_bc63d7f9-f46a-4cb9-85c8-261c177d796f.dat\n+galaxy.model.metadata DEBUG 2023-05-09 13:02:54,265 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 133\n+galaxy.model.metadata DEBUG 2023-05-09 13:02:54,279 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 134\n+\n+galaxy.jobs DEBUG 2023-05-09 13:02:54,498 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] job_wrapper.finish for job 88 executed (295.746 ms)\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 4 test(s) - out of 31 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_affiliation_filters (Test #1): passed\n+FROGS_affiliation_filters (Test #2): passed\n+FROGS_affiliation_postprocess (Test #1): passed\n+FROGS_affiliation_stats (Test #1): passed\n+FROGS_biom_to_stdBiom (Test #1): passed\n+FROGS_biom_to_tsv (Test #1): passed\n+FROGS_cluster_filters (Test #1): passed\n+FROGS_clustering (Test #1): passed\n+FROGS_clustering (Test #2): passed\n+FROGS_cluster_stats (Test #1): passed\n+FROGS_demultiplex (Test #1): passed\n+FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n+FROGSSTAT_DESeq2_Visualisation (Test #1): passed\n+FROGSFUNC_step3_functions (Test #1): passed\n+FROGSFUNC_step4_pathways (Test #1): passed\n+FROGSFUNC_step1_placeseqs (Test #1): failed\n+FROGS_itsx (Test #1): passed\n+FROGS_normalisation (Test #1): passed\n+FROGSSTAT_Phyloseq_Alpha_Diversity (Test #1): passed\n+FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): passed\n+FROGSSTAT_Phyloseq_Sample_Clustering (Test #1): passed\n+FROGSSTAT_Phyloseq_Composition_Visualisation (Test #1): passed\n+FROGSSTAT_Phyloseq_Import_Data (Test #1): passed\n+FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance (Test #1): passed\n+FROGSSTAT_Phyloseq_Structure_Visualisation (Test #1): passed\n+FROGS_preprocess (Test #1): failed\n+FROGS_preprocess (Test #2): failed\n+FROGS_remove_chimera (Test #1): passed\n+FROGS_taxonomic_affiliation (Test #1): passed\n+FROGS_Tree (Test #1): passed\n+FROGS_tsv_to_biom (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/preprocess.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocess.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,2187 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpf5nu7q0b/galaxy-dev\n+Clonage dans \'/tmp/tmpf5nu7q0b/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/.local/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n+\n+[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n+[notice] To update, run: pip install --upgrade pip\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirement'..b'770-4665-adca-3be38edd13ce.dat\' --R1-size 267 --R2-size 266 --mismatch-rate 0.15 --merge-software vsearch --keep-unmerged]\n+galaxy.jobs.runners DEBUG 2023-05-19 19:24:28,921 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] (4) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpf5nu7q0b/job_working_directory/000/4/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpf5nu7q0b/job_working_directory/000/4/galaxy_4.ec; \n+if [ -f "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/dereplicated.fasta" ] ; then cp "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/dereplicated.fasta" "/tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_e2c97707-a166-4579-98d6-4bf7516ad47e.dat" ; fi; \n+if [ -f "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/count.tsv" ] ; then cp "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/count.tsv" "/tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_bb215308-43aa-40e3-8098-0818c25d88ab.dat" ; fi; \n+if [ -f "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/report.html" ] ; then cp "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/report.html" "/tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_670e9a4e-8a70-45a7-94f7-638ffe0f2430.dat" ; fi; cd \'/tmp/tmpf5nu7q0b/job_working_directory/000/4\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-19 19:24:28,943 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] (4) executing job script: /tmp/tmpf5nu7q0b/job_working_directory/000/4/galaxy_4.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-19 19:25:08,489 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 370281\n+galaxy.jobs.runners.local DEBUG 2023-05-19 19:25:08,489 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmpf5nu7q0b/job_working_directory/000/4/galaxy_4.sh\n+galaxy.jobs DEBUG 2023-05-19 19:25:08,529 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_e2c97707-a166-4579-98d6-4bf7516ad47e.dat to /tmp/tmpf5nu7q0b/files/e/2/c/dataset_e2c97707-a166-4579-98d6-4bf7516ad47e.dat\n+galaxy.jobs DEBUG 2023-05-19 19:25:08,529 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_bb215308-43aa-40e3-8098-0818c25d88ab.dat to /tmp/tmpf5nu7q0b/files/b/b/2/dataset_bb215308-43aa-40e3-8098-0818c25d88ab.dat\n+galaxy.jobs DEBUG 2023-05-19 19:25:08,529 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_670e9a4e-8a70-45a7-94f7-638ffe0f2430.dat to /tmp/tmpf5nu7q0b/files/6/7/0/dataset_670e9a4e-8a70-45a7-94f7-638ffe0f2430.dat\n+galaxy.model.metadata DEBUG 2023-05-19 19:25:08,606 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 6\n+galaxy.model.metadata DEBUG 2023-05-19 19:25:08,638 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 7\n+galaxy.model.metadata DEBUG 2023-05-19 19:25:08,647 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 8\n+galaxy.jobs DEBUG 2023-05-19 19:25:08,726 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] job_wrapper.finish for job 4 executed (203.612 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 2 test(s) executed passed.\n+FROGS_preprocess (Test #1): passed\n+FROGS_preprocess (Test #2): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/01-prepro-flash.fasta --- a/test-data/references/01-prepro-flash.fasta Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,140562 +0,0 @@\n->01_3118;size=12 reference=AB747657_SH134902.07FU_refs position=1..151 \n-CTGAGTATTTGTCTTTTAAAGACATCTCTCTATCCATACACTCTTTTTTTTAAAAAGACATGATTTATACAGTTAGTCTGAATGATTTTTTAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->01_7682;size=17 reference=KJ922376_SH187578.07FU_refs position=1..170 errors=108%G \n-TACCCTTGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCTCCAGGACCACACCATAAACCTTTTTTATGCAGTTGCAATCAGCGTCAGTACAACAAATGTAAATCATTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->01_72347;size=10 reference=JN192372_SH093189.07FU_refs position=1..193 errors=129%C \n-GCGGCCGGCTGAATATTTTTTTTCACCCATGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCAAACCATAAACCTTTTTCTTATGCAGTTTCCATCAGCGTCAGTAAAAACAATGTAATTATTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->01_52289;size=9 reference=JX272968_SH208843.07FU_refs position=1..194 \n-CCGAGTGAGGGTCCCCTCCGGGGGGCCCAACCTCCCACCCGTGTCTACTGTACCATGTTGCTTCGGCGGGCGCGCCCGTGCCCGCCGGAGACCCCTTGAACGCTGTTGTGAATGAGGTTGTCTGAGTGAGATTGCAAACTGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n->01_8007;size=9 reference=KJ638312_SH419903.07FU_refs position=1..194 \n-GATCATTACCGAGTTCTCGGGCTTCGGCTCGACTCTCCCACCCTTTGTGAACGTACCTCTGTTGCTTTGGCGGCTCCGGCCGCCAAAGGACCTCCAAACTCCAGTCAGTAAACGCAGACGTCTGATAAACAAGTTAATAAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->01_1497;size=12 reference=GU237816_SH186616.07FU_refs position=1..198 \n-ATCATTACCTAGAGTTGTGGGCTCTGCCTACCATCTCTTACCCATGTCTTTTGAGTACCTTCGTTTCCTCGGCGGGTCCGCCCGCCGATCGGACAACACTTAAACCCTTTGTAATTGAAATCAGCGTCTGAAAAAACTTTAATAGTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->01_17752;size=6 reference=KP744516_SH528288.07FU_refs position=1..198 \n-CCGAGTGAGGGTCTTCAAAGGCTCAACCTCCCAAACCCCTTGTATATCACCGAGAGTTTTATTGTTGCTTCGGTGGGTCCACAGTGCCCACCGAAGACCCACCAAAAATCCTAGTAAGAGTGTCGTCTGAGTAATTAAAAAATAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGC\n->01_21530;size=5 reference=DQ103550_SH211946.07FU_refs position=1..202 \n-GGAAGGATCATTACCGAGTTCTCGAGCTTCGGCTCGACTCTCCCACCCTTTGTGAACACACCTCTGTTGCCTCGGCGGCCGCTCCGGCCGCCGAAGGACCTTCAAACTCCAGTCAGTAAACGCAGACGTCTGATAAACAAGTCAATGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->01_83487;size=12 reference=HE861827_SH187575.07FU_refs position=1..202 \n-TACAATATGAAGGCTTCGGCTGGATTATTTATTTCACCCTTGTCTTTTGCGCACTTGTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCACACCATAAACCTTTTTTGTTAATGCAGTCAGCGTCAGTACAACAAATGTAAATCATTTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->01_10273;size=9 reference=JQ746601_SH188617.07FU_refs position=1..210 errors=109%C \n-TTGAAATAAACCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTGTAGACTTTCCAAGTCTATGTTGCTTCATTTACCCCAATGTATGTTAATAGAATGTTGTCTTTTATAATATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->01_19311;size=12 reference=HQ880789_SH123218.07FU_refs position=1..211 errors=22%G \n-CCGAGTTTTCAACTCCCTAACCCTTTTGTGAACCTACCTATTGTTGCTTCGGCGGACTCGCCCCAGCCGGACGCGGACTGGACCAGCGGCCGCCGGGGACCCTCAAACTCTTGTATTATCAGCATCTTCTGAATACGCCGCAAGGCAAAACAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGC\n->01_12586;size=12 reference=KP165574_SH188638.07FU_refs position=1..213 errors=93%G \n-TTGAAATAAACCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTTGTAGACCTTTCAGGTCTATGTTTTCTCATTTTACCCCAATGTATGTCGATAGAATGTTGTGCCTTTATAATGTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->01_96708;size=5 reference=KP013190_SH094425.07FU_refs position=1..213 \n-TTGAAATAAATCTGATGGGTTGTTGCTGGTTCTCTAGGGAGCATGTGCACGCCTTGTCATCTTTATATCTCCACCTGTGCACTTTTTGTAGACCCTTCAAGGTCTATGTCGCTTAATTTACCCCAAACAAATAATAGAATGTTGTGCCTTTGAAAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->01_235;size=10 reference=EF652441_SH091530.07FU_refs_singleton position=1..215 \n-AAGGATCATTACCGAGTGTAGGGTGCCTCCGGGCGCCCAACCTCCCACCCGTGACTACCTAACCCTGTTGCTTCGGCGGGGCGCCCCCCCGGGGGGCCGCCGCCGGGGACTACTGAACCTCCTGTCTGAGCCTGATGCAGTCTGAGCTTTGATATTAAATAGTCAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n->01_53715;size=15 reference=JX436920_SH182391.07FU_refs position=1..216 \n-CGTGCACGCCCGAG'..b'TCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->01_36531_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=178%T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=95+A \n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTTAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATTGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->03_11710_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=157+G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=42%A \n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCGATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCTACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->03_1160_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=126%G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=75+C \n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTGCTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->01_7615_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=101+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=15%G \n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAATAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCCATGAAGAACGCAGC\n->02_91186_FROGS_combined;size=1 R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=52+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=82%C \n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCGTTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/01-prepro-flash.html --- a/test-data/references/01-prepro-flash.html Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,828 +0,0 @@\n-<!DOCTYPE html>\n-<!--\n-# Copyright (C) 2015 INRA\n-#\n-# This program is free software: you can redistribute it and/or modify\n-# it under the terms of the GNU General Public License as published by\n-# the Free Software Foundation, either version 3 of the License, or\n-# (at your option) any later version.\n-#\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n-# GNU General Public License for more details.\n-#\n-# You should have received a copy of the GNU General Public License\n-# along with this program. If not, see <https://www.gnu.org/licenses/>.\n--->\n-<html>\n- <head>\n- <title>FROGS Pre-process</title>\n- <meta charset="UTF-8">\n- <meta name="version" content="4.0.1">\n- <!-- CSS -->\n- \n- \n-\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n-\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n-\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"></link>\n- <style type="text/css">\n- #js-alert {\n- width: 90%;\n- margin-right: auto;\n- margin-left: auto;\n- }\n- #content {\n- width: 90%;\n- margin-right: auto;\n- margin-left: auto;\n- }\n- .clear {\n- clear: both;\n- height: 0px;\n- width: 100%;\n- float: none !important;\n- }\n- ul.nav-tabs {\n-\t\t\t\tmargin-bottom: 30px;\n-\t\t\t}\n-\t\t\t.page-item.active .page-link {\n-\t\t\t\tz-index: 1;\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tbackground-color: #8EADAC;\n-\t\t\t\tborder-color: #8EADAC;\n-\t\t\t\toutline: none !important;\n-\t\t\t\tbox-shadow: none !important;\n-\t\t\t}\n-\t\t\t.btn {\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tborder:#8EADAC;\n-\t\t\t\tbackground-color: #8EADAC;\n-\t\t\t}\n-\t\t\t.btn:focus, .btn:active {\n-\t\t\t\toutline: none !important;\n-\t\t\t\tbox-shadow: none !important;\n-\t\t\t}\n-\t\t\t.btn:hover:enabled{\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tborder:#648a89;\n-\t\t\t\tbackground-color: #648a89;\n-\t\t\t\tcursor:pointer !important;\n-\t\t\t}\n-\t\t\t.pb-2, .py-2 {\n-\t\t\t\tpadding-bottom: 1.5rem !important;\n-\t\t\t\tmargin-bottom: 2rem !important;\n-\t\t\t\tmargin-top: 4rem !important;\n-\t\t\t}\n-\t\t\t.pb-2-first{\n-\t\t\t\tpadding-bottom: 1.5rem !important;\n-\t\t\t\tmargin-bottom: 2rem !important;\n-\t\t\t\tmargin-top: 1rem !important;\n-\t\t\t}\n-\t\t\t/* ##### THEME FOR CHECKBOXES ##### */\n-\t\t\t.container {\n-\t\t\t\tposition: relative;\n-\t\t\t\tpadding-left: 0px;\n-\t\t\t\tmargin-bottom: 15px;\n-\t\t\t\tcursor: pointer;\n-\t\t\t\t-webkit-user-select: none;\n-\t\t\t\t-moz-user-select: none;\n-\t\t\t\t-ms-user-select: none;\n-\t\t\t\tuser-select: none;\n-\t\t\t}\n-\n-\t\t\t/* Hide the browser\'s default checkbox */\n-\t\t\t.container input {\n-\t\t\t\tposition: absolute;\n-\t\t\t\topacity: 0;\n-\t\t\t\tcursor: pointer;\n-\t\t\t}\n-\n-\t\t\t/* Create a custom checkbox */\n-\t\t\t.checkmark {\n-\t\t\t\tposition: absolute;\n-\t\t\t\ttop: 0;\n-\t\t\t\tleft: 0;\n-\t\t\t\theight: 20px;\n-\t\t\t\twidth: 20px;\n-\t\t\t\tbackground-color: #8EADAC;\n-\t\t\t\tborder-radius: 5px;\n-\t\t\t\topacity:0.65;\n-\t\t\t}\n-\n-\t\t\t/* On mouse-over, add a grey background color */\n-\t\t\t.container:hover input ~ .checkmark {\n-\t\t\t\tbackground-color: #648a89;\n-\t\t\t}\n-\n-\t\t\t/* When the checkbox is checked, add a blue background */\n-\t\t\t.container input:checked ~ .checkmark {\n-\t\t\t\tbackground-color: #8EADAC;\n-\t\t\t\topacity:1;\n-\t\t\t}\n-\n-\t\t\t/* Create the checkmark/indicator (hidden when not checked) */\n-\t\t\t.checkmark:after {\n-\t\t\t\tcontent: "";\n-\t\t\t\tposition: absolute;\n-\t\t\t\tdisplay: none;\n-\t\t\t}\n-\n-\t\t\t/* Show the checkmark when checked */\n-\t\t\t.container input:checked ~ .checkmark:after {\n-\t\t\t\tdisplay: block;\n-\t\t\t}\n-\n-\t\t\t/* Style the checkmark/indicator */\n-\t\t\t.container .checkmark:after {\n-\t\t\t\tleft: 7px;\n-\t\t\t\ttop: 3px;\n-\t\t\t\twidth: 6px;\n-\t\t\t\theight: 10px;\n-\t\t\t\tborder: solid white;\n-\t\t\t\tborder-width:'..b'oad("artificial combined", false, "filterBySample-table-artificialCombined", false); \n- }else{\n- $("#filterBySample-table-artificialCombined").prev("h2").remove();\n- $("#filterBySample-table-artificialCombined").remove();\n- }\n- /*$("select").addClass("selectpicker");\n- $(".dataTables_length select").selectpicker({\n-\t\t\t\t\tstyle: \'btn-info\',\n-\t\t\t\t\tsize: 2,\n-\t\t\t\t\twidth : \'60px\'\n-\t\t\t\t});\n-\t\t\t\t$(\'.selectpicker\').selectpicker(\'refresh\');\n-\t\t\t\t//$(\'select\').selectpicker(\'refresh\');\n-\t\t\t\t*/\n- });\n- </script>\n- </head>\n- <body>\n- <!-- Alert -->\n- <p id="js-alert" class="alert alert-warning">\n- javascript is needed to display data.<br />\n- If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n- </p>\n- \n- <!-- Content -->\n- <div id="content" class="hidden">\n-\t\t\t<h2 class="pb-2-first mt-4 mb-2 border-bottom" style="margin-top: 1rem">Preprocess summary</h2>\n- <div id="filter-summary"></div>\n- \n- <div id="filter-log">\n-\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Details on merged sequences</h2>\n- <table id="filterBySample-table-combined" class="table table-striped">\n- <thead>\n-\t\t\t\t\t\t<!--\n- <tr>\n- <th class="title">Filtering by sample : details on full length amplicon reads</th>\n- </tr>\n- -->\n- </thead>\n- <tbody></tbody>\n- <tfoot>\n- <tr>\n- <th>\n- <span class="table-action">With selection:</span> \n- <button id="display-spl-lengths" class="btn table-action fusion-right" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="before-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display amplicon lengths</span> </button>\n- <button id="display-after-spl-lengths" class="btn table-action" disabled data-toggle="modal" data-target="#lengths-modal" data-whatever="after-process" ><span class="fa fa-line-chart" aria-hidden="true"> Display preprocessed amplicon lengths</span></button>\n- </th>\n- </tr>\n- </tfoot>\n- </table>\n- <h2 class="pb-2 mt-4 mb-2 border-bottom">Details on artificial combined sequences</h2>\n- <table id="filterBySample-table-artificialCombined" class="table table-striped">\n- <thead>\n- </thead>\n- <tbody></tbody>\n- </table>\n- </div>\n- </div>\n- \n- \n- \n- <!-- Modals -->\n- <div class="modal" id="lengths-modal" tabindex="-1" role="dialog" aria-hidden="true">\n- <div class="modal-dialog modal-lg">\n- <div class="modal-content">\n- <div class="modal-header">\n- <h4 class="modal-title">Amplicons lengths</h4>\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- \n- \n- </div>\n- <div class="modal-body">\n- <div id="lengths-chart"></div>\n- </div>\n- <div class="modal-footer">\n- <button class="btn table-action fusion-right" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n- </div>\n- </div>\n- </div>\n- </div>\n- </body>\n-</html>\n' |
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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/01-prepro-vsearch.html --- a/test-data/references/01-prepro-vsearch.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/01-prepro-vsearch.html Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Pre-process</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <!-- CSS --> |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/02-clustering_denoising.biom --- a/test-data/references/02-clustering_denoising.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/02-clustering_denoising.biom Tue May 23 07:59:04 2023 +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": "2022-06-15T10:03:09", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_74803"}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_22"}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_103"}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_222"}}, {"id": "Cluster_5", "metadata": {"comment": [], "seed_id": "01_94"}}, {"id": "Cluster_6", "metadata": {"comment": [], "seed_id": "01_69140"}}, {"id": "Cluster_7", "metadata": {"comment": [], "seed_id": "01_108"}}, {"id": "Cluster_8", "metadata": {"comment": [], "seed_id": "01_19"}}, {"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_60"}}, {"id": "Cluster_10", "metadata": {"comment": [], "seed_id": "01_97858"}}, {"id": "Cluster_11", "metadata": {"comment": [], "seed_id": "01_60934"}}, {"id": "Cluster_12", "metadata": {"comment": [], "seed_id": "01_67210"}}, {"id": "Cluster_13", "metadata": {"comment": [], "seed_id": "01_85419"}}, {"id": "Cluster_14", "metadata": {"comment": [], "seed_id": "01_81"}}, {"id": "Cluster_15", "metadata": {"comment": [], "seed_id": "01_66997"}}, {"id": "Cluster_16", "metadata": {"comment": [], "seed_id": "01_54"}}, {"id": "Cluster_17", "metadata": {"comment": [], "seed_id": "01_92546"}}, {"id": "Cluster_18", "metadata": {"comment": [], "seed_id": "01_59"}}, {"id": "Cluster_19", "metadata": {"comment": [], "seed_id": "01_96725"}}, {"id": "Cluster_20", "metadata": {"comment": [], "seed_id": "01_71661"}}, {"id": "Cluster_21", "metadata": {"comment": [], "seed_id": "01_25"}}, {"id": "Cluster_22", "metadata": {"comment": [], "seed_id": "01_201"}}, {"id": "Cluster_23", "metadata": {"comment": [], "seed_id": "01_76"}}, {"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_38"}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_10"}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_97506"}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_190"}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_85242"}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id": "01_91819"}}, {"id": "Cluster_30", "metadata": {"comment": [], "seed_id": "01_91485"}}, {"id": "Cluster_31", "metadata": {"comment": [], "seed_id": "01_264"}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_90"}}, {"id": "Cluster_33", "metadata": {"comment": [], "seed_id": "01_155"}}, {"id": "Cluster_34", "metadata": {"comment": [], "seed_id": "01_54706"}}, {"id": "Cluster_35", "metadata": {"comment": [], "seed_id": "01_259"}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_51488"}}, {"id": "Cluster_37", "metadata": {"comment": [], "seed_id": "01_40"}}, {"id": "Cluster_38", "metadata": {"comment": [], "seed_id": "01_151"}}, {"id": "Cluster_39", "metadata": {"comment": [], "seed_id": "01_65"}}, {"id": "Cluster_40", "metadata": {"comment": [], "seed_id": "01_91964"}}, {"id": "Cluster_41", "metadata": {"comment": [], "seed_id": "01_76743"}}, {"id": "Cluster_42", "metadata": {"comment": [], "seed_id": "01_90304"}}, {"id": "Cluster_43", "metadata": {"comment": [], "seed_id": "01_54589"}}, {"id": "Cluster_44", "metadata": {"comment": [], "seed_id": "01_101"}}, {"id": "Cluster_45", "metadata": {"comment": [], "seed_id": "01_67"}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_410"}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_66"}}, {"id": "Cluster_48_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined"}}, {"id": "Cluster_49", "metadata": {"comment": [], "seed_id": "01_86"}}, {"id": "Cluster_50", "metadata": {"comment": [], "seed_id": "01_88865"}}, {"id": "Cluster_51", "metadata": {"comment": [], "seed_id": "01_210"}}, {"id": "Cluster_52", "metadata": 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[74063, 0, 1], [74064, 0, 1], [74065, 0, 1], [74066, 0, 1], [74067, 0, 1], [74068, 0, 1], [74069, 0, 1], [74070, 0, 1], [74071, 0, 1], [74072, 0, 1], [74073, 0, 1], [74074, 0, 1], [74075, 0, 1], [74076, 0, 1], [74077, 0, 1], [74078, 0, 1], [74079, 0, 1], [74080, 0, 1], [74081, 0, 1], [74082, 0, 1], [74083, 0, 1], [74084, 0, 1], [74085, 0, 1], [74086, 0, 1], [74087, 0, 1], [74088, 0, 1], [74089, 0, 1], [74090, 0, 1], [74091, 0, 1], [74092, 0, 1], [74093, 0, 1], [74094, 0, 1], [74095, 0, 1], [74096, 0, 1], [74097, 0, 1], [74098, 0, 1], [74099, 0, 1], [74100, 0, 1], [74101, 0, 1], [74102, 0, 1], [74103, 0, 1], [74104, 0, 1], [74105, 0, 1], [74106, 0, 1], [74107, 0, 1], [74108, 0, 1], [74109, 0, 1], [74110, 0, 1], [74111, 0, 1], [74112, 0, 1], [74113, 0, 1], [74114, 0, 1], [74115, 0, 1], [74116, 0, 1], [74117, 0, 1], [74118, 0, 1], [74119, 0, 1], [74120, 0, 1], [74121, 0, 1], [74122, 0, 1], [74123, 0, 1], [74124, 0, 1], [74125, 0, 1], [74126, 0, 1]], "shape": [74127, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/02-clustering_denoising.fasta --- a/test-data/references/02-clustering_denoising.fasta Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,148254 +0,0 @@\n->Cluster_1 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n-AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n->Cluster_2 reference=JX118731_SH218995.07FU_refs position=1..250 errors=164%A\n-GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_3 reference=HG007976_SH219743.07FU_refs position=1..250 errors=127%C,210%A\n-AAGGATCATTATTGAATGAACTTGGCGTGGTTGTTGCTGGTCCTCTCGGGGGCATGTGCACACCCGTCATCTTTATCTTTCCACCTGTGCACGTTTTGTAGGTCCAAAAAATTTTTCCGAGGCAACTCGTTTTAGGGGACTGGCGTTCGTTACTGTCGCCTTTCCCTGGATTTTAGGCCTATGTTTTCACATACACCATAACAATGTAATAGAATGTTATTAATGGGCTTTATTGCCTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_4 reference=UDB002317_SH221025.07FU_refs position=1..250 errors=99%A\n-CTGAACGAAATGGGTGGCAAGGCTGTCGCTGGCTCAAATGAGCATGTGCACGTCTTTTGCTGCTTACTTCATTCTCTTTTCCACCTGTGCACTCTTTGTAAACACTTGGGATGTGAGAGAGGGTTGGCATTTATTGTTGAACCTCTCTTGATATTGAAAAAGTCTGGGTGTTTATGTATTTTTTGACATACACGGTCGAATGTCTATAGAATGAAATTAATAGGCTCTTGTCAGCCTTTAAATGATAAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_5 reference=GU234142_SH201120.07FU_refs position=1..250\n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->Cluster_6 reference=UDB015350_SH176685.07FU_refs position=1..250 errors=205%A\n-GTGACTGCGGAGGATCATTATCGAATAAACTTGAGCATGCTGTTTGCTGGCCCCTGCCCTGGGGTATGTGCACGCTTGTTCTTTTGTTATTTCTCCAACCTGTGCACATTTTGTAGACCCTGGAGATTTTATGAATTTTGATTCGATTCGGGACTGCTGATGCTTCCCTTTGTTGAAGCCGGCTTTGCCTTGCACCTCCAGGTCTATGTCATTTTTCACAACCTCTTTTTAAAAAAACATGTTTGGAAAAAATATAAATGAAATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_7 reference=KF732310_SH222414.07FU_refs position=1..250 errors=173%G\n-TTGAAATAAACCTGATGAGTTGCTGCTGGCTCTCTTGGGAGCATGTGCACACTTGTCGTCTTTATATCTCCACCTGTGCACCTTTTGTAGACTTTGGATATCTTTCTGAGTGCTTGTCACTCAGGTTCTTGAGGATTGACTTTACGTCTCTCTTTACATTTCCAAGTCTATGTTTCTTCATATACTCAATGTATGTCTTAGAGTGTAATTAATGGGCCATTGTGCCTATAAACTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_8 reference=JQ320113_SH190746.07FU_refs position=1..250 errors=210%G\n-TCGAAATAAAAACTTGGTTTGGGTTGTTGCTGGCTTCTAGAAGCATGTGCACACTTACTCCATTTTTTCAACCACCTGTGCACTTTGTGTAGACCTGAAACACTTTTTCAAGGTAGTTAAACTAACTACTCTTGGTTTGAGAATCGTCGCTACATGGCTTTTCTCGCGTCTCAGGTTTATGTTCTTTTATATGTACCCTACGAGAATGTATATGAATGTCTACAATTGGCCTCGTGCCTTTTAAAAATTAAAACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_10 reference=JQ621972_SH177703.07FU_refs position=1..250\n-TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->Cluster_9 reference=JQ279537_SH175098.07FU_refs position=1..250\n-CTGAGGTTACCGGGGGTGAGTTGCGAGTCGTTTGTTGCTGGCGCTTCACGGCGCATGTGCACGGCGCTCCTCCTCATCTTCGTTCCTTCTATCAACCCCTGTGCACTATGATGGGATTAGAGAGAAGCGCGTCTTCTTAGGGATTAACGTAGTAGTTGTGGGTCCGCCCGCGGCAAAAGGTTAATCTTTGATCGGCGGCGTCGTGGTACCTCGAAGTCTCCGTTATTTCAAACTACTATATATGTCTTGTCAGAATGATTAGTCCTTCGTTGGACGCTAATGAAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_11 reference=JX536175_SH183774.07FU_refs position=1..250 errors=71%T\n-AACTTCTTTGGAGATAGTACTGTTGCTGGCCTTGTAATGAGGTATGTGCACGTTCTATTGCCAATTTATTCATCCACCTGTGCACTTTTTGTAGGAGTTCTTTGGGGTTATTTTGTACTTGGTGCAATTTGGCTTTGAAAGGCTTCTATGTCTTATAAACCATTAGTATGTCTCTGAATGTTTTTTATTGGGACTTGATTGGCCCTTTAAACTTGT'..b'CAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_52229_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=122+T;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=47%A\n-TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCTAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAATTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_8899_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=105%G;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=100+G\n-TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTGTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCACATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_65152_FROGS_combined R1_desc:reference=KF732603_SH223051.07FU_refs position=1..250 errors=92%T;R2_desc=R2_desc=reference=KF732603_SH223051.07FU_refs position=1..250 errors=107+T\n-TTGAAATAAATCTGGCGAGTTGCTGCTGGTTCTCCAGGGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGATCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCATGTGCACACTTGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATATCTCTCTGGATGGGTTGCTATTCAGGATTGAGGATTGACTTTTATGTCTCTCCTTCCATTTCCAGGCCTATGTTTCTTCATAATACTCCAATGTATGTCATAGAATGTAATCAATGGCCTTTGTGCCTATAAATCTTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_10490_FROGS_combined R1_desc:reference=UDB001581_SH219736.07FU_refs position=1..250 errors=237%G;R2_desc=R2_desc=reference=UDB001581_SH219736.07FU_refs position=1..250 errors=165+A\n-TTGAATGAACTTGGCTTGGTTGCTGCTGGTCTTTTCGAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATGCAACTTTCAGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACATGTGCACGCCATGTCATCTTTATATCTCCACCTGTGCACCTTTTGTAGACCTGGATTCAATTTTCCGAGGTAACTCGGTTCGTGAGGAACTGCTTAACGGCTTTCCTTGTTAGTTTCCAGGCCTATGTTTTCATATACACCATACGAATGTAACAGAATGTCATTATTAGGCTTAATTGTCTTATAAACTATATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_6064_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=197+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=181%C\n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCGGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/02-clustering_fastidious.biom --- a/test-data/references/02-clustering_fastidious.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/02-clustering_fastidious.biom Tue May 23 07:59:04 2023 +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": "2022-06-15T10:02:11", "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', 2, 1], [74661, 2, 1], [74662, 2, 1], [74663, 2, 1], [74664, 2, 1], [74665, 2, 1], [74666, 2, 1], [74667, 2, 1], [74668, 2, 1], [74669, 2, 1], [74670, 2, 1], [74671, 2, 1], [74672, 2, 1], [74673, 2, 1], [74674, 2, 1], [74675, 2, 1], [74676, 2, 1], [74677, 2, 1], [74678, 2, 1], [74679, 2, 1], [74680, 2, 1], [74681, 2, 1], [74682, 2, 1], [74683, 2, 1], [74684, 2, 1], [74685, 2, 1], [74686, 2, 1], [74687, 2, 1], [74688, 2, 1], [74689, 2, 1], [74690, 2, 1], [74691, 2, 1], [74692, 2, 1], [74693, 2, 1], [74694, 2, 1], [74695, 2, 1], [74696, 2, 1], [74697, 2, 1], [74698, 2, 1], [74699, 2, 1], [74700, 2, 1], [74701, 2, 1], [74702, 2, 1], [74703, 2, 1], [74704, 2, 1], [74705, 2, 1], [74706, 2, 1], [74707, 2, 1], [74708, 2, 1], [74709, 2, 1], [74710, 2, 1], [74711, 2, 1], [74712, 2, 1], [74713, 2, 1], [74714, 2, 1], [74715, 2, 1], [74716, 2, 1], [74717, 2, 1], [74718, 2, 1], [74719, 2, 1], [74720, 2, 1], [74721, 2, 1], [74722, 2, 1], [74723, 2, 1], [74724, 2, 1], [74725, 2, 1], [74726, 2, 1], [74727, 2, 1], [74728, 2, 1], [74729, 2, 1], [74730, 2, 1], [74731, 2, 1], [74732, 2, 1], [74733, 2, 1], [74734, 2, 1], [74735, 2, 1], [74736, 2, 1], [74737, 2, 1], [74738, 2, 1], [74739, 2, 1], [74740, 2, 1], [74741, 2, 1], [74742, 2, 1], [74743, 2, 1], [74744, 2, 1], [74745, 2, 1], [74746, 2, 1], [74747, 2, 1], [74748, 2, 1], [74749, 2, 1], [74750, 2, 1], [74751, 2, 1], [74752, 2, 1], [74753, 2, 1], [74754, 2, 1], [74755, 2, 1], [74756, 2, 1], [74757, 2, 1], [74758, 2, 1], [74759, 2, 1], [74760, 2, 1], [74761, 2, 1], [74762, 2, 1], [74763, 2, 1], [74764, 2, 1], [74765, 2, 1], [74766, 2, 1], [74767, 2, 1], [74768, 2, 1], [74769, 2, 1], [74770, 2, 1], [74771, 2, 1], [74772, 2, 1], [74773, 2, 1], [74774, 2, 1], [74775, 2, 1], [74776, 2, 1], [74777, 2, 1], [74778, 2, 1], [74779, 2, 1], [74780, 2, 1], [74781, 2, 1], [74782, 2, 1], [74783, 2, 1], [74784, 2, 1], [74785, 2, 1], [74786, 2, 1], [74787, 2, 1], [74788, 2, 1], [74789, 2, 1], [74790, 2, 1], [74791, 2, 1], [74792, 2, 1], [74793, 2, 1], [74794, 2, 1], [74795, 2, 1], [74796, 2, 1], [74797, 2, 1], [74798, 2, 1], [74799, 2, 1], [74800, 2, 1], [74801, 2, 1], [74802, 2, 1], [74803, 2, 1], [74804, 2, 1], [74805, 2, 1], [74806, 2, 1], [74807, 2, 1], [74808, 2, 1], [74809, 2, 1], [74810, 2, 1], [74811, 2, 1], [74812, 2, 1], [74813, 2, 1], [74814, 2, 1], [74815, 2, 1], [74816, 2, 1], [74817, 2, 1], [74818, 2, 1], [74819, 2, 1], [74820, 2, 1], [74821, 2, 1], [74822, 2, 1], [74823, 2, 1], [74824, 2, 1], [74825, 2, 1], [74826, 2, 1], [74827, 2, 1], [74828, 2, 1], [74829, 2, 1], [74830, 2, 1], [74831, 2, 1], [74832, 2, 1], [74833, 2, 1], [74834, 2, 1], [74835, 2, 1], [74836, 2, 1], [74837, 2, 1], [74838, 2, 1], [74839, 2, 1], [74840, 2, 1], [74841, 2, 1], [74842, 2, 1], [74843, 2, 1], [74844, 2, 1], [74845, 2, 1], [74846, 2, 1], [74847, 2, 1], [74848, 2, 1], [74849, 2, 1], [74850, 2, 1], [74851, 2, 1], [74852, 2, 1], [74853, 2, 1], [74854, 2, 1], [74855, 2, 1], [74856, 2, 1], [74857, 2, 1], [74858, 2, 1], [74859, 2, 1], [74860, 2, 1], [74861, 2, 1], [74862, 2, 1], [74863, 2, 1], [74864, 2, 1], [74865, 2, 1], [74866, 2, 1], [74867, 2, 1], [74868, 2, 1], [74869, 2, 1], [74870, 2, 1], [74871, 2, 1], [74872, 2, 1], [74873, 2, 1], [74874, 2, 1], [74875, 2, 1], [74876, 2, 1], [74877, 2, 1], [74878, 2, 1], [74879, 2, 1], [74880, 2, 1], [74881, 2, 1], [74882, 2, 1], [74883, 2, 1], [74884, 2, 1], [74885, 2, 1], [74886, 2, 1], [74887, 2, 1], [74888, 2, 1], [74889, 2, 1], [74890, 2, 1], [74891, 2, 1], [74892, 2, 1], [74893, 2, 1], [74894, 2, 1], [74895, 2, 1], [74896, 2, 1], [74897, 2, 1], [74898, 2, 1], [74899, 2, 1], [74900, 2, 1], [74901, 2, 1], [74902, 2, 1], [74903, 2, 1], [74904, 2, 1], [74905, 2, 1], [74906, 2, 1], [74907, 2, 1], [74908, 2, 1], [74909, 2, 1], [74910, 2, 1], [74911, 2, 1], [74912, 2, 1], [74913, 2, 1], [74914, 2, 1], [74915, 2, 1], [74916, 2, 1], [74917, 2, 1], [74918, 2, 1], [74919, 2, 1], [74920, 2, 1], [74921, 2, 1]], "shape": [74922, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/02-clustering_fastidious.fasta --- a/test-data/references/02-clustering_fastidious.fasta Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,149844 +0,0 @@\n->Cluster_1 reference=JF747094_SH197643.07FU_refs position=1..249 errors=112%A\n-ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->Cluster_2 reference=DQ898183_SH216206.07FU_refs position=1..249 errors=21%G\n-CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->Cluster_3 reference=JN711441_SH022548.07FU_refs_singleton position=1..248 errors=206%T\n-AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n->Cluster_4 reference=AF456924_SH097201.07FU_refs position=1..250\n-CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->Cluster_5 reference=JX399009_SH268556.07FU_refs position=1..249 errors=185%C\n-CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->Cluster_6 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n-AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n->Cluster_7 reference=JF417478_SH216679.07FU_refs position=1..250 errors=99%T\n-CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n->Cluster_8 reference=EU837224_SH182725.07FU_refs position=1..249 errors=132%T\n-TTGAATTCTATGGAGGGGGGAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCTTCCTTTCTCTCATACACACACCTGTGCACCTGTTGTAGGTCCTCGAAAGAGGAGCTATGTTTTTCACATCACACCCCGTCGTATGTCTATAGAATGTGTTGAAAACGTCGACCTGTTTGACAGGCCGGCGGACAATAAAATTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_9 reference=JQ621972_SH177703.07FU_refs position=1..250\n-TACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATATCTGCCCCGGGCGCGTCGCCGCCCCGGACCAAGGCGCCCGCCGGGGGACCAACCCAAAAATCTTTTGTACACCCCCTCGCGGGTTTTTTTTTTTTTATATCTGAGCCTTGTCGGCGCCCCCAGCGGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->Cluster_10 reference=HQ714785_SH330547.07FU_refs position=1..250 errors=136%A\n-GTGAGGGGCATGTGAGGGCTGTCGCTGACTCAAAGTCGTGCACGCCCGAGTGTGTCCTCTCACATAATAATCCATCTCACCCTTTGTGCATCGCCGCGTGAGCACCCTTTGGGATCATCTCGGAGGGGGCTCGCGTTTTCACACAAACCCCCCTTTTAAAAGTGTAGAATGACCTCATTTATGCGCTAACACGCAATCAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n->Cluster_11 reference=AB594796_SH278638.07FU_refs position=1..248 errors=111%C\n-GATCATTACAGAGTTATCTAACTCCCAAACCCATGTGAACTTACCATTTGTTGCCTCGGCAGAGGCTACCCGGTACCTACCCTGGAGCAGCTACCCTGTAGCTACCCTGGAACGGCCTACCCTGTAGCGCATCCTGCCGGTGGACCTTTAAACTCTTGTTATTTTAAAGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n->Cluster_12 reference=JX118731_SH218995.07FU_refs position=1..250 errors=164%A\n-GGCTCTTCGGGGCATGTGCTCGCCTGTCACCTTTATCTTTCCACCTGTGCACACACTGTAGTCCTGGATACCTCTCGCCGCAAGGCGGATGCAGAGACTGCTGCTCAGCCTCCGAAAGGGGGAGGACGGCTATCTTTGAATTTCCAGGTCTACGATTATCACATACCCCAATTGAATGTTACAGAATGTTATCAAAGGGCCTTGTGCCTATAAACCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGA'..b'TTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->Cluster_7577_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=178%T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=95+A\n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTTAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATTGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->Cluster_50507_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=157+G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=42%A\n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCGATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCTACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->Cluster_50479_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=126%G;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=75+C\n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTGCTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n->Cluster_18841_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=101+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=15%G\n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAATAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCCATGAAGAACGCAGC\n->Cluster_47898_FROGS_combined R1_desc:reference=GU234142_SH201120.07FU_refs position=1..250 errors=52+T;R2_desc=R2_desc=reference=GU234142_SH201120.07FU_refs position=1..250 errors=82%C\n-TTGAATTAACTTGTTGGGTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCATTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTAGCTGGCTCTTAGGAGCATGTGCACACCCTTCATTGTTTTTCCACCTGTGCACTTTATGTAGTCCTGGAAGTCTTGCAAAAGATACACCAGCTCAAAAGGTTTACTCCTATCTGAGTTTCCAGGTCTATGTTCTCATATACCCCATTAGAATGTTCAGAATGTCGTTTATAGGCTTTAATGCCATTAAACTTAATACAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/03-chimera.biom --- a/test-data/references/03-chimera.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/03-chimera.biom Tue May 23 07:59:04 2023 +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": "2022-06-15T10:02:11", "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": 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newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/03-chimera.html --- a/test-data/references/03-chimera.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/03-chimera.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Remove Chimera</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <!-- 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> @@ -276,7 +276,7 @@ $(function() { var detection_categories = ["Clusters kept", "% Clusters kept", "Cluster abundance kept", "% Cluster abundance kept", "Chimeric clusters removed", "Chimeric abundance removed", "Abundance of the most abundant chimera removed", "Individual chimera detected", "Individual chimera abundance detected", "Abundance of the most abundant individual chimera detected"] ; - var detection_series = [{"name": "01_subsample", "data": [25127.0, 100.0, 50000.0, 100.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]}, {"name": "02_subsample", "data": [24947.0, 99.99599166265833, 49999.0, 99.998, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}, {"name": "03_subsample", "data": [24960.0, 99.99599375025039, 49999.0, 99.998, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}] ; + var detection_series = [{"name": "01_subsample", "data": ["25127", 100.0, "50000", 100.0, "0", "0", "0", "0", "0", "0"]}, {"name": "02_subsample", "data": ["24947", 99.99599166265833, "49999", 99.998, "1", "1", "1", "1", "1", "1"]}, {"name": "03_subsample", "data": ["24960", 99.99599375025039, "49999", 99.998, "1", "1", "1", "1", "1", "1"]}] ; var remove_info = {"nb_removed": 2, "nb_kept": 74920, "abundance_removed": 2, "abundance_kept": 149998, "nb_ambiguous": 0, "abundance_ambiguous": 0} ; // Remove alert |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/04-filters.biom --- a/test-data/references/04-filters.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/04-filters.biom Tue May 23 07:59:04 2023 +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": "2022-06-16T10:03:28", "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": 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"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": [], 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newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/04-filters.excluded --- a/test-data/references/04-filters.excluded Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/04-filters.excluded Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,74866 +1,74866 @@\n-#Present in less than 50.0% of replicates of all replicate groups.\tAbundance < 0.005% (i.e 8 sequences )\tPresent in databank of contaminants\n-\tCluster_56\t\n-\tCluster_57_FROGS_combined\t\n-\tCluster_58_FROGS_combined\t\n-\tCluster_59_FROGS_combined\t\n-\tCluster_60_FROGS_combined\t\n-\tCluster_61_FROGS_combined\t\n-\tCluster_62_FROGS_combined\t\n-\tCluster_63_FROGS_combined\t\n-\tCluster_64_FROGS_combined\t\n-\tCluster_65_FROGS_combined\t\n-\tCluster_66_FROGS_combined\t\n-\tCluster_67_FROGS_combined\t\n-\tCluster_68_FROGS_combined\t\n-\tCluster_69_FROGS_combined\t\n-\tCluster_70_FROGS_combined\t\n-\tCluster_71_FROGS_combined\t\n-\tCluster_72_FROGS_combined\t\n-\tCluster_73_FROGS_combined\t\n-\tCluster_74_FROGS_combined\t\n-\tCluster_75_FROGS_combined\t\n-\tCluster_76_FROGS_combined\t\n-\tCluster_77_FROGS_combined\t\n-\tCluster_78_FROGS_combined\t\n-\tCluster_79_FROGS_combined\t\n-\tCluster_80_FROGS_combined\t\n-\tCluster_81_FROGS_combined\t\n-\tCluster_82_FROGS_combined\t\n-\tCluster_83_FROGS_combined\t\n-\tCluster_84_FROGS_combined\t\n-\tCluster_85_FROGS_combined\t\n-\tCluster_86_FROGS_combined\t\n-\tCluster_87_FROGS_combined\t\n-\tCluster_88_FROGS_combined\t\n-\tCluster_89_FROGS_combined\t\n-\tCluster_90_FROGS_combined\t\n-\tCluster_91_FROGS_combined\t\n-\tCluster_92_FROGS_combined\t\n-\tCluster_93_FROGS_combined\t\n-\tCluster_94_FROGS_combined\t\n-\tCluster_95_FROGS_combined\t\n-\tCluster_96_FROGS_combined\t\n-\tCluster_97_FROGS_combined\t\n-\tCluster_98_FROGS_combined\t\n-\tCluster_99_FROGS_combined\t\n-\tCluster_100_FROGS_combined\t\n-\tCluster_101_FROGS_combined\t\n-\tCluster_102_FROGS_combined\t\n-\tCluster_103_FROGS_combined\t\n-\tCluster_104_FROGS_combined\t\n-\tCluster_105_FROGS_combined\t\n-\tCluster_106_FROGS_combined\t\n-\tCluster_107_FROGS_combined\t\n-\tCluster_108_FROGS_combined\t\n-\tCluster_109_FROGS_combined\t\n-\tCluster_110_FROGS_combined\t\n-\tCluster_111_FROGS_combined\t\n-\tCluster_112_FROGS_combined\t\n-\tCluster_113_FROGS_combined\t\n-\tCluster_114_FROGS_combined\t\n-\tCluster_115_FROGS_combined\t\n-\tCluster_116_FROGS_combined\t\n-\tCluster_117_FROGS_combined\t\n-\tCluster_118_FROGS_combined\t\n-\tCluster_119_FROGS_combined\t\n-\tCluster_120_FROGS_combined\t\n-\tCluster_121_FROGS_combined\t\n-\tCluster_122_FROGS_combined\t\n-\tCluster_123_FROGS_combined\t\n-\tCluster_124_FROGS_combined\t\n-\tCluster_125_FROGS_combined\t\n-\tCluster_126_FROGS_combined\t\n-\tCluster_127_FROGS_combined\t\n-\tCluster_128_FROGS_combined\t\n-\tCluster_129_FROGS_combined\t\n-\tCluster_130_FROGS_combined\t\n-\tCluster_131_FROGS_combined\t\n-\tCluster_132_FROGS_combined\t\n-\tCluster_133_FROGS_combined\t\n-\tCluster_134_FROGS_combined\t\n-\tCluster_135_FROGS_combined\t\n-\tCluster_136_FROGS_combined\t\n-\tCluster_137_FROGS_combined\t\n-\tCluster_138_FROGS_combined\t\n-\tCluster_139_FROGS_combined\t\n-\tCluster_140_FROGS_combined\t\n-\tCluster_141_FROGS_combined\t\n-\tCluster_142_FROGS_combined\t\n-\tCluster_143_FROGS_combined\t\n-\tCluster_144_FROGS_combined\t\n-\tCluster_145_FROGS_combined\t\n-\tCluster_146_FROGS_combined\t\n-\tCluster_147_FROGS_combined\t\n-\tCluster_148_FROGS_combined\t\n-\tCluster_149_FROGS_combined\t\n-\tCluster_150_FROGS_combined\t\n-\tCluster_151_FROGS_combined\t\n-\tCluster_152_FROGS_combined\t\n-\tCluster_153_FROGS_combined\t\n-\tCluster_154_FROGS_combined\t\n-\tCluster_155_FROGS_combined\t\n-\tCluster_156_FROGS_combined\t\n-\tCluster_157_FROGS_combined\t\n-\tCluster_158_FROGS_combined\t\n-\tCluster_159_FROGS_combined\t\n-\tCluster_160_FROGS_combined\t\n-\tCluster_161_FROGS_combined\t\n-\tCluster_162_FROGS_combined\t\n-\tCluster_163_FROGS_combined\t\n-\tCluster_164_FROGS_combined\t\n-\tCluster_165_FROGS_combined\t\n-\tCluster_166_FROGS_combined\t\n-\tCluster_167_FROGS_combined\t\n-\tCluster_168_FROGS_combined\t\n-\tCluster_169_FROGS_combined\t\n-\tCluster_170_FROGS_combined\t\n-\tCluster_171_FROGS_combined\t\n-\tCluster_172_FROGS_combined\t\n-\tCluster_173_FROGS_combined\t\n-\tCluster_174_FROGS_combined\t\n-\tCluster_175_FROGS_combined\t\n-\tCluster_176_FROGS_combined\t\n-\tCluster_177_FROGS_combined\t\n-\tCluster_178_FROGS_combined\t\n-\tCluster_179_FROGS_combined\t\n-\tCluster_180_FROGS_combined\t\n-\tCluster_181_FROGS_combined\t\n-\tCluster_182_FROGS_combined\t\n-\tCluster_183_FROGS_combined\t\n-\tCluster_184_FROGS_combined\t\n-\tCluster_185_FROGS_c'..b'FROGS_combined\n+Cluster_74856_FROGS_combined\tCluster_74855_FROGS_combined\n+Cluster_74857_FROGS_combined\tCluster_74856_FROGS_combined\n+Cluster_74858_FROGS_combined\tCluster_74857_FROGS_combined\n+Cluster_74859_FROGS_combined\tCluster_74858_FROGS_combined\n+Cluster_74860_FROGS_combined\tCluster_74859_FROGS_combined\n+Cluster_74861_FROGS_combined\tCluster_74860_FROGS_combined\n+Cluster_74862_FROGS_combined\tCluster_74861_FROGS_combined\n+Cluster_74863_FROGS_combined\tCluster_74862_FROGS_combined\n+Cluster_74864_FROGS_combined\tCluster_74863_FROGS_combined\n+Cluster_74865_FROGS_combined\tCluster_74864_FROGS_combined\n+Cluster_74866_FROGS_combined\tCluster_74865_FROGS_combined\n+Cluster_74867_FROGS_combined\tCluster_74866_FROGS_combined\n+Cluster_74868_FROGS_combined\tCluster_74867_FROGS_combined\n+Cluster_74869_FROGS_combined\tCluster_74868_FROGS_combined\n+Cluster_74870_FROGS_combined\tCluster_74869_FROGS_combined\n+Cluster_74871_FROGS_combined\tCluster_74870_FROGS_combined\n+Cluster_74872_FROGS_combined\tCluster_74871_FROGS_combined\n+Cluster_74873_FROGS_combined\tCluster_74872_FROGS_combined\n+Cluster_74874_FROGS_combined\tCluster_74873_FROGS_combined\n+Cluster_74875_FROGS_combined\tCluster_74874_FROGS_combined\n+Cluster_74876_FROGS_combined\tCluster_74875_FROGS_combined\n+Cluster_74877_FROGS_combined\tCluster_74876_FROGS_combined\n+Cluster_74878_FROGS_combined\tCluster_74877_FROGS_combined\n+Cluster_74879_FROGS_combined\tCluster_74878_FROGS_combined\n+Cluster_74880_FROGS_combined\tCluster_74879_FROGS_combined\n+Cluster_74881_FROGS_combined\tCluster_74880_FROGS_combined\n+Cluster_74882_FROGS_combined\tCluster_74881_FROGS_combined\n+Cluster_74883_FROGS_combined\tCluster_74882_FROGS_combined\n+Cluster_74884_FROGS_combined\tCluster_74883_FROGS_combined\n+Cluster_74885_FROGS_combined\tCluster_74884_FROGS_combined\n+Cluster_74886_FROGS_combined\tCluster_74885_FROGS_combined\n+Cluster_74887_FROGS_combined\tCluster_74886_FROGS_combined\n+Cluster_74888_FROGS_combined\tCluster_74887_FROGS_combined\n+Cluster_74889_FROGS_combined\tCluster_74888_FROGS_combined\n+Cluster_74890_FROGS_combined\tCluster_74889_FROGS_combined\n+Cluster_74891_FROGS_combined\tCluster_74890_FROGS_combined\n+Cluster_74892_FROGS_combined\tCluster_74891_FROGS_combined\n+Cluster_74893_FROGS_combined\tCluster_74892_FROGS_combined\n+Cluster_74894_FROGS_combined\tCluster_74893_FROGS_combined\n+Cluster_74895_FROGS_combined\tCluster_74894_FROGS_combined\n+Cluster_74896_FROGS_combined\tCluster_74895_FROGS_combined\n+Cluster_74897_FROGS_combined\tCluster_74896_FROGS_combined\n+Cluster_74898_FROGS_combined\tCluster_74897_FROGS_combined\n+Cluster_74899_FROGS_combined\tCluster_74898_FROGS_combined\n+Cluster_74900_FROGS_combined\tCluster_74899_FROGS_combined\n+Cluster_74901_FROGS_combined\tCluster_74900_FROGS_combined\n+Cluster_74902_FROGS_combined\tCluster_74901_FROGS_combined\n+Cluster_74903_FROGS_combined\tCluster_74902_FROGS_combined\n+Cluster_74904_FROGS_combined\tCluster_74903_FROGS_combined\n+Cluster_74905_FROGS_combined\tCluster_74904_FROGS_combined\n+Cluster_74906_FROGS_combined\tCluster_74905_FROGS_combined\n+Cluster_74907_FROGS_combined\tCluster_74906_FROGS_combined\n+Cluster_74908_FROGS_combined\tCluster_74907_FROGS_combined\n+Cluster_74909_FROGS_combined\tCluster_74908_FROGS_combined\n+Cluster_74910_FROGS_combined\tCluster_74909_FROGS_combined\n+Cluster_74911_FROGS_combined\tCluster_74910_FROGS_combined\n+Cluster_74912_FROGS_combined\tCluster_74911_FROGS_combined\n+Cluster_74913_FROGS_combined\tCluster_74912_FROGS_combined\n+Cluster_74914_FROGS_combined\tCluster_74913_FROGS_combined\n+Cluster_74915_FROGS_combined\tCluster_74914_FROGS_combined\n+Cluster_74916_FROGS_combined\tCluster_74915_FROGS_combined\n+Cluster_74917_FROGS_combined\tCluster_74916_FROGS_combined\n+Cluster_74918_FROGS_combined\tCluster_74917_FROGS_combined\n+Cluster_74919_FROGS_combined\tCluster_74918_FROGS_combined\n+Cluster_74920_FROGS_combined\tCluster_74919_FROGS_combined\n+Cluster_74921_FROGS_combined\tCluster_74920_FROGS_combined\n+Cluster_74922_FROGS_combined\tCluster_74921_FROGS_combined\n+\tCluster_74922_FROGS_combined\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/04-filters.html --- a/test-data/references/04-filters.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/04-filters.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -17,9 +17,9 @@ --> <html> <head> - <title>FROGS OTU Filters</title> + <title>FROGS ASV Filters</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <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"> @@ -432,7 +432,7 @@ ['Kept', global_results['nb_clstr_kept']], ['Removed', (global_results['nb_clstr_ini'] - global_results['nb_clstr_kept'])] ]; - $('#nb-filtered').highcharts( pie_param('OTUs', nb_filtered_data, 'OTUs') ); + $('#nb-filtered').highcharts( pie_param('ASVs', nb_filtered_data, 'ASVs') ); // Results by sequences var abundance_filtered_data = [ @@ -536,7 +536,7 @@ } sample_table_data.push( sample_data ); } - $('#' + container_id).append( table("OTUs removed by sample", sample_table_titles, sample_table_data) ); + $('#' + container_id).append( table("ASVs removed by sample", sample_table_titles, sample_table_data) ); $('#' + container_id + ' table').prop( 'id', 'details-table' ); $('#' + container_id + ' table').DataTable({ dom: "<'#details-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" + @@ -557,7 +557,7 @@ group_data = [group, replicate_groups[group]['Replicates']] ; group_table_data.push( group_data ); } - $('#' + container_id).append( table("OTUs removed by sample", group_table_titles, group_table_data) ); + $('#' + container_id).append( table("ASVs removed by sample", group_table_titles, group_table_data) ); $('#' + container_id + ' table').prop( 'id', 'details-table' ); $('#' + container_id + ' table').DataTable({ dom: "<'#details-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" + @@ -576,7 +576,7 @@ // Data // /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - 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"] ; + var processed_filters = ["Present in less than 3 samples", "Abundance < 0.005% (i.e 8 sequences )"] ; /* Example: ['filterA', 'filterB', 'filterC'] */ @@ -589,7 +589,7 @@ 'nb_seq_ini': 100000 } */ - 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}} ; + 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}} ; /* Example: { 'sampleA':{ @@ -609,10 +609,10 @@ } } */ - var replicate_groups = {"group_1": {"Replicates": "01_subsample, 02_subsample"}, "group_2": {"Replicates": "03_subsample"}} ; + var replicate_groups = {} ; - var by_filters_results = [{"filters": ["Abundance < 0.005% (i.e 8 sequences )"], "count": 74865}] ; + 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}] ; /* Example: [ {'filters':['filterA'], 'count': 10}, @@ -669,7 +669,7 @@ <!-- Content --> <div id="content" class="hidden"> <ul class="nav nav-tabs"> - <li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by OTUs</a></li> + <li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by ASVs</a></li> <li class="nav-item"><a class="nav-link" href="#view-by-samples">Filters by samples</a></li> <li class="nav-item" id="view-by-replicates-nav"><a class="nav-link" href="#view-by-replicates">Replicate Groups</a></li> </ul> @@ -688,7 +688,7 @@ <div class="row"> <div class="col-md-2 col-ld-3"></div> <div id="venn-filters" class="col-md-8 col-ld-6"> - <p> Draw a Venn to see which OTUs had been deleted by the filters chosen (Maximum 6 options): </p> + <p> Draw a Venn to see which ASVs had been deleted by the filters chosen (Maximum 6 options): </p> <ul id="byFilters-jvenn-chkbx"></ul> <button id="byFilters-jvenn-btn" class="btn d-block mx-auto" disabled><span class="fa fa-gears" aria-hidden="true"> Venn</span></button> </div> @@ -714,7 +714,7 @@ <div class="modal-dialog modal-lg"> <div class="modal-content"> <div class="modal-header"> - <h4 class="modal-title">Venn on removed OTUs</h4> + <h4 class="modal-title">Venn on removed ASVs</h4> <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button> </div> <div class="modal-body"> |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/05-itsx.biom --- a/test-data/references/05-itsx.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/05-itsx.biom Tue May 23 07:59:04 2023 +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": "2022-06-15T10:02:11", "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 37e6f0c959bb -r b2967b704d6b test-data/references/05-itsx.fasta --- a/test-data/references/05-itsx.fasta Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/05-itsx.fasta Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,110 +1,110 @@\n >Cluster_1 reference=JF747094_SH197643.07FU_refs position=1..249 errors=112%A\n-ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCA\n+ATCATTAACGAGTTAGGGTCTCTCTGGCCCGACCTCCCAACCCTTTGTCTACTTGACCATCGTTGCTTCGGCGAGCCCGTCCTCACGGACCGCCGGAGGGACCTTCACCGGCCCTCTGGTCCGCGCTCGTCGGTAGCCCAACCATTAAAATCTTTAACCAAACGTGCCTTAATCTAAGTACAATTATTAAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n >Cluster_2 reference=DQ898183_SH216206.07FU_refs position=1..249 errors=21%G\n-CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTA\n+CCAATATCTAGGGTCTCATATAGGACTCCTAATCAAACACATTCCTGTGTATTCTTCCATGTTGCTTTCCCAAACCAGTAGCCACTGCTGCCAGCCGATATCCTAATGGTTTGAGGTGTTTGGGGAAGGGCCAGTTATTAAACCTTTATACCAATTAGCTGTCTGAGAAGGCCATGTGCCCTAATCTTTAAACATATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC\n >Cluster_3 reference=JN711441_SH022548.07FU_refs_singleton position=1..248 errors=206%T\n-AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAA\n+AGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n >Cluster_4 reference=AF456924_SH097201.07FU_refs position=1..250\n-CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCA\n+CCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n >Cluster_5 reference=JX399009_SH268556.07FU_refs position=1..249 errors=185%C\n-CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCA\n+CATTATAGAGTTTTTTAAACTCCCAACCCATGTGAACTTACCATTGTTGCCTCGGCAGAGGCTACCCGGTACACCTTACCCTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGAACGGCTTACCCTGTAGCGGCTGCCGGTGGACTACTAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n >Cluster_6 reference=KM668101_SH491630.07FU_refs_singleton position=1..250\n-AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAA\n+AGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAATTGGTTGAGTTATGAATGCTTTTCAATTTACACATTTTGAAATTTGGGGTCATTATATTGGAATAATATATAATAACTTTCAGCAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGC\n >Cluster_7 reference=JF417478_SH216679.07FU_refs position=1..250 errors=99%T\n-CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCA\n+CCGAGTGAGGGTCCCCTTTGCGGGCCCGACCTCCCACCCGTGTCTACCGTACCGTGTTGCTTCGGCGGGCCCGCCAGGGGGGCTCCTGTCCCTGGCCGCCGGGGGGCCATCTCCCGTGCCTCCGGGCCCGTGCCCGCCGGAGACCCTCGTGAACGCTGTCTTGAACAAAGGTTGCGGTCTGAGTGGAAAACACAATCGTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n >Cluster_8 reference=EU837224_SH182725.07FU_refs position=1..249 errors=132%T\n-TTGAATTCTATGGAGGGGGGAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCTTCCTTTCTCTCATACACACACCTGTGCACCTGTTGTAGGTCCTCGAAAGAGGAGCTATGTTTTTCACATCACACCCCGTCGTATGTCTATAGAATGTGTT'..b'AGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n >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\n-GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTA\n+GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n >Cluster_51 reference=AJ786644_SH470265.07FU_refs_singleton position=1..243 errors=78%G\n-CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTA\n+CATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n >Cluster_52 reference=EF669607_SH109271.07FU_refs_singleton position=1..243\n-CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTA\n+CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\n >Cluster_53 reference=FJ860822_SH177722.07FU_refs position=1..242 errors=22%A\n-CATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCA\n+CATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\n >Cluster_54 reference=UDB016470_SH189377.07FU_refs position=1..242 errors=108%A\n-CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATA\n+CCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\n >Cluster_55 reference=UDB011541_SH194446.07FU_refs position=1..241 errors=109%G\n-GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATA\n+GGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/05-itsx.html --- a/test-data/references/05-itsx.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/05-itsx.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS ITSx</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <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"> @@ -288,7 +288,7 @@ ['Kept', global_results['nb_clstr_kept']], ['Removed', (global_results['nb_clstr_ini'] - global_results['nb_clstr_kept'])] ]; - $('#nb-filtered').highcharts( pie_param('OTUs', nb_filtered_data, 'OTUs') ); + $('#nb-filtered').highcharts( pie_param('ASVs', nb_filtered_data, 'ASVs') ); // Results by sequences var abundance_filtered_data = [ @@ -307,7 +307,7 @@ sample_table_data.push( sample_data ); } - $('#' + container_id).append( table("OTUs removed by sample", sample_table_titles, sample_table_data) ); + $('#' + container_id).append( table("ASVs removed by sample", sample_table_titles, sample_table_data) ); $('#' + container_id + ' table').prop( 'id', 'details-table' ); $('#' + container_id + ' table').DataTable({ "sDom": '<"top"<"#details-csv-export"><"clear">lf>rt<"bottom"ip><"clear">' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/06-affiliation.html --- a/test-data/references/06-affiliation.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/06-affiliation.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <!-- 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> @@ -463,7 +463,7 @@ ["With affiliation", global_results["nb_clstr_with_affi"]], ["Without affiliation", (global_results["nb_clstr"] - global_results["nb_clstr_with_affi"])] ] - $('#clstr-ratio-affi').highcharts( pie_param("OTUs affiliation", pie_series, 'OTUs') ); + $('#clstr-ratio-affi').highcharts( pie_param("ASVs affiliation", pie_series, 'ASVs') ); var pie_series = [ ["With affiliation", global_results["nb_seq_with_affi"]], @@ -475,7 +475,7 @@ var histogram_series = [ { - 'name': 'OTUs', + 'name': 'ASVs', 'data': global_results["nb_clstr_ambiguous"].map(function(num) { var prct = (num/global_results["nb_clstr"])*10000/100 ; return( parseFloat(numberDisplay(prct)) ); @@ -491,7 +491,7 @@ $('#clstr-multi-affi').highcharts( histogram_param('Multi-affiliation by taxonomic rank', '% of multi-affiliated', taxonomy_ranks, histogram_series, '%') ); // Display data by sample - var table_categories = [ 'Sample', 'Nb OTUs', '% OTUs affiliated by blast', 'Nb seq', '% seq affiliated by blast' ]; + var table_categories = [ 'Sample', 'Nb Clusters', '% affiliated clusters by blast', 'Nb seq', '% Affiliated sequences by blast' ]; var table_series = new Array(); for( var sample_name in sample_results ){ table_series.push([ |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-affiliation_deleted.biom --- a/test-data/references/07-affiliation_deleted.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/07-affiliation_deleted.biom Tue May 23 07:59:04 2023 +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": "2022-06-15T10:04:29", "rows": [{"id": "Cluster_24", "metadata": {"comment": [], "seed_id": "01_10", "blast_affiliations": [{"subject": "UDB003291_SH182302.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "evalue": "7.05e-153", "aln_length": 286, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Hydnellum", "s__Hydnellum_peckii"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_25", "metadata": {"comment": [], "seed_id": "01_97506", "blast_affiliations": [{"subject": "KC992854_SH220410.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "evalue": "2.53e-152", "aln_length": 285, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Psathyrellaceae", "g__Psathyrella", "s__Psathyrella_sublatispora"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_26", "metadata": {"comment": [], "seed_id": "01_151", "blast_affiliations": [{"subject": "JX179268_SH178540.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "evalue": "2.53e-152", "aln_length": 285, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Agaricaceae", "g__Lepiota", "s__Lepiota_geogenia"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_27", "metadata": {"comment": [], "seed_id": "01_108", "blast_affiliations": [{"subject": "KF732310_SH222414.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "evalue": "5.49e-154", "aln_length": 288, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_gentianeus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_28", "metadata": {"comment": [], "seed_id": "01_71661", "blast_affiliations": [{"subject": "UDB001581_SH219736.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "evalue": "1.97e-153", "aln_length": 287, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Strophariaceae", "g__Hypholoma", "s__Hypholoma_capnoides"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_29", "metadata": {"comment": [], "seed_id"'..b'idiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Hymenochaete", "s__Hymenochaete_longispora"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_46", "metadata": {"comment": [], "seed_id": "01_91485", "blast_affiliations": [{"subject": "JQ716403_SH219241.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "evalue": "7.94e-178", "aln_length": 331, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Hymenochaetales", "f__Hymenochaetaceae", "g__Pseudochaete", "s__Pseudochaete_subrigidula"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_47", "metadata": {"comment": [], "seed_id": "01_410", "blast_affiliations": [{"subject": "EU623745_SH215851.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "evalue": "0.0", "aln_length": 390, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Marasmiaceae", "g__Megacollybia", "s__Megacollybia_subfurfuracea"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_50_FROGS_combined", "metadata": {"comment": ["FROGS_combined"], "seed_id": "01_71070_FROGS_combined", "blast_affiliations": [{"subject": "JF419897_SH181470.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "evalue": "-1", "aln_length": 1017, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Dothideomycetes", "o__Pleosporales", "f__Lindgomycetaceae", "g__Lindgomyces", "s__Lindgomyces_breviappendiculatus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 515], [0, 1, 500], [0, 2, 515], [1, 0, 491], [1, 1, 506], [1, 2, 533], [2, 0, 494], [2, 1, 513], [2, 2, 509], [3, 0, 536], [3, 1, 490], [3, 2, 547], [4, 0, 545], [4, 1, 507], [4, 2, 493], [5, 0, 498], [5, 1, 515], [5, 2, 524], [6, 0, 525], [6, 1, 530], [6, 2, 510], [7, 0, 511], [7, 1, 550], [7, 2, 469], [8, 0, 509], [8, 1, 522], [8, 2, 515], [9, 0, 508], [9, 1, 544], [9, 2, 545], [10, 0, 480], [10, 1, 504], [10, 2, 515], [11, 0, 525], [11, 1, 499], [11, 2, 483], [12, 0, 536], [12, 1, 534], [12, 2, 521], [13, 0, 499], [13, 1, 538], [13, 2, 539], [14, 0, 473], [14, 1, 528], [14, 2, 524], [15, 0, 518], [15, 1, 508], [15, 2, 486], [16, 0, 534], [16, 1, 524], [16, 2, 514], [17, 0, 518], [17, 1, 517], [17, 2, 494], [18, 0, 540], [18, 1, 524], [18, 2, 516], [19, 0, 497], [19, 1, 505], [19, 2, 514], [20, 0, 511], [20, 1, 518], [20, 2, 502], [21, 0, 530], [21, 1, 513], [21, 2, 541], [22, 0, 507], [22, 1, 530], [22, 2, 498], [23, 0, 499], [23, 1, 513], [23, 2, 520], [24, 0, 526], [24, 1, 518], [24, 2, 553]], "shape": [25, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-affiliation_deleted.html --- a/test-data/references/07-affiliation_deleted.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/07-affiliation_deleted.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation Filters</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <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"> @@ -433,7 +433,7 @@ [mode, global_results['cluster'][mode]], ['Modified', global_results['cluster']['Modified']] ]; - $('#nb-filtered').highcharts( pie_param('OTUs', nb_filtered_data, 'OTUs') ); + $('#nb-filtered').highcharts( pie_param('ASVs', nb_filtered_data, 'ASVs') ); // Results by sequences var abundance_filtered_data = [ @@ -556,7 +556,7 @@ } sample_table_data.push( sample_data ); } - $('#' + container_id).append( table("OTUs removed by sample", sample_table_titles, sample_table_data) ); + $('#' + container_id).append( table("ASVs removed by sample", sample_table_titles, sample_table_data) ); $('#' + container_id + ' table').prop( 'id', 'details-table' ); $('#' + container_id + ' table').DataTable({ dom: "<'#details-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" + @@ -576,7 +576,7 @@ // Data // /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - var processed_filters = ["Blast evalue > 1e-150", "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma", "Blast identity < 1.0"] ; + var processed_filters = ["Blast evalue > 1e-150", "Blast identity < 100.0"] ; /* Example: ['filterA', 'filterB', 'filterC'] */ @@ -623,7 +623,7 @@ } } ; */ - var by_samples_results = {"01_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma": 6, "Blast identity < 1.0": 1}, "kept": 25}, "02_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma": 6, "Blast identity < 1.0": 1}, "kept": 25}, "03_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma": 6, "Blast identity < 1.0": 1}, "kept": 25}} ; + var by_samples_results = {"01_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast identity < 100.0": 1}, "kept": 25}, "02_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast identity < 100.0": 1}, "kept": 25}, "03_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast identity < 100.0": 1}, "kept": 25}} ; /* Example: { 'sampleA':{ @@ -643,7 +643,7 @@ } } */ - var by_filters_results = [{"filters": ["Blast evalue > 1e-150"], "count": 23}, {"filters": ["Blast evalue > 1e-150", "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma"], "count": 6}, {"filters": ["Blast evalue > 1e-150", "Blast identity < 1.0"], "count": 1}] ; + var by_filters_results = [{"filters": ["Blast evalue > 1e-150"], "count": 29}, {"filters": ["Blast evalue > 1e-150", "Blast identity < 100.0"], "count": 1}] ; /* Example: [ {'filters':['filterA'], 'count': 10}, @@ -693,7 +693,7 @@ <!-- Content --> <div id="content" class="hidden"> <ul class="nav nav-tabs"> - <li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by OTUs</a></li> + <li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by ASVs</a></li> <li class="nav-item"><a class="nav-link" href="#view-by-samples">Filters by samples</a></li> </ul> @@ -709,7 +709,7 @@ <h2 class="pb-2 mt-4 mb-2 border-bottom">Taxon lost summary</h2> Filtering criteria are applied by affiliation. So for blast, filters are not only applied on the blast consensus taxonomy but on each blast hit (cf multihit.tsv file).<br> - For each OTU, none, part or all blast affiliations may be removed, resulting in unchanged / updated or deleted blast consensus taxonomy.<br> + For each ASV, none, part or all blast affiliations may be removed, resulting in unchanged / updated or deleted blast consensus taxonomy.<br> The detailed number of lost affiliations (not only the consensus) by rank are summarised. It may also precise if blast consensus multi-affiliation are lost.<br><br> <div id="taxon_lost"></div> @@ -717,7 +717,7 @@ <div class="row"> <div class="col-md-2 col-ld-3"></div> <div id="venn-filters" class="col-md-8 col-ld-6"> - <p> Draw a Venn to see which OTUs had been deleted by the filters chosen (Maximum 6 options): </p> + <p> Draw a Venn to see which ASVs had been deleted by the filters chosen (Maximum 6 options): </p> <ul id="byFilters-jvenn-chkbx"></ul> <button id="byFilters-jvenn-btn" class="btn d-block mx-auto" disabled><span class="fa fa-gears" aria-hidden="true"> Venn</span></button> </div> @@ -726,7 +726,7 @@ </div> <div id="view-by-samples" role="tabpanel" class="tab-pane disabled"> - <h2 class="pb-2 mt-4 mb-2 border-bottom">Details by samples of removed OTUs</h2> + <h2 class="pb-2 mt-4 mb-2 border-bottom">Details by samples</h2> <div id="filter-log"></div> </div> </div> @@ -738,7 +738,7 @@ <div class="modal-dialog modal-lg"> <div class="modal-content"> <div class="modal-header"> - <h4 class="modal-title">Venn on removed OTUs</h4> + <h4 class="modal-title">Venn on removed ASVs</h4> <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button> </div> <div class="modal-body"> |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-affiliation_masked.biom --- a/test-data/references/07-affiliation_masked.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/07-affiliation_masked.biom Tue May 23 07:59:04 2023 +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": "2022-06-15T10:04:29", "rows": [{"id": "Cluster_1", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_54", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_2", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_92546", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_3", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_59", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_4", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_81", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_5", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_25", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_6", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_74803", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Bankeraceae", "g__Sarcodon", "s__Sarcodon_quercophilus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_7", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_38", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Rasamsonia", "s__Rasamsonia_emersonii"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_8", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_90", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Boletales", "f__Suillaceae", "g__Truncocolumella", "s__Truncocolumella_rubra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_9", "metadata": {"comment": ["blast_eval_gt_1e-150", "undesired_tax_in_blast"], "seed_id": "01_97858", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_mienum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_10", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_259", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Russulales", "f__Russulaceae", "g__Lactarius", "s__Lactarius_cyathuliformis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.98]}}, {"id": "Cluster_11", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_90304", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__A'..b'sphaeria_polylepidis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_52", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_1953", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_microcysticus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_53", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_4641", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_rhododendri"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_54", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_3904", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Thelephorales", "f__Thelephoraceae", "g__Thelephora", "s__Thelephora_atra"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_55", "metadata": {"comment": ["blast_eval_gt_1e-150"], "seed_id": "01_67609", "blast_affiliations": null, "blast_taxonomy": null, "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_friabilis"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}], "columns": [{"id": "01_subsample", "metadata": null}, {"id": "02_subsample", "metadata": null}, {"id": "03_subsample", "metadata": null}], "matrix_element_type": "int", "data": [[0, 0, 512], [0, 1, 515], [0, 2, 534], [1, 0, 508], [1, 1, 512], [1, 2, 536], [2, 0, 514], [2, 1, 502], [2, 2, 534], [3, 0, 503], [3, 1, 515], [3, 2, 546], [4, 0, 521], [4, 1, 550], [4, 2, 473], [5, 0, 512], [5, 1, 574], [5, 2, 545], [6, 0, 509], [6, 1, 492], [6, 2, 532], [7, 0, 526], [7, 1, 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"sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-affiliation_masked.html --- a/test-data/references/07-affiliation_masked.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/07-affiliation_masked.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Affiliation Filters</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <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"> @@ -433,7 +433,7 @@ [mode, global_results['cluster'][mode]], ['Modified', global_results['cluster']['Modified']] ]; - $('#nb-filtered').highcharts( pie_param('OTUs', nb_filtered_data, 'OTUs') ); + $('#nb-filtered').highcharts( pie_param('ASVs', nb_filtered_data, 'ASVs') ); // Results by sequences var abundance_filtered_data = [ @@ -556,7 +556,7 @@ } sample_table_data.push( sample_data ); } - $('#' + container_id).append( table("OTUs removed by sample", sample_table_titles, sample_table_data) ); + $('#' + container_id).append( table("ASVs removed by sample", sample_table_titles, sample_table_data) ); $('#' + container_id + ' table').prop( 'id', 'details-table' ); $('#' + container_id + ' table').DataTable({ dom: "<'#details-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" + @@ -576,7 +576,7 @@ // Data // /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - var processed_filters = ["Blast evalue > 1e-150", "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma", "Blast identity < 1.0"] ; + var processed_filters = ["Blast evalue > 1e-150", "Blast identity < 100.0"] ; /* Example: ['filterA', 'filterB', 'filterC'] */ @@ -623,7 +623,7 @@ } } ; */ - var by_samples_results = {"01_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma": 6, "Blast identity < 1.0": 1}, "kept": 25}, "02_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma": 6, "Blast identity < 1.0": 1}, "kept": 25}, "03_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma": 6, "Blast identity < 1.0": 1}, "kept": 25}} ; + var by_samples_results = {"01_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast identity < 100.0": 1}, "kept": 25}, "02_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast identity < 100.0": 1}, "kept": 25}, "03_subsample": {"initial": 55, "filtered": {"Blast evalue > 1e-150": 30, "Blast identity < 100.0": 1}, "kept": 25}} ; /* Example: { 'sampleA':{ @@ -643,7 +643,7 @@ } } */ - var by_filters_results = [{"filters": ["Blast evalue > 1e-150"], "count": 23}, {"filters": ["Blast evalue > 1e-150", "Blast taxonomies belong to undesired taxon: g__Sarcodon / s__Trichoderma"], "count": 6}, {"filters": ["Blast evalue > 1e-150", "Blast identity < 1.0"], "count": 1}] ; + var by_filters_results = [{"filters": ["Blast evalue > 1e-150"], "count": 29}, {"filters": ["Blast evalue > 1e-150", "Blast identity < 100.0"], "count": 1}] ; /* Example: [ {'filters':['filterA'], 'count': 10}, @@ -693,7 +693,7 @@ <!-- Content --> <div id="content" class="hidden"> <ul class="nav nav-tabs"> - <li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by OTUs</a></li> + <li class="nav-item active"><a class="nav-link active" href="#view-by-filters">Filters by ASVs</a></li> <li class="nav-item"><a class="nav-link" href="#view-by-samples">Filters by samples</a></li> </ul> @@ -709,7 +709,7 @@ <h2 class="pb-2 mt-4 mb-2 border-bottom">Taxon lost summary</h2> Filtering criteria are applied by affiliation. So for blast, filters are not only applied on the blast consensus taxonomy but on each blast hit (cf multihit.tsv file).<br> - For each OTU, none, part or all blast affiliations may be removed, resulting in unchanged / updated or deleted blast consensus taxonomy.<br> + For each ASV, none, part or all blast affiliations may be removed, resulting in unchanged / updated or deleted blast consensus taxonomy.<br> The detailed number of lost affiliations (not only the consensus) by rank are summarised. It may also precise if blast consensus multi-affiliation are lost.<br><br> <div id="taxon_lost"></div> @@ -717,7 +717,7 @@ <div class="row"> <div class="col-md-2 col-ld-3"></div> <div id="venn-filters" class="col-md-8 col-ld-6"> -Draw a Venn to see which OTUs had its taxonomy masked by the filters chosen (Maximum 6 options): <ul id="byFilters-jvenn-chkbx"></ul> +Draw a Venn to see which ASVs had its taxonomy masked by the filters chosen (Maximum 6 options): <ul id="byFilters-jvenn-chkbx"></ul> <button id="byFilters-jvenn-btn" class="btn d-block mx-auto" disabled><span class="fa fa-gears" aria-hidden="true"> Venn</span></button> </div> <div class="col-md-2 col-ld-3"></div> @@ -725,7 +725,7 @@ </div> <div id="view-by-samples" role="tabpanel" class="tab-pane disabled"> - <h2 class="pb-2 mt-4 mb-2 border-bottom">Details by samples of masked OTUs</h2> + <h2 class="pb-2 mt-4 mb-2 border-bottom">Details by samples</h2> <div id="filter-log"></div> </div> </div> @@ -737,7 +737,7 @@ <div class="modal-dialog modal-lg"> <div class="modal-content"> <div class="modal-header"> - <h4 class="modal-title">Venn on removed OTUs</h4> + <h4 class="modal-title">Venn on removed ASVs</h4> <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button> </div> <div class="modal-body"> |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-impacted_OTU_deleted.tsv --- a/test-data/references/07-impacted_OTU_deleted.tsv Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,31 +0,0 @@\n-#comment\tstatus\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-blast_eval_gt_1e-150\tOTU_deleted\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\t1561\t512\t515\t534\n-blast_eval_gt_1e-150\tOTU_deleted\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\t1556\t508\t512\t536\n-blast_eval_gt_1e-150\tOTU_deleted\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\t1550\t514\t502\t534\n-blast_eval_gt_1e-150;undesired_tax_in_blast\tOTU_deleted\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\t1564\t503\t515\t546\n-blast_eval_gt_1e-150\tOTU_deleted\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\t1544\t521\t550\t473\n-blast_eval_gt_1e-150;undesired_tax_in_blast\tOTU_deleted\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\tAGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTT'..b'GTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t544\t177\t203\t164\n-blast_eval_gt_1e-150\tOTU_deleted\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\t245\t80\t83\t82\n-blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Leptosphaeriaceae;(1.0);g__Leptosphaeria;(1.0);s__Leptosphaeria_polylepidis;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Leptosphaeriaceae;g__Leptosphaeria;s__Leptosphaeria_polylepidis\tAJ786644_SH470265.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_210\tCATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_51\t83\t22\t28\t33\n-blast_eval_gt_1e-150\tOTU_deleted\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\t59\t26\t16\t17\n-blast_eval_gt_1e-150;undesired_tax_in_blast\tOTU_deleted\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_rhododendri;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rhododendri\tFJ860822_SH177722.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_4641\tCATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_53\t45\t17\t12\t16\n-blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Thelephoraceae;(1.0);g__Thelephora;(1.0);s__Thelephora_atra;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Thelephora;s__Thelephora_atra\tUDB016470_SH189377.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_3904\tCCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_54\t37\t9\t13\t15\n-blast_eval_gt_1e-150\tOTU_deleted\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Amanitaceae;(1.0);g__Amanita;(1.0);s__Amanita_friabilis;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_friabilis\tUDB011541_SH194446.07FU_refs\t100.0\t100.0\t6.09e-128\t241\t01_67609\tGGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\tCluster_55\t10\t2\t6\t2\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-impacted_OTU_deleted_multihit.tsv --- a/test-data/references/07-impacted_OTU_deleted_multihit.tsv Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -#observation_name blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-impacted_OTU_masked.tsv --- a/test-data/references/07-impacted_OTU_masked.tsv Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,31 +0,0 @@\n-#comment\tstatus\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-blast_eval_gt_1e-150\tAffiliation_masked\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\t1561\t512\t515\t534\n-blast_eval_gt_1e-150\tAffiliation_masked\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\t1556\t508\t512\t536\n-blast_eval_gt_1e-150\tAffiliation_masked\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\t1550\t514\t502\t534\n-blast_eval_gt_1e-150;undesired_tax_in_blast\tAffiliation_masked\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\t1564\t503\t515\t546\n-blast_eval_gt_1e-150\tAffiliation_masked\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\t1544\t521\t550\t473\n-blast_eval_gt_1e-150;undesired_tax_in_blast\tAffiliation_masked\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\tAGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAA'..b'CGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t544\t177\t203\t164\n-blast_eval_gt_1e-150\tAffiliation_masked\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\t245\t80\t83\t82\n-blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Leptosphaeriaceae;(1.0);g__Leptosphaeria;(1.0);s__Leptosphaeria_polylepidis;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Leptosphaeriaceae;g__Leptosphaeria;s__Leptosphaeria_polylepidis\tAJ786644_SH470265.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_210\tCATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_51\t83\t22\t28\t33\n-blast_eval_gt_1e-150\tAffiliation_masked\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\t59\t26\t16\t17\n-blast_eval_gt_1e-150;undesired_tax_in_blast\tAffiliation_masked\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_rhododendri;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rhododendri\tFJ860822_SH177722.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_4641\tCATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_53\t45\t17\t12\t16\n-blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Thelephoraceae;(1.0);g__Thelephora;(1.0);s__Thelephora_atra;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Thelephora;s__Thelephora_atra\tUDB016470_SH189377.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_3904\tCCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_54\t37\t9\t13\t15\n-blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Amanitaceae;(1.0);g__Amanita;(1.0);s__Amanita_friabilis;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_friabilis\tUDB011541_SH194446.07FU_refs\t100.0\t100.0\t6.09e-128\t241\t01_67609\tGGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\tCluster_55\t10\t2\t6\t2\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-impacted_OTU_masked_multihit.tsv --- a/test-data/references/07-impacted_OTU_masked_multihit.tsv Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -#observation_name blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-impacted_clusters_deleted.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/07-impacted_clusters_deleted.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,31 @@\n+#comment\tstatus\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+blast_eval_gt_1e-150\tASV_deleted\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\t1561\t512\t515\t534\n+blast_eval_gt_1e-150\tASV_deleted\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\t1556\t508\t512\t536\n+blast_eval_gt_1e-150\tASV_deleted\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\t1550\t514\t502\t534\n+blast_eval_gt_1e-150\tASV_deleted\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\t1564\t503\t515\t546\n+blast_eval_gt_1e-150\tASV_deleted\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\t1544\t521\t550\t473\n+blast_eval_gt_1e-150\tASV_deleted\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\tAGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTATTACCCTTGTGCACAACCTGTAGCTTGACCATTTTAACAAAAT'..b'CCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t544\t177\t203\t164\n+blast_eval_gt_1e-150\tASV_deleted\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\t245\t80\t83\t82\n+blast_eval_gt_1e-150\tASV_deleted\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Leptosphaeriaceae;(1.0);g__Leptosphaeria;(1.0);s__Leptosphaeria_polylepidis;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Leptosphaeriaceae;g__Leptosphaeria;s__Leptosphaeria_polylepidis\tAJ786644_SH470265.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_210\tCATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_51\t83\t22\t28\t33\n+blast_eval_gt_1e-150\tASV_deleted\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\t59\t26\t16\t17\n+blast_eval_gt_1e-150\tASV_deleted\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_rhododendri;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rhododendri\tFJ860822_SH177722.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_4641\tCATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_53\t45\t17\t12\t16\n+blast_eval_gt_1e-150\tASV_deleted\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Thelephoraceae;(1.0);g__Thelephora;(1.0);s__Thelephora_atra;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Thelephora;s__Thelephora_atra\tUDB016470_SH189377.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_3904\tCCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_54\t37\t9\t13\t15\n+blast_eval_gt_1e-150\tASV_deleted\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Amanitaceae;(1.0);g__Amanita;(1.0);s__Amanita_friabilis;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_friabilis\tUDB011541_SH194446.07FU_refs\t100.0\t100.0\t6.09e-128\t241\t01_67609\tGGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\tCluster_55\t10\t2\t6\t2\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-impacted_clusters_deleted_multihit.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/07-impacted_clusters_deleted_multihit.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +#observation_name blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-impacted_clusters_masked.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/07-impacted_clusters_masked.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -0,0 +1,31 @@\n+#comment\tstatus\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+blast_eval_gt_1e-150\tAffiliation_masked\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\t1561\t512\t515\t534\n+blast_eval_gt_1e-150\tAffiliation_masked\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\t1556\t508\t512\t536\n+blast_eval_gt_1e-150\tAffiliation_masked\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\t1550\t514\t502\t534\n+blast_eval_gt_1e-150\tAffiliation_masked\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\t1564\t503\t515\t546\n+blast_eval_gt_1e-150\tAffiliation_masked\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\t1544\t521\t550\t473\n+blast_eval_gt_1e-150\tAffiliation_masked\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\tAGGGAAAACATTTACATTGTATGTGAAGGGTTGTAGCCAGCCTCTTATAGGAATTGTGCACACCTGAATCATCATGTAATAACCATTTAATACTTTTAT'..b'CACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t544\t177\t203\t164\n+blast_eval_gt_1e-150\tAffiliation_masked\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\t245\t80\t83\t82\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Dothideomycetes;(1.0);o__Pleosporales;(1.0);f__Leptosphaeriaceae;(1.0);g__Leptosphaeria;(1.0);s__Leptosphaeria_polylepidis;(1.0);\tk__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Leptosphaeriaceae;g__Leptosphaeria;s__Leptosphaeria_polylepidis\tAJ786644_SH470265.07FU_refs_singleton\t100.0\t100.0\t4.75e-129\t243\t01_210\tCATTAGTCTCTATTGGGGGGGACGAGATTCAGATTGCTAAATCAGGGCTTCGGCCCGGCTTTACAGCTTTTGCCCTTTCTGATTATACCCATGTTTTGTGTGTACCAGTTGTTTTCTTGGTGGGCTTGTCCACCAATAAGGCCCTGCTAAACCTTTTGTAATTGCAGTCAGCGTCAGTAAAACCTAATTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_51\t83\t22\t28\t33\n+blast_eval_gt_1e-150\tAffiliation_masked\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\t59\t26\t16\t17\n+blast_eval_gt_1e-150\tAffiliation_masked\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_rhododendri;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rhododendri\tFJ860822_SH177722.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_4641\tCATTACCGAGTTTACAACTCCCAAACCCCAATGTGAACGTTACCACACCGTTGCCTCGGCGGGATCGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAATAAACTCTATTGTATTTATGTATTTTTACTTCTGAGCTTTCTCGGCGCTCCCAGCGAGCGTTTCGAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_53\t45\t17\t12\t16\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Thelephorales;(1.0);f__Thelephoraceae;(1.0);g__Thelephora;(1.0);s__Thelephora_atra;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Thelephora;s__Thelephora_atra\tUDB016470_SH189377.07FU_refs\t100.0\t100.0\t1.70e-128\t242\t01_3904\tCCGAATCGTCAAACACGGGTTGTTGCTGGCCCCCGAACGGGGGCACGTGCACGCTCTGTTTACGCATCCACTCACACCTGTGCACCCTCGGTAGTTCTATGGTTTGGGAGACCCCGTCTTCCTTCCGTGGCTCTACGTCTTTACACACACAACGTCTCATGGAATGTTTTTCGCGTTTAACGCAATAAAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_54\t37\t9\t13\t15\n+blast_eval_gt_1e-150\tAffiliation_masked\tk__Fungi;(1.0);p__Basidiomycota;(1.0);c__Agaricomycetes;(1.0);o__Agaricales;(1.0);f__Amanitaceae;(1.0);g__Amanita;(1.0);s__Amanita_friabilis;(1.0);\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_friabilis\tUDB011541_SH194446.07FU_refs\t100.0\t100.0\t6.09e-128\t241\t01_67609\tGGTGACTGCGGAGGATCATTATTGATGAACCTCTGGCTAGATGCCTGTTGTGCTGGCCCTTTGGGGGCAATGTGCACACCTCTGGTCATTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCTGTGTCTATGATATGTTACACACACACAATTGGTTGGCATATTACAAAAAATAAATAAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGC\tCluster_55\t10\t2\t6\t2\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/07-impacted_clusters_masked_multihit.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/07-impacted_clusters_masked_multihit.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +#observation_name blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/09-normalisation.biom --- a/test-data/references/09-normalisation.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/09-normalisation.biom Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "Sampling 100 elements by sample from test_4.0.1/08-affiliation_postprocessed.biom", "date": "2022-06-15T10:04:33", "rows": [{"id": "Cluster_9", "metadata": {"comment": [], "seed_id": "01_97858", "blast_affiliations": [{"subject": "JQ621972_SH177703.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_mienum"], "evalue": "2.32e-137", "aln_length": 258, "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_mienum"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_mienum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_36", "metadata": {"comment": [], "seed_id": "01_222", "blast_affiliations": [{"subject": "UDB002317_SH221025.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "evalue": "9.52e-162", "aln_length": 302, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"], "rdp_bootstrap": [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_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_41", "metadata": {"comment": [], "seed_id": "01_91819", "blast_affiliations": [{"subject": "UDB011569_SH190415.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Tricholomataceae", "g__Tricholoma", "s__Tricholoma_portentosum"], "evalue": "2.72e-167", "aln_length": 312, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Tricholomataceae", "g__Tricholoma", "s__Tricholoma_portentosum"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Tricholomataceae", "g__Tricholoma", "s__Tricholoma_portentosum"]'..b'tstrap": [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_49", "metadata": {"comment": [], "seed_id": "01_88865", "blast_affiliations": [{"subject": "GQ159830_SH222371.07FU_refs", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"], "evalue": "1.33e-129", "aln_length": 244, "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_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]}}, {"id": "Cluster_32", "metadata": {"comment": [], "seed_id": "01_96725", "blast_affiliations": [{"subject": "KF732249_SH136099.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_amnicola"], "evalue": "1.19e-155", "aln_length": 291, "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_amnicola"], "rdp_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_amnicola"], "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, 6], [0, 1, 2], [0, 2, 1], [1, 0, 4], [1, 1, 1], [1, 2, 2], [2, 0, 4], [2, 2, 4], [3, 0, 2], [3, 1, 1], [3, 2, 1], [4, 0, 4], [4, 2, 1], [5, 0, 2], [5, 2, 3], [6, 0, 5], [6, 1, 1], [6, 2, 2], [7, 0, 2], [7, 1, 2], [7, 2, 1], [8, 0, 2], [8, 1, 4], [8, 2, 4], [9, 0, 2], [9, 1, 1], [9, 2, 1], [10, 0, 3], [10, 1, 3], [10, 2, 5], [11, 0, 3], [11, 1, 2], [11, 2, 2], [12, 0, 1], [12, 1, 1], [12, 2, 2], [13, 0, 2], [13, 1, 3], [13, 2, 3], [14, 0, 3], [14, 1, 4], [14, 2, 2], [15, 0, 2], [15, 1, 2], [16, 0, 6], [16, 1, 1], [16, 2, 8], [17, 0, 4], [17, 1, 3], [17, 2, 1], [18, 0, 4], [19, 0, 1], [19, 1, 5], [19, 2, 5], [20, 0, 4], [20, 2, 2], [21, 0, 2], [22, 0, 2], [22, 1, 4], [23, 0, 3], [23, 2, 3], [24, 0, 1], [24, 1, 2], [24, 2, 1], [25, 0, 1], [25, 1, 1], [25, 2, 1], [26, 0, 1], [26, 1, 1], [26, 2, 1], [27, 0, 6], [27, 1, 3], [27, 2, 2], [28, 0, 1], [28, 1, 2], [28, 2, 1], [29, 0, 2], [29, 1, 1], [29, 2, 3], [30, 0, 2], [31, 0, 2], [31, 1, 1], [31, 2, 4], [32, 0, 2], [32, 1, 5], [32, 2, 1], [33, 0, 3], [33, 1, 2], [33, 2, 4], [34, 0, 1], [34, 2, 2], [35, 0, 1], [35, 1, 1], [35, 2, 1], [36, 0, 2], [36, 1, 3], [37, 0, 1], [37, 1, 4], [37, 2, 3], [38, 0, 1], [38, 1, 4], [38, 2, 3], [39, 1, 3], [40, 1, 6], [41, 1, 3], [41, 2, 1], [42, 1, 4], [42, 2, 1], [43, 1, 3], [43, 2, 4], [44, 1, 3], [44, 2, 3], [45, 1, 4], [45, 2, 2], [46, 1, 1], [46, 2, 5], [47, 1, 2], [47, 2, 3], [48, 1, 1], [49, 2, 1]], "shape": [50, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/09-normalisation.fasta --- a/test-data/references/09-normalisation.fasta Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/09-normalisation.fasta Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -98,5 +98,3 @@ 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_52 reference=EF669607_SH109271.07FU_refs_singleton position=1..243 -CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/09-normalisation.html --- a/test-data/references/09-normalisation.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/09-normalisation.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Abundance Normalisation</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <!-- 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> @@ -363,11 +363,11 @@ $(function() { - var categories = ["Nb OTU before normalisation", "Nb OTU after normalisation"] ; + var categories = ["Nb ASV before normalisation", "Nb ASV after normalisation"] ; var del_categories = ["Nb sequences"] ; - var series_by_sample = [{"name": "01_subsample", "data": [55, 41]}, {"name": "02_subsample", "data": [55, 46]}, {"name": "03_subsample", "data": [55, 40]}] ; + var series_by_sample = [{"name": "01_subsample", "data": [55, 39]}, {"name": "02_subsample", "data": [55, 40]}, {"name": "03_subsample", "data": [55, 41]}] ; var del_by_sample = [] ; - var remove_info = {"abundance_kept": 300, "abundance_removed": 74828, "nb_kept": 51, "nb_removed": 4} ; + var remove_info = {"abundance_kept": 300, "abundance_removed": 74828, "nb_kept": 50, "nb_removed": 5} ; // Remove alert $('#js-alert').remove(); @@ -411,7 +411,7 @@ ['Kept', remove_info['nb_kept']], ['Removed', remove_info['nb_removed']] ]; - $('#nb-filtered').highcharts( pie_param('Clusters', nb_filtered_data, 'Clusters') ); + $('#nb-filtered').highcharts( pie_param('ASVs', nb_filtered_data, 'ASVs') ); var abundance_filtered_data = [ ['Kept', remove_info['abundance_kept']], ['Removed', remove_info['abundance_removed']] |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/10-clustersStat.html --- a/test-data/references/10-clustersStat.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/10-clustersStat.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| @@ -19,7 +19,7 @@ <head> <title>FROGS Cluster stat</title> <meta charset="UTF-8"> - <meta name="version" content="4.0.1"> + <meta name="version" content="4.1.0"> <!-- CSS --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> @@ -838,14 +838,14 @@ // Data // /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// - var clusters_sizes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11] ; + var clusters_sizes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15] ; var series = [{ 'name': "All", - 'data': [4, 2, 2, 9, 7, 7, 7, 3, 3, 4, 3] + 'data': [2, 2, 5, 8, 6, 8, 4, 7, 3, 1, 3, 1] }]; var sum_series = new Array() ; - 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);" ; + var samples_distrib = {"01_subsample": {"shared_seq": 92, "shared_observations": 36, "own_seq": 8, "own_observations": 3}, "02_subsample": {"shared_seq": 90, "shared_observations": 37, "own_seq": 10, "own_observations": 3}, "03_subsample": {"shared_seq": 99, "shared_observations": 40, "own_seq": 1, "own_observations": 1}} ; + var newick = "((01_subsample,(02_subsample,03_subsample):0.410):0.470);" ; /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/11-affiliationsStat.html --- a/test-data/references/11-affiliationsStat.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/11-affiliationsStat.html Tue May 23 07:59:04 2023 +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="4.0.1">\n+\t\t<meta name="version" content="4.1.0">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -611,7 +611,7 @@\n \t\t\t\t\n \t\t\t\t// Parameters\n \t\t\t\tvar clean_type = {\n-\t\t\t\t\t"clstr": "OTUs",\n+\t\t\t\t\t"clstr": "ASVs",\n \t\t\t\t\t"seq": "sequences"\n \t\t\t\t}\n \t\t\t\tvar categories_ident = [1, 50, 80, 90, 95, 99, 100, 101];\n@@ -737,7 +737,7 @@\n \t\t\t\t\n \t\t\t\t// Parameters\n \t\t\t\tvar clean_type = {\n-\t\t\t\t\t"clstr": "OTUs",\n+\t\t\t\t\t"clstr": "ASVs",\n \t\t\t\t\t"seq": "sequences"\n \t\t\t\t}\n \t\t\t\tvar bootstrap_categories = [50, 80, 90, 95, 100, 101];\n@@ -868,7 +868,7 @@\n \t\t\t\tfor( var rank = 0 ; rank < taxonomic_ranks.length ; rank++ ){\n \t\t\t\t\ttitles.push( "Nb " + taxonomic_ranks[rank].toLowerCase() );\n \t\t\t\t}\n-\t\t\t\ttitles.push( "Nb otus" );\n+\t\t\t\ttitles.push( "Nb asv" );\n \t\t\t\ttitles.push( "Nb sequences" );\n \t\t\t\t$(\'#taxBySample-table thead\').append( \'<tr><th>\' + titles.join("</th><th>") + \'</th></tr>\' );\n \t\t\t\t$(\'#taxBySample-table .title\').attr( "colspan", titles.length );\n@@ -886,7 +886,7 @@\n \t\t\t\t\tfor( var rank = 0 ; rank < taxonomic_ranks.length ; rank++ ){\n \t\t\t\t\t\tsample_data.push( numberDisplay(tree.getNodeByDepth(rank+1).length) );\n \t\t\t\t\t}\n-\t\t\t\t\tsample_data.push( numberDisplay(rarefaction[sample_name][\'nb_otus\']) );\n+\t\t\t\t\tsample_data.push( numberDisplay(rarefaction[sample_name][\'nb_asv\']) );\n \t\t\t\t\tsample_data.push( numberDisplay(rarefaction[sample_name][\'nb_seq\']) );\n \t\t\t\t\t// Add row data\n \t\t\t\t\t$(\'#taxBySample-table tbody\').append( \'<tr><td>\' + sample_data.join("</td><td>") + \'</td></tr>\' );\n@@ -978,7 +978,7 @@\n \t\t\tvar bootstrap_score_load = function( cotainer_id ){\n \t\t\t\t$(\'#\' + cotainer_id).highcharts( bootstrap_param() );\n \t\t\t\t\n-\t\t\t\t$(\'#bootstrap-clstr-btn\').on(\'click\', function (e) { // Display view by OTUs\n+\t\t\t\t$(\'#bootstrap-clstr-btn\').on(\'click\', function (e) { // Display view by ASVs\n \t\t\t\t\tif( $(\'#bootstrap-clstr-btn\').hasClass("btn-default") ){\n \t\t\t\t\t\t$(\'#bootstrap-clstr-btn\').removeClass( "btn-default" );\n \t\t\t\t\t\t$(\'#bootstrap-clstr-btn\').addClass( "btn-primary" );\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__Trichoderma_mienum\\":{\\"0\\": 3, \\"1\\": 3, \\"2\\": 5},\\"s__Trichoderma_cremeum\\":{\\"0\\": 3, \\"1\\": 3, \\"2\\": 5},\\"s__Trichoderma_aggressivum\\":{\\"0\\": 3, \\"1\\": 2, \\"2\\": 1},\\"s__Trichoderma_rodmanii\\":{\\"0\\": 1, \\"2\\": 1})\\"g__Trichoderma\\")\\"f__Hypocreaceae\\")\\"o__Hypocreales\\",(((\\"s__Pestalotiopsis_diversiseta\\":{\\"0\\": 3, \\"1\\": 2, \\"2\\": 1})\\"g__Pestalotiopsis\\",(\\"s__Adisciso_tricellulare\\":{\\"0\\": 1, \\"1\\": 2, \\"2\\": 1})\\"g__Adisciso\\")\\"f__Amphisphaeriaceae\\",((\\"s__Hypoxylon_fragiforme\\":{\\"0\\": 1, \\"1\\": 4, \\"2\\": 1})\\"g__Hypoxylon\\")\\"f__Xylariaceae\\")\\"o__Xylariales\\",(((\\"s__Phaeoacremonium_rubrigenum\\":{\\"0\\": 1, \\"1\\": 3, \\"2\\": 2})\\"g__Phaeoacremonium\\")\\"f__Togniniaceae\\")\\"o__Diaporthales\\")\\"c__Sordariomycetes\\",((((\\"s__Elaphomyces_compleximurus\\":{\\"0\\": 2, \\"1\\": 2, \\"2\\": 2})\\"g__Elaphomyces\\")\\"f__Elaphomycetaceae\\",((\\"s__Rasamsonia_emersonii\\":{\\"0\\": 5, \\"1\\": 3, \\"2\\": 1})\\"g__Rasamsonia\\",(\\"s__Aspergillus_caninus\\":{\\"1\\": 1},\\"s__Aspergillus_microcysticus\\":{\\"2\\": 1})\\"g__Aspergillus\\")\\"f__Trichocomaceae\\")\\"o__Eurotiales\\",(((\\"s__Exophiala_equina\\":{\\"0\\": 4, \\"1\\": 3, \\"2\\": 4})\\"g__Exophiala\\")\\"f__Herpotrichiellaceae\\")\\"o__Chaetothyriales\\")\\"c__Eurotiomycetes\\",((((\\"s__Lindgomyces_breviappendiculatus\\":{\\"0\\": 3, \\"1\\": 3, \\"2\\": 4})\\"g__Lindgomyces\\")\\"f__Lindgomycetaceae\\")\\"o__Pleosporales\\")\\"c__Dothideomycetes\\",((((\\"s__Terfezia_claveryi\\":{\\"0\\": 4, \\"1\\": 3})\\"g__Terfezia\\")\\"f__Pezizaceae\\",((\\"s__Tuber_latisporum\\":{\\"0\\": 1, \\"1\\": 2})\\"g__Tuber\\")\\"f__Tubera'..b', 7, 7, 8, 10, 11, 11, 13, 14, 15, 15, 15, 15, 15, 15, 15, 17, 19, 19, 20, 20, 20, 20, 21, 22, 23, 23, 24, 24, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 27, 28, 28, 28, 28, 28, 29, 29], "Species": [2, 4, 6, 8, 10, 11, 13, 14, 15, 17, 18, 19, 20, 20, 21, 21, 21, 21, 23, 25, 25, 26, 26, 26, 26, 27, 28, 29, 29, 31, 31, 33, 33, 33, 33, 33, 33, 33, 34, 34, 34, 34, 35, 36, 36, 37, 38, 38, 39, 39], "ASVs": [2, 3, 4, 6, 8, 9, 11, 11, 13, 14, 16, 16, 16, 17, 19, 21, 23, 24, 25, 26, 26, 27, 29, 29, 30, 30, 30, 30, 31, 32, 32, 32, 33, 33, 33, 34, 35, 35, 36, 37, 38, 38, 38, 38, 39, 39, 39, 39, 39, 39]}, "02_subsample": {"nb_asv": 40, "nb_seq": 100, "Family": [2, 4, 5, 7, 9, 10, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 15, 16, 16, 16, 16, 16, 17, 17, 17, 18, 18, 19, 19, 19, 19, 19, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22], "Genus": [2, 4, 6, 8, 10, 11, 12, 12, 12, 12, 13, 15, 15, 15, 15, 15, 17, 18, 19, 20, 20, 20, 21, 22, 22, 23, 23, 24, 24, 24, 24, 24, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28], "Species": [2, 4, 6, 8, 10, 11, 12, 12, 12, 14, 16, 18, 20, 20, 20, 21, 23, 24, 25, 26, 28, 29, 31, 33, 33, 34, 34, 35, 35, 35, 35, 35, 37, 37, 38, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 40, 40], "ASVs": [2, 4, 6, 7, 8, 10, 12, 13, 15, 17, 18, 19, 20, 22, 24, 24, 25, 25, 26, 27, 28, 28, 28, 29, 29, 29, 30, 31, 31, 31, 32, 32, 32, 33, 33, 33, 33, 34, 35, 36, 36, 36, 38, 38, 38, 39, 40, 40, 40, 40]}, "03_subsample": {"nb_asv": 41, "nb_seq": 100, "Family": [2, 4, 6, 7, 9, 11, 12, 13, 14, 14, 15, 16, 17, 18, 18, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 25, 25, 25, 25, 25, 26, 26, 26], "Genus": [2, 4, 6, 8, 10, 12, 13, 14, 15, 15, 16, 17, 18, 20, 20, 21, 21, 22, 22, 23, 23, 24, 24, 25, 25, 26, 26, 26, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 30, 30, 30, 30, 30, 31, 31, 31], "Species": [2, 4, 6, 8, 10, 12, 13, 14, 15, 17, 18, 20, 21, 23, 23, 24, 24, 25, 27, 28, 28, 29, 30, 32, 32, 33, 33, 34, 35, 35, 36, 36, 36, 37, 37, 37, 37, 37, 37, 38, 39, 39, 40, 40, 40, 40, 40, 41, 41, 41], "ASVs": [1, 3, 5, 7, 9, 11, 12, 14, 15, 17, 17, 17, 18, 18, 19, 21, 22, 24, 25, 26, 27, 28, 28, 29, 29, 30, 30, 30, 31, 31, 33, 34, 35, 36, 36, 36, 36, 36, 36, 38, 38, 39, 39, 39, 39, 39, 39, 40, 41, 41]}} ;\n \t\t\t/* Example:\n \t\t\t\t{\n \t\t\t\t\t"Surface-01": {\n@@ -1037,11 +1037,11 @@\n \t\t\t/* Example:\n \t\t\t\t1000\n \t\t\t*/\n-\t\t\tvar rarefaction_ranks = ["Family", "Genus", "Species", "OTUs"] ;\n+\t\t\tvar rarefaction_ranks = ["Family", "Genus", "Species", "ASVs"] ;\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": 50, "seq": 296}], [99.627, 100.0, {"clstr": 1, "seq": 4}]] ;\n+\t\t\tvar alignment_scores = [[100.0, 100.0, {"clstr": 49, "seq": 294}], [99.627, 100.0, {"clstr": 1, "seq": 6}]] ;\n \t\t\t/* Example:\n \t\t\t\t[\n \t\t\t\t\t[100, 100, { "clstr": 53, "seq": 20500 }],\n@@ -1143,14 +1143,14 @@\n \t\t\t\t<div id="bootstrap-distrib" role="tabpanel" class="tab-pane disabled">\n \t\t\t\t\t<div id="bootstrap-barplot"></div>\n \t\t\t\t\t<div id="set-bootstrap-barplot" class="set-datatype">\n-\t\t\t\t\t\t<button id="bootstrap-clstr-btn" type="button" class="btn btn-md btn-block">by OTUs</button>\n+\t\t\t\t\t\t<button id="bootstrap-clstr-btn" type="button" class="btn btn-md btn-block">by ASVs</button>\n \t\t\t\t\t\t<button id="bootstrap-seq-btn" type="button" class="btn btn-md btn-block">by sequences</button>\n \t\t\t\t\t</div>\n \t\t\t\t</div>\n \t\t\t\t<div id="alignment-distrib" role="tabpanel" class="tab-pane disabled">\n \t\t\t\t\t<div id="alignment-heatmap"></div>\n \t\t\t\t\t<div id="set-alignment-heatmap" class="set-datatype">\n-\t\t\t\t\t\t<button id="heatmap-clstr-btn" type="button" class="btn btn-md btn-block" disabled>by OTUs</button>\n+\t\t\t\t\t\t<button id="heatmap-clstr-btn" type="button" class="btn btn-md btn-block" disabled>by ASVs</button>\n \t\t\t\t\t\t<button id="heatmap-seq-btn" type="button" class="btn btn-md btn-block">by sequences</button>\n \t\t\t\t\t</div>\n \t\t\t\t</div>\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/12-biom2tsv.tsv --- a/test-data/references/12-biom2tsv.tsv Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/12-biom2tsv.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,52 +1,51 @@\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\t11\t4\t3\t4\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\t3\t1\t2\t0\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Elaphomycetaceae;(1.0);g__Elaphomyces;(1.0);s__Elaphomyces_compleximurus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Elaphomycetaceae;g__Elaphomyces;s__Elaphomyces_compleximurus\tJN711441_SH022548.07FU_refs_singleton\t100.0\t100.0\t8.06e-132\t248\t01_59\tAGGATCATTACCGAGTGAGGGTCTCTGCGTGGGCCCGACCTCTCCACCCGTGTCTACCGTACCAGTGTTGCTTCGGCGGGCCCGCCGTTCAGGCCGCCGGGGGGTGAGGTGTTGCACCCGCCTCCGGGCCCGTGTCCGCCGGGGATGAGGGAACTACTGCTGTTGGAGTGTTGTCTGAGTGGGTGATAGAATAGTTAAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_3\t6\t2\t2\t2\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Sordariomycetes;(1.0);o__Hypocreales;(1.0);f__Hypocreaceae;(1.0);g__Trichoderma;(1.0);s__Trichoderma_aggressivum;(1.0);\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_aggressivum\tAF456924_SH097201.07FU_refs\t100.0\t100.0\t4.90e-134\t252\t01_81\tCCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCCAAAACTCTTATTGTATACCCCCTCGCGGGTTATTTTTACTATCTGAGCCTTCTCGGCGCCTCTCGTAGGCGTTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC\tCluster_4\t6\t3\t2\t1\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\t6\t3\t2\t1\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\t5\t1\t1\t3\n-no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycet'..b'TTGATAAAGTCTTGATGAATGATAGATTGGTCTTTTGAACCAATATAAAAGTTGTACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC\tCluster_47\t11\t1\t5\t5\n+no data\tk__Fungi;(1.0);p__Ascomycota;(1.0);c__Eurotiomycetes;(1.0);o__Eurotiales;(1.0);f__Trichocomaceae;(1.0);g__Aspergillus;(1.0);s__Aspergillus_caninus;(1.0);\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Trichocomaceae;g__Aspergillus;s__Aspergillus_caninus\tGQ169315_SH195598.07FU_refs\t100.0\t100.0\t3.70e-130\t245\t01_86\tTGCGGAAGGATCATTAACGAGTGCGGCCCCTCCGGGGTGCCAACCTCCCACCCGTGTCTATCGTACCACGTTGCTTCGGCGGGACCGCCCCTATCCGTAGGGGCCGTCGGGAGCCTCGCTCCGGGCGTGCGCCCGCCGAAGACCCCACGAACGCTGTCTGAAGACTGCCGTCTGAGTGGATTATCGAATCAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC\tCluster_48\t2\t2\t0\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+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\t3\t1\t1\t1\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/13-affiliation_multihit.tsv --- a/test-data/references/13-affiliation_multihit.tsv Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/13-affiliation_multihit.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,52 +1,51 @@\n-#OTUID\ttaxonomy\tsubject\tevalue\tperc_identity\tperc_query_coverage\taln_length\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+ASVID\ttaxonomy\tsubject\tevalue\tperc_identity\tperc_query_coverage\taln_length\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_30\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Psathyrella;s__Psathyrella_multipedata\tKC992888_SH220378.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n+Cluster_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_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_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_40\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_limonius\tUDB001086_SH222381.07FU_refs\t7.59e-168\t100.0\t100.0\t313\n+Cluster_16\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Xylariales;f__Xylariaceae;g__Hypoxylon;s__Hypoxylon_fragiforme\tAY616689_SH196294.07FU_refs\t8.56e-142\t100.0\t100.0\t266\n+Cluster_12\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_pachyderma\tJX118731_SH218995.07FU_refs\t5.20e-144\t100.0\t100.0\t270\n+Cluster_46\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Hymenochaetales;f__Hymenochaetaceae;g__Pseudochaete;s__Pseudochaete_subrigidula\tJQ716403_SH219241.07FU_refs\t7.94e-178\t100.0\t100.0\t331\n Cluster_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_1\tk__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Chaetothyriales;f__Herpotrichiellaceae;g__Exophiala;s__Exophiala_equina\tJF747094_SH197643.07FU_refs\t2.25e-132\t100.0\t100.0\t249\n+Cluster_14\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Diaporthales;f__Togniniaceae;g__Phaeoacremonium;s__Phaeoacremonium_rubrigenum\tAF118139_SH214931.07FU_refs\t3.94e-140\t100.0\t100.0\t263\n+Cluster_29\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_caesiocolor\tKF732603_SH223051.07FU_refs\t5.4'..b'0.0\t390\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_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_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_8\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__Suillaceae;g__Truncocolumella;s__Truncocolumella_rubra\tEU837224_SH182725.07FU_refs\t2.25e-132\t100.0\t100.0\t249\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_6\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Bankeraceae;g__Sarcodon;s__Sarcodon_quercophilus\tKM668101_SH491630.07FU_refs_singleton\t3.94e-140\t100.0\t100.0\t263\n+Cluster_35\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_aurantiobasis\tJX045670_SH303923.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n+Cluster_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_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_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_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_18\tk__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_rodmanii\tEU330948_SH316773.07FU_refs\t8.56e-142\t100.0\t100.0\t266\n-Cluster_29\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Cortinariaceae;g__Cortinarius;s__Cortinarius_caesiocolor\tKF732603_SH223051.07FU_refs\t5.49e-154\t100.0\t100.0\t288\n-Cluster_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_30\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Psathyrella;s__Psathyrella_multipedata\tKC992888_SH220378.07FU_refs\t1.19e-155\t100.0\t100.0\t291\n-Cluster_12\tk__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Psathyrellaceae;g__Coprinopsis;s__Coprinopsis_pachyderma\tJX118731_SH218995.07FU_refs\t5.20e-144\t100.0\t100.0\t270\n-Cluster_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_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_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 37e6f0c959bb -r b2967b704d6b test-data/references/13-affiliation_std.biom --- a/test-data/references/13-affiliation_std.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/13-affiliation_std.biom Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "Sampling 100 elements by sample from test_4.0.1/08-affiliation_postprocessed.biom", "date": "2022-06-15T10:04:33", "rows": [{"id": "Cluster_9", "metadata": {"comment": "", "seed_id": "01_97858", "blast_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_mienum", "rdp_taxonomy": "k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Hypocreaceae;g__Trichoderma;s__Trichoderma_mienum", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_mienum"]}}, {"id": "Cluster_36", "metadata": {"comment": "", "seed_id": "01_222", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Amanitaceae;g__Amanita;s__Amanita_franchetii", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Amanitaceae", "g__Amanita", "s__Amanita_franchetii"]}}, {"id": "Cluster_5", "metadata": {"comment": "", "seed_id": "01_25", "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", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Xylariales", "f__Amphisphaeriaceae", "g__Pestalotiopsis", "s__Pestalotiopsis_diversiseta"]}}, {"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_41", "metadata": {"comment": "", "seed_id": "01_91819", "blast_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Tricholoma;s__Tricholoma_portentosum", "rdp_taxonomy": "k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Agaricales;f__Tricholomataceae;g__Tricholoma;s__Tricholoma_portentosum", "rdp_bootstrap": "1.0;1.0;1.0;1.0;1.0;1.0;1.0", "taxonomy": ["k__Fungi", 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3], [41, 2, 1], [42, 1, 4], [42, 2, 1], [43, 1, 3], [43, 2, 4], [44, 1, 3], [44, 2, 3], [45, 1, 4], [45, 2, 2], [46, 1, 1], [46, 2, 5], [47, 1, 2], [47, 2, 3], [48, 1, 1], [49, 2, 1]], "shape": [50, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/14-tsv2biom.biom --- a/test-data/references/14-tsv2biom.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/14-tsv2biom.biom Tue May 23 07:59:04 2023 +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": "2022-06-15T10:04:34", "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", 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"perc_query_coverage": "100.0", "evalue": "2.25e'..b' "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_caninus"], "seed_id": "01_86", "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], "blast_affiliations": [{"taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Trichocomaceae", "g__Aspergillus", "s__Aspergillus_caninus"], "subject": "GQ169315_SH195598.07FU_refs", "perc_identity": "100.0", "perc_query_coverage": "100.0", "evalue": "3.70e-130", "aln_length": "245"}]}}, {"id": "Cluster_49", "metadata": {"comment": ["no data"], "blast_taxonomy": ["k__Fungi", "p__Basidiomycota", "c__Agaricomycetes", "o__Agaricales", "f__Cortinariaceae", "g__Cortinarius", "s__Cortinarius_parkeri"], 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1, 1], [13, 2, 2], [14, 0, 1], [14, 1, 2], [14, 2, 1], [15, 0, 2], [15, 1, 2], [15, 2, 1], [16, 0, 2], [16, 1, 2], [17, 0, 1], [17, 1, 4], [17, 2, 3], [18, 0, 4], [18, 2, 2], [19, 1, 3], [19, 2, 4], [20, 1, 4], [20, 2, 1], [21, 0, 4], [21, 2, 1], [22, 1, 3], [23, 0, 6], [23, 1, 3], [23, 2, 2], [24, 0, 2], [24, 1, 5], [24, 2, 1], [25, 1, 1], [25, 2, 5], [26, 0, 1], [26, 2, 2], [27, 0, 2], [28, 0, 2], [28, 1, 3], [28, 2, 3], [29, 0, 4], [29, 1, 1], [29, 2, 2], [30, 0, 1], [30, 1, 4], [30, 2, 3], [31, 2, 1], [32, 0, 4], [33, 0, 3], [33, 1, 4], [33, 2, 2], [34, 1, 4], [34, 2, 2], [35, 0, 2], [35, 1, 1], [35, 2, 1], [36, 0, 6], [36, 1, 1], [36, 2, 8], [37, 0, 2], [37, 1, 3], [38, 0, 2], [38, 2, 3], [39, 0, 5], [39, 1, 1], [39, 2, 2], [40, 0, 3], [40, 1, 3], [40, 2, 5], [41, 0, 1], [41, 1, 2], [41, 2, 1], [42, 0, 1], [42, 1, 1], [42, 2, 1], [43, 1, 6], [44, 1, 2], [44, 2, 3], [45, 0, 2], [45, 1, 1], [45, 2, 1], [46, 0, 1], [46, 1, 5], [46, 2, 5], [47, 0, 2], [48, 1, 1], [49, 0, 1], [49, 1, 1], [49, 2, 1]], "shape": [50, 3], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/14-tsv2biom.fasta --- a/test-data/references/14-tsv2biom.fasta Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/14-tsv2biom.fasta Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -98,5 +98,3 @@ TGATGAGTTGCTGCTGGTTCTCTAGGGAGCATTGTGCACACTTGTCATTTTTTATATTTCCACTTGTGCACCTTTTGTAGACCTGAATAGTTGTAAGGAATTAACTTTCCTTATATTTTCAGGCCTATGTTTCTTCATATACTCCTTAATGCATGTTATAGAGTGTAACAGGCCCTATGTGCCTATAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC >Cluster_50_FROGS_combined GATACTCTGGCCAAGTGAGCGTTGCGTTTGGGCTCTTTTGAGTATTCCAACTTGAAATCAAAAAGGCAGTTGGAGAGCTACTGGGGTGTAAGAAATCCCCGGGAGTCTCGACAGCTGGTACAGCGGTCAAATTCCACGAAGACGGAGCATAGATAGCTAACCCCTGCGTCGTTGCACAAAAAAACAAAAAACGAGTGCCTTACAAAGGGACGCTTTGCTCTCGAGAGGTCAGCTGCGTACTTGGACTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCCTGAGCGCCCTTTGGAATGCTCGCGCAAGCGGGCCTGACGTTGGGCGCCCTTGGGAGAGTCGATCCTATGCCAACTCCCGGACCCCTTGTTTATGTGTATCCTTCGTTTCCTCGGCAGGCTTGCTTGCCAATGGGGACACCAACAAACTCTTTTTGTAGTGGCAGTGTCTGTGGAATTATCAAATCTTATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC ->Cluster_52 -CGAGAGAGGGTCTTCCAGGCCCGACCTCCCACCCGTGTCTCTTTCTGACCCTGTTGCTTCGGCGGGCCGCGCCAGCGCCCCGTGCCTGGCCGCCGGGGGGCCCCTGTGCCCCCGGGTCCGCGCCCGCCGGAGACCTCCAATGGAATTCTGTTCTGAAAGCCTGTCGTCTGAGTGATTGTCTTGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGC |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/15-tree-mafft.html --- a/test-data/references/15-tree-mafft.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/15-tree-mafft.html Tue May 23 07:59:04 2023 +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="4.0.1">\n+\t\t<meta name="version" content="4.1.0">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -182,7 +182,7 @@\n }\n #phylocanvas {\n width: 1150px;\n- height: 727px;\n+ height: 716px;\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": 51, "otu_removed": 0, "abundance_kept": 300, "abundance_removed": 0} ;\n+\t\t\t\tvar summary = {"otu_kept": 50, "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@@ -443,25 +443,25 @@\n \t\t\t\t\t[\'In Tree\', summary[\'otu_kept\']],\n \t\t\t\t\t[\'Out of Tree\', summary[\'otu_removed\']]\n \t\t\t\t];\n-\t\t\t\t$(\'#nb-otu\').highcharts( pie_param(\'OTUs\', nb_otu, \'OTUs\') );\n+\t\t\t\t$(\'#nb-otu\').highcharts( pie_param(\'ASVs\', nb_otu, \'ASVs\') );\n \t\t\t\tvar nb_abundance = [\n \t\t\t\t\t[\'In Tree\', summary[\'abundance_kept\']],\n \t\t\t\t\t[\'Out of Tree\', summary[\'abundance_removed\']]\n \t\t\t\t];\n \t\t\t\t$(\'#nb-abundance\').highcharts( pie_param(\'Abundance\', nb_abundance, \'Sequences\') );\n \t\t\t\t\n-\t\t\t\t// Display failed OTUs table\n+\t\t\t\t// Display failed ASVs table\n \t\t\t\tvar table_categories = removed_details_categories.slice() ;\n-\t\t\t\ttable_categories.unshift( "OTU Name" );\n+\t\t\t\ttable_categories.unshift( "ASV Name" );\n \t\t\t\tvar table_series = new Array();\n \t\t\t\tfor( var spl_idx = 0 ; spl_idx < removed_details_data.length ; spl_idx++ ){\n \t\t\t\t\tvar nb_by_step = removed_details_data[spl_idx][\'data\'].slice() ;\n \t\t\t\t\tnb_by_step.unshift( removed_details_data[spl_idx][\'name\'] );\n \t\t\t\t\ttable_series.push( nb_by_step );\n \t\t\t\t};\n-\t\t\t\t$(\'#OTUs-fail\').append( table(table_categories, table_series) );\n-\t\t\t\t$(\'#OTUs-fail table\').prop( \'id\', \'details-table\' );\n-\t\t\t\t$(\'#OTUs-fail table\').DataTable({\n+\t\t\t\t$(\'#ASVs-fail\').append( table(table_categories, table_series) );\n+\t\t\t\t$(\'#ASVs-fail table\').prop( \'id\', \'details-table\' );\n+\t\t\t\t$(\'#ASVs-fail table\').DataTable({\n \t\t\t\t\tdom: \t"<\'#details-csv-export\'><\'row\'<\'col-sm-5\'l><\'col-sm-7\'f>>" +\n \t\t\t\t\t\t\t"<\'row\'<\'col-sm-12\'tr>>" +\n \t\t\t\t\t\t\t"<\'row\'<\'col-sm-5\'i><\'col-sm-7\'p>>"\n@@ -488,7 +488,7 @@\n });\n tree.branchColour = "#8EADAC";\n tree.selectedColour = "#DE9F73";\n- tree.load(\'((((((((Cluster_21 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_cremeum:0.078518609,(Cluster_18 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_rodmanii:0.060934408,Cluster_9 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_mienum:0.031124161)0.740:0.007475077)0.465:0.014999311,Cluster_4 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Hypocreaceae g__Trichoderma s__Trichoderma_aggressivum:0.018679151)1.000:0.451763845,(Cluster_16 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Xylariaceae g__Hypoxylon s__Hypoxylon_fragiforme:0.231638797,(Cluster_5 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Amphisphaeriaceae g__Pestalotiopsis s__Pestalotiopsis_diversiseta:0.078204987,Cluster_11 k__Fungi p__Ascomycota c__Sordariomycetes o__Xylariales f__Amphisphaeriaceae g__Adisciso s__Adisciso_tricellulare:'..b'_Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_aurantiobasis:0.026928271,Cluster_38 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_sinapivelus:0.072298)0.590:0.002099848,((Cluster_29 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_caesiocolor:0.047819839,((Cluster_40 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_limonius:0.064924365,(Cluster_31 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_calojanthinus:0.026320982,Cluster_32 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_amnicola:0.032415696)0.963:0.02807349)0.061:0.005719258,Cluster_49 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_parkeri:0.091082619)0.745:0.00555978)0.476:0.009522841,Cluster_27 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Cortinariaceae g__Cortinarius s__Cortinarius_gentianeus:0.063518897)0.706:0.008938396)0.996:0.101585622)0.755:0.025418261)0.583:0.013002361,((Cluster_43 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Paxillaceae g__Alpova s__Alpova_alpestris:0.0770561,Cluster_44 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Paxillaceae g__Alpova s__Alpova_corsicus:0.016333891)0.996:0.25265363,(Cluster_8 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Suillaceae g__Truncocolumella s__Truncocolumella_rubra:0.108132476,Cluster_39 k__Fungi p__Basidiomycota c__Agaricomycetes o__Boletales f__Boletaceae g__Xerocomus s__Xerocomus_porophyllus:0.163074547)0.544:0.06978195)1.000:0.297040136)0.795:0.032943001,Cluster_13 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Tricholomataceae g__Gamundia s__Gamundia_leucophylla:0.158367262)0.688:0.033893059,(Cluster_36 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Amanitaceae g__Amanita s__Amanita_franchetii:0.219265966,(Cluster_45 k__Fungi p__Basidiomycota c__Agaricomycetes o__Hymenochaetales f__Hymenochaetaceae g__Hymenochaete s__Hymenochaete_longispora:0.385750698,(Cluster_22 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_semisanguifluus:0.099729168,(Cluster_10 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_cyathuliformis:0.007325427,Cluster_17 k__Fungi p__Basidiomycota c__Agaricomycetes o__Russulales f__Russulaceae g__Lactarius s__Lactarius_sp:0.008423931)0.691:0.035761733)0.993:0.31064026)0.912:0.131912668)0.490:0.03563371)0.925:0.151566685,(Cluster_46 k__Fungi p__Basidiomycota c__Agaricomycetes o__Hymenochaetales f__Hymenochaetaceae g__Pseudochaete s__Pseudochaete_subrigidula:0.417849611,(Cluster_6 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Sarcodon s__Sarcodon_quercophilus:0.480759519,(Cluster_24 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Hydnellum s__Hydnellum_peckii:0.151520149,Cluster_34 k__Fungi p__Basidiomycota c__Agaricomycetes o__Thelephorales f__Bankeraceae g__Hydnellum s__Hydnellum_suaveolens:0.189302877)0.835:0.092429593)0.706:0.071145205)0.709:0.059899274)0.998:0.1747282845)NA;\');\n tree.backColour = true;\n tree.draw();\n \t\t\t});\n@@ -511,8 +511,8 @@\n <div id="nb-otu" class="col-md-6"></div>\n <div id="nb-abundance" class="col-md-6"></div>\n </div>\n- <div id="OTUs-fail" style="display:none;">\n- \t<h2 class="pb-2 mt-4 mb-2 border-bottom">Table of failed OTUs</h2>\n+ <div id="ASVs-fail" style="display:none;">\n+ \t<h2 class="pb-2 mt-4 mb-2 border-bottom">Table of failed ASVs</h2>\n </div>\n <h1 class="page-header">Tree View\n <h5>Enabling zoom:</h5>\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/15-tree-mafft.nwk --- a/test-data/references/15-tree-mafft.nwk Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/15-tree-mafft.nwk Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,1 +1,1 @@ -((((((((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; +((((((Cluster_2:0.478207033,Cluster_20:0.354953051)0.766:0.095968545,Cluster_14:0.232700865)0.863:0.094767868,(Cluster_1:0.225049392,(Cluster_3:0.168511418,(Cluster_7:0.066213201,Cluster_48:0.155548872)0.926:0.084554056)0.982:0.161573855)0.892:0.097427259)0.760:0.05845986,((Cluster_16:0.263256816,(Cluster_5:0.055889034,Cluster_11:0.016912705)0.696:0.077142368)0.113:0.136583521,(Cluster_18:0.03758883,(Cluster_9:0.02961912,(Cluster_4:0.037533542,Cluster_21:0.079552597)0.743:0.010235142)0.799:0.025155658)0.991:0.269509509)0.730:0.072590175)0.936:0.191455672,Cluster_50_FROGS_combined:0.409304334)0.998:0.1010219175,(((((((Cluster_26:0.192853513,(Cluster_15:0.339146845,Cluster_37:0.201592282)0.368:0.064878447)0.835:0.043396312,(Cluster_23:0.187495916,Cluster_47:0.49292884)0.705:0.039691239)0.187:0.010305467,(((Cluster_41:0.109135579,(Cluster_42:0.285483589,(Cluster_28:0.09901092,Cluster_33:0.108834953)0.924:0.055167003)0.649:0.025803756)0.864:0.041630632,((Cluster_25:0.033874049,Cluster_30:0.053174939)0.999:0.12287502,(Cluster_12:0.053089478,Cluster_19:0.096505604)0.905:0.047939155)0.989:0.119683565)0.857:0.059674621,((Cluster_35:0.026928271,Cluster_38:0.072298)0.590:0.002099848,((Cluster_29:0.047819839,((Cluster_40:0.064924365,(Cluster_31:0.026320982,Cluster_32:0.032415696)0.963:0.02807349)0.061:0.005719258,Cluster_49:0.091082619)0.745:0.00555978)0.476:0.009522841,Cluster_27:0.063518897)0.706:0.008938396)0.996:0.101585622)0.755:0.025418261)0.583:0.013002361,((Cluster_43:0.0770561,Cluster_44:0.016333891)0.996:0.25265363,(Cluster_8:0.108132476,Cluster_39:0.163074547)0.544:0.06978195)1.000:0.297040136)0.795:0.032943001,Cluster_13:0.158367262)0.688:0.033893059,(Cluster_36:0.219265966,(Cluster_45:0.385750698,(Cluster_22:0.099729168,(Cluster_10:0.007325427,Cluster_17:0.008423931)0.691:0.035761733)0.993:0.31064026)0.912:0.131912668)0.490:0.03563371)0.925:0.151566685,(Cluster_46:0.417849611,(Cluster_6:0.480759519,(Cluster_24:0.151520149,Cluster_34:0.189302877)0.835:0.092429593)0.706:0.071145205)0.709:0.059899274)0.998:0.1747282845)NA; |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/16-phylo_import.nb.html --- a/test-data/references/16-phylo_import.nb.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/16-phylo_import.nb.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -11,7 +11,7 @@\n \n \n \n-<title>FROGS Phyloseq: Import Data (version 4.0.1)</title>\n+<title>FROGS Phyloseq: Import Data (version 4.1.0)</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@@ -30,7 +30,7 @@\n !function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],r=Object.getPrototypeOf,s=t.slice,g=t.flat?function(e){return t.flat.call(e)}:function(e){return t.concat.apply([],e)},u=t.push,i=t.indexOf,n={},o=n.toString,v=n.hasOwnProperty,a=v.toString,l=a.call(Object),y={},m=function(e){return"function"==typeof e&&"number"!=typeof e.nodeType&&"function"!=typeof e.item},x=function(e){return null!=e&&e===e.window},E=C.document,c={type:!0,src:!0,nonce:!0,noModule:!0};function b(e,t,n){var r,i,o=(n=n||E).createElement("script");if(o.text=e,t)for(r in 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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/25-frogsfunc_copynumbers_marker.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/25-frogsfunc_copynumbers_marker.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -0,0 +1,11 @@ +sequence 16S_rRNA_Count metadata_NSTI +Cluster_1 1 0.033280000000000004 +Cluster_10 1 0.132638 +Cluster_11 1 0.048261 +Cluster_12 1 0.000101 +Cluster_2 3 0.010731999999999998 +Cluster_3 1 0.206031 +Cluster_4 1 0.939349 +Cluster_5 1 0.776856 +Cluster_6 1 0.067849 +Cluster_7 1 0.000102 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/25-frogsfunc_placeseqs.biom --- a/test-data/references/25-frogsfunc_placeseqs.biom Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/25-frogsfunc_placeseqs.biom Tue May 23 07:59:04 2023 +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": "2018-10-04T16:37:49", "rows": [{"id": "Cluster_1", "metadata": {"blast_taxonomy": ["Bacteria", "Firmicutes", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Oscillibacter", "unknown species"], "seed_id": "M02944:219:000000000-B6TML:1:1102:9099:12653", "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Bacteria", "Firmicutes", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Oscillibacter", "unknown species"], "evalue": "0.0", "aln_length": 403, "perc_query_coverage": 100.0, "subject": "HQ785790.1.1449"}], "picrust2_affiliations": "Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;unclassified;Oscillospiraceae_bacterium_VE202-24"}}, {"id": "Cluster_2", "metadata": {"blast_taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Multi-affiliation"], "seed_id": "M02944:219:000000000-B6TML:1:1102:5178:4304", "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "LXJJ02000010.3161.4631"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli S88"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CU928161.4443202.4444743"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CU651637.2709763.2711303"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli O157:H7"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP033605.4932246.4933797"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Shigella flexneri"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP033510.2312050.2313603"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli O32:H37 str. P4"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "AJQW01000057.1.1280"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP032515.4680373.4681924"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP032265.2506313.2507866"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli DEC8C"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "AIGH01000069.160053.161583"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "unknown species"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "JX984110.1.1220"}, {"perc_identity":'..b' [5, 23, 3386], [5, 24, 3607], [5, 25, 2661], [5, 26, 4604], [5, 27, 2104], [5, 28, 5], [5, 29, 7], [5, 30, 3], [5, 31, 4], [5, 32, 4], [5, 33, 2], [5, 34, 11], [5, 35, 108], [5, 36, 5], [5, 37, 4], [5, 38, 21], [5, 39, 13], [5, 40, 87], [5, 41, 16], [5, 42, 5819], [5, 43, 610], [5, 44, 1198], [5, 45, 5003], [5, 46, 6177], [5, 47, 2239], [5, 48, 5907], [5, 49, 38], [5, 50, 596], [5, 51, 27], [5, 52, 86], [5, 53, 18], [5, 54, 35], [5, 55, 18], [5, 56, 224], [5, 57, 1154], [5, 58, 2566], [5, 59, 389], [5, 60, 83], [5, 61, 163], [5, 62, 256], [6, 0, 1148], [6, 1, 1468], [6, 2, 1044], [6, 3, 1396], [6, 4, 552], [6, 5, 612], [6, 6, 1846], [6, 7, 13], [6, 8, 13], [6, 9, 15], [6, 10, 35], [6, 11, 9], [6, 12, 24], [6, 13, 21], [6, 14, 2666], [6, 15, 728], [6, 16, 4407], [6, 17, 3321], [6, 18, 9514], [6, 19, 1597], [6, 20, 2373], [6, 21, 969], [6, 22, 372], [6, 23, 97], [6, 24, 697], [6, 25, 42], [6, 26, 836], [6, 27, 399], [6, 28, 1], [6, 29, 2], [6, 30, 6], [6, 31, 8], [6, 32, 6], [6, 33, 7], [6, 34, 4], [6, 35, 5184], [6, 36, 1406], [6, 37, 2379], [6, 38, 1471], [6, 39, 4165], [6, 40, 2616], [6, 41, 473], [6, 42, 1876], [6, 43, 1757], [6, 44, 3013], [6, 45, 1270], [6, 46, 2225], [6, 47, 1771], [6, 48, 3610], [6, 49, 41], [6, 50, 20], [6, 51, 32], [6, 52, 76], [6, 53, 34], [6, 54, 22], [6, 55, 11], [6, 56, 15266], [6, 57, 4545], [6, 58, 2580], [6, 59, 2981], [6, 60, 1403], [6, 61, 638], [6, 62, 3822], [7, 0, 2], [7, 1, 4], [7, 2, 7], [7, 3, 19], [7, 4, 4], [7, 5, 7], [7, 6, 7], [7, 7, 290], [7, 8, 369], [7, 9, 3062], [7, 10, 948], [7, 11, 1596], [7, 12, 231], [7, 13, 1769], [7, 14, 824], [7, 15, 152], [7, 16, 165], [7, 17, 190], [7, 18, 350], [7, 19, 57], [7, 20, 344], [7, 21, 1], [7, 23, 1], [7, 24, 9], [7, 28, 1634], [7, 29, 963], [7, 30, 3978], [7, 31, 1161], [7, 32, 398], [7, 33, 15], [7, 34, 1884], [7, 35, 278], [7, 36, 2075], [7, 37, 333], [7, 38, 629], [7, 39, 1036], [7, 40, 1579], [7, 41, 4682], [7, 42, 26], [7, 46, 1], [7, 48, 1], [7, 49, 717], [7, 50, 1213], [7, 51, 4106], [7, 52, 167], [7, 53, 1136], [7, 54, 1806], [7, 55, 513], [7, 56, 58], [7, 57, 995], [7, 58, 5041], [7, 59, 610], [7, 60, 160], [7, 61, 3817], [7, 62, 993], [8, 0, 762], [8, 1, 2421], [8, 2, 812], [8, 3, 1403], [8, 4, 859], [8, 5, 973], [8, 6, 2543], [8, 7, 107], [8, 8, 152], [8, 9, 233], [8, 10, 186], [8, 11, 639], [8, 12, 85], [8, 13, 364], [8, 14, 177], [8, 15, 222], [8, 16, 525], [8, 17, 249], [8, 18, 311], [8, 19, 947], [8, 20, 411], [8, 21, 355], [8, 22, 114], [8, 23, 736], [8, 24, 720], [8, 25, 257], [8, 26, 940], [8, 27, 314], [8, 28, 358], [8, 29, 720], [8, 30, 41], [8, 31, 22], [8, 32, 727], [8, 33, 348], [8, 34, 205], [8, 35, 49], [8, 36, 18], [8, 37, 176], [8, 38, 152], [8, 39, 31], [8, 40, 48], [8, 41, 376], [8, 42, 1781], [8, 43, 6486], [8, 44, 2989], [8, 45, 4222], [8, 46, 3170], [8, 47, 3299], [8, 48, 2726], [8, 49, 167], [8, 50, 434], [8, 51, 198], [8, 52, 453], [8, 53, 281], [8, 54, 304], [8, 55, 295], [8, 56, 266], [8, 57, 269], [8, 58, 274], [8, 59, 179], [8, 60, 61], [8, 61, 134], [8, 62, 66], [9, 0, 175], [9, 1, 168], [9, 2, 505], [9, 3, 260], [9, 4, 140], [9, 5, 338], [9, 6, 316], [9, 7, 1055], [9, 8, 491], [9, 9, 4500], [9, 10, 1006], [9, 11, 448], [9, 12, 1647], [9, 13, 1191], [9, 14, 323], [9, 15, 682], [9, 16, 771], [9, 17, 510], [9, 18, 839], [9, 19, 1232], [9, 20, 708], [9, 21, 11], [9, 22, 198], [9, 23, 26], [9, 24, 224], [9, 25, 32], [9, 26, 50], [9, 27, 11], [9, 28, 559], [9, 29, 263], [9, 30, 281], [9, 31, 2647], [9, 32, 71], [9, 33, 526], [9, 34, 875], [9, 35, 1022], [9, 36, 612], [9, 37, 103], [9, 38, 269], [9, 39, 371], [9, 40, 382], [9, 41, 271], [9, 42, 358], [9, 43, 869], [9, 44, 296], [9, 45, 348], [9, 46, 586], [9, 47, 368], [9, 48, 627], [9, 49, 1384], [9, 50, 1800], [9, 51, 613], [9, 52, 3138], [9, 53, 1499], [9, 54, 978], [9, 55, 3175], [9, 56, 1861], [9, 57, 1951], [9, 58, 1888], [9, 59, 1655], [9, 60, 1355], [9, 61, 911], [9, 62, 1416]], "shape": [10, 63], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/25-frogsfunc_placeseqs_closests_ref_sequences.txt --- a/test-data/references/25-frogsfunc_placeseqs_closests_ref_sequences.txt Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/25-frogsfunc_placeseqs_closests_ref_sequences.txt Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,11 +1,11 @@\n-Cluster\tNb sequences\tFROGS Taxonomy\tPICRUSt2 closest ID\tPICRUSt2 closest reference name\tPICRUSt2 closest taxonomy\tNSTI\tNSTI Confidence\tFROGS and PICRUSt2 lowest same taxonomic rank\tComment\tCluster sequence\tPICRUSt2 closest reference sequence\n-Cluster_2\t217042\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Multi-affiliation\t2609459821\tEscherichia coli 6-175-07_S1_C2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli\t7e-06\tGood\tFamily\tidentical sequence\tTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAAC\tGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTACAGGAAGCAGCTTGCTGCTTTGCGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTACC\n-Cluster_7\t100935\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Multi-affiliation\t2731957973\tCampylobacter coli BIGS0003\tBacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\t0.013\tGood\tSpecies\tidentical sequence\tTAGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGGAGGATGACACTTTTCGGAGCGTAAACTCCTTTTCTTAGGGAAGAATTCTGACGGTACCTAAGGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGATTATCAAGTCTCTTGTGAAATCTAATGGCTTAACCATTAAACTGCTTGGGAAACTGATAGTCTAGAGTGAGGGAGAGGCAGATGGAATTGGTGGTGTAGGGGTAAAATCCGTAGATATCACCAAGAATACCCATTGCGAAGGCGATCTGCTGGAACTCAACTGACGCTAAGGCGCGAAAGCGTGGGGAGCAAAC\tTTTTTATGGAGAGTTTGATCCTGGCTCAGAGTGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGATGAAGCTTCTAGCTTGCTAGAAGTGGATTAGTGGCGCACGGGTGAGTAAGGTATAGTTAATCTGCCCTACACAAGAGGACAACAGTTGGAAACGACTGCTAATACTCTATACTCCTGCTTAACACAAGTTGAGTAGGGAAAGTTTTCGGTGTAGGATGAGACTATATAGTATCAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCTATGACGCTTAACTGGTCTGAGAGGATGATCAGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGGAGGATGACACTTTTCGGAGCGTAAACTCCTTTTCTTAGGGAAGAATTCTGACGGTACCTAAGGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGATTATCAAGTCTCTTGTGAAATCTAATGGCTTAACCATTAAACTGCTTGGGAAACTGATAGTCTAGAGTGAGGGAGAGGCAGATGGAATTGGTGGTGTAGGGGTAAAATCCGTAGATATCACCAAGAATACCCATTGCGAAGGCGATCTGCTGGAACTCAACTG'..b'CGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATAGGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTTTATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC\tGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAGCGAACAGCTTAGATCTTCGGATGAAGAGGTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTCATACAGGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGACCACAGCACCGCATGGTGCGGGGGTAAAAACTCCGGTGGTATGAGATGGACCCGCGTCTGATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGGCCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGGGCAAGTCTGATGTGAAAACCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTTCATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGACTACTAGGTGTCGGGTGGCAAAGCCATTCGGTGCCGCAGCAAACGCAATAAGTAGTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGCTCTTGACATCCCGCTACCGGACGGTAATGCGTCCTTCCCTTCGGGGAGCGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATCTTTAGTAGCCAGCGGCCAGGCCGGGCACTCTAGAGAGACTGCCGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGAGCAGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGCGAGACCGCGAGGTGGAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTCAGTAACGCCCGAAGTCAGTGACCCAACCGTAAGGAGGGAGCTGCCGAAGGCGGGACCGATAACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTT\t98.5\t100.0\t383.0\n+Cluster_12\t53185\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\t2645727658\tClostridia bacterium UC5.1-2H11\tBacteria;Firmicutes;Clostridia;unclassified;unclassified;unclassified;Clostridia bacterium UC5.1-2H11\t0.0001\tGood\tUp to Class\tidentical sequence\tTGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCGGGGACGAAACAAATGACGGTACCCGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC\tATTTTATTGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGGGGCGACGGAGGATTCGTCCAACGGATACCTAGTGGCGGACGGGTGAGTAACGCGTGAGGAACCTGCCTTGGAGAGGGGAATAACACTCCGAAAGGAGTGCTAATACCGCATGATGCAGTTGGGTCGCATGGCTTGACTGCCAAAGATTTATCGCTCTGAGATGGCCTCGCGTCTGATTAGCTAGTAGGCGGGGTAACGGCCCACCTAGGCGACGATCAGTAGCCGGACTGAGAGGTTGACCGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCGGGGACGAAACAAATGACGGTACCCGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGATACTAGGTGTGGGGGGTCTGACCCCTCCGTGCCGCAGTTAACACAATAAGTATCCCACCTGGGGAGTACGATCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGGCTTGACATCCCACTAACGAGGCAGAGATGCGTTAGTGCCTTCGGGAAAGTGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAGTCCCGCAACGAGCGCAACCCTTATTGTTAGTTGCTACGCAAGAGCACTCTAGCGAGACTGCCGTTGACAAAACGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGTCCTGGGCCACACACGTACTACAATGGTGGTTACAGAGGGAGGCAATACCGCGAGGTGGAGCAAATCCCTAAAAGCCATCCCAGTTCGGATTGCAGGCTGAAACCCGCCTGTATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGAGAGTCGGGAACACCCGAAGTCCGTAGCCTAACCGCAAGGAGGGCGCGGCCGAAGGTGGGTTCGATAATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCT\t100.0\t100.0\t404.0\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/25-frogsfunc_placeseqs_report.html --- a/test-data/references/25-frogsfunc_placeseqs_report.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/25-frogsfunc_placeseqs_report.html Tue May 23 07:59:04 2023 +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="4.0.1">\n+\t\t<meta name="version" content="4.1.0">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -116,11 +116,54 @@\n \t\t\tdiv.dtsp-panesContainer div.dtsp-searchPanes div.dtsp-searchPane div.dtsp-selected {\n \t\t\t\tborder: 2px solid #e1e5e8;\n \t\t\t}\n+\t\t\t\t\t\t.highcharts-figure,\n+\t\t\t.highcharts-data-table table {\n+\t\t\t\tmin-width: 360px;\n+\t\t\t\tmax-width: 800px;\n+\t\t\t\tmargin: 1em auto;\n+\t\t\t}\n+\n+\t\t\t.highcharts-data-table table {\n+\t\t\t\tfont-family: Verdana, sans-serif;\n+\t\t\t\tborder-collapse: collapse;\n+\t\t\t\tborder: 1px solid #ebebeb;\n+\t\t\t\tmargin: 10px auto;\n+\t\t\t\ttext-align: center;\n+\t\t\t\twidth: 100%;\n+\t\t\t\tmax-width: 500px;\n+\t\t\t}\n+\n+\t\t\t.highcharts-data-table caption {\n+\t\t\t\tpadding: 1em 0;\n+\t\t\t\tfont-size: 1.2em;\n+\t\t\t\tcolor: #555;\n+\t\t\t}\n+\n+\t\t\t.highcharts-data-table th {\n+\t\t\t\tfont-weight: 600;\n+\t\t\t\tpadding: 0.5em;\n+\t\t\t}\n+\n+\t\t\t.highcharts-data-table td,\n+\t\t\t.highcharts-data-table th,\n+\t\t\t.highcharts-data-table caption {\n+\t\t\t\tpadding: 0.5em;\n+\t\t\t}\n+\n+\t\t\t.highcharts-data-table thead tr,\n+\t\t\t.highcharts-data-table tr:nth-child(even) {\n+\t\t\t\tbackground: #f8f8f8;\n+\t\t\t}\n+\n+\t\t\t.highcharts-data-table tr:hover {\n+\t\t\t\tbackground: #f1f7ff;\n+\t\t\t}\n \t\t</style>\n \t\t<!-- JS -->\n \t\t<script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script>\n \t\t<script type="text/javascript" src="https://code.highcharts.com/8.2.0/highcharts.js"></script>\n \t\t<script type="text/javascript" src="https://code.highcharts.com/8.2.0/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://code.highcharts.com/modules/export-data.js"></script>\n \t\t<!--<script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>\n \t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script>\n \t\t<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/js/bootstrap.min.js" integrity="sha384-smHYKdLADwkXOn1EmN1qk/HfnUcbVRZyYmZ4qpPea6sjB/pTJ0euyQp0Mk8ck+5T" crossorigin="anonymous"></script>-->\n@@ -206,7 +249,7 @@\n \t\t\t * @return {Hash} The hash.\n \t\t\t * @warning This method use HightChart xAxis.categories.\n \t\t\t */\n-\t\t\t var chartplot = function( pTitle, pXTitle, pYTitle, pXCategories, pData ) {\n+\t\t\t var chartplot_pie = function( pTitle, pXTitle, pYTitle, pXCategories, pData ) {\n \t\t\t \tvar chart = {\n \t\t\t \t title: {\n \t\t\t \t text: pTitle\n@@ -255,14 +298,75 @@\n \t\t\t \t}\n \t\t\t \treturn chart ;\n \t\t\t }\n-\t\t\t\n+\n+\t\t\t var chartplot_line = function( pTitle, pXTitle, f_pYTitle, s_pYTitle, max_fY, max_sY, pXCategories, pData ) {\n+\t\t\t \tvar chart = {\n+\t\t\t \t title: {\n+\t\t\t \t text: pTitle\n+\t\t\t \t },\n+\t\t\t \t xAxis: {\n+\t\t\t \t \tallowDecimals: true\n+\t\t\t \t },\n+\t\t\t \t yAxis: [{\n+\t\t\t \t title: {\n+\t\t\t \t text: f_pYTitle,\n+\t\t\t \t style: {\n+ \t\t\t\t\tcolor: Highcharts.getOptions().colors[1]\n+ \t\t\t\t\t}\n+\t\t\t \t },\n+\t\t\t \t dataSorting: {\n+ \t\t\t\t\tenabled: true\n+ \t\t\t\t\t\t},\n+\t\t\t \t max: max_fY,\n+\t\t\t \t startOnTick: false,\n+\t\t\t \t endOnTick:false\n+\t\t\t \t } , {\n+\t\t\t \t \t//Secondary Y axis\n+\t\t\t \t \tgridLineWidth: 0,\n+\t\t\t \t \topposite: true,\n+\t\t\t \t \ttitle: {\n+\t\t\t \t \t\ttext: s_pYTitle,\n+\t\t\t \t \t\tstyle: {\n+ \t\t\t\t\tcolor: Highcharts.getOptions().colors[0]\n+ \t\t\t\t\t}\n+\t\t\t \t \t},\n+\t\t\t \t \tlabels: {\n+ \t\t\t\t\tstyle: {\n+ \t\t\t\t\tcolor: Highcharts.getOptions().colors[0]\n+ \t\t\t\t\t\t}\n+ \t\t\t\t\t\t\t},\n+ \t\t\t\t\t\tmax: max_sY\n+\t\t\t \t }] ,\n+\t\t\t \t tooltip: {\n+\t\t\t \t \tshared: true\n+\t\t'..b'AGTTGCTACGCAAGAGCACTCTAGCGAGACTGCCGTTGACAAAACGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGTCCTGGGCCACACACGTACTACAATGGTGGTTACAGAGGGAGGCAATACCGCGAGGTGGAGCAAATCCCTAAAAGCCATCCCAGTTCGGATTGCAGGCTGAAACCCGCCTGTATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGAGAGTCGGGAACACCCGAAGTCCGTAGCCTAACCGCAAGGAGGGCGCGGCCGAAGGTGGGTTCGATAATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCT", "100.0", "100.0"]}] ;\n \t\t\t\tvar remove_info = {"nb_kept": 10, "nb_removed": 0, "abundance_kept": 1221250, "abundance_removed": 0} ;\n \n+\n+\t\t\t\tvar alignment_series = [];\n+\t\t\t\tvar coverage_series = [];\n+\n+\t\t\t\tfor(var cluster in detection_series) {\n+\t\t\t\t\tdict_a = {};\n+\t\t\t\t\tdict_c = {};\n+\t\t\t\t\tdict_a.name = detection_series[cluster].name;\n+\t\t\t\t\tdict_c.name = detection_series[cluster].name;\n+\t\t\t\t\tdict_a.x = parseFloat(detection_series[cluster].data[5]);\n+\t\t\t\t\tdict_c.x = parseFloat(detection_series[cluster].data[5]);\n+\t\t\t\t\tdict_a.y = parseFloat(detection_series[cluster].data[11].split(" ")[0]);\n+\t\t\t\t\tdict_c.y = parseFloat(detection_series[cluster].data[12].split(" ")[0]);\n+\t\t\t\t\talignment_series.push(dict_a);\n+\t\t\t\t\tcoverage_series.push(dict_c);\n+\t\t\t\t}\n+\t\t\t\t// alert(JSON.stringify(scatter_series, null, 4));\n \t\t\t\t// Remove alert\n \t\t\t\t$(\'#js-alert\').remove();\n \t\t\t\t$(\'#content\').removeClass("hidden");\n@@ -342,7 +526,7 @@\n \t\t\t\t\n \t\t\t\t// Display chimera detection data\n \t\t\t\tvar table_categories = detection_categories.slice() ;\n-\t\t\t\ttable_categories.unshift( "Cluster" );\n+\t\t\t\ttable_categories.unshift( "ASV" );\n \t\t\t\tvar table_series = new Array();\n \t\t\t\tfor( var spl_idx = 0 ; spl_idx < detection_series.length ; spl_idx++ ){\n \t\t\t\t\tvar nb_by_step = detection_series[spl_idx][\'data\'].slice() ;\n@@ -362,7 +546,78 @@\n \t\t\t\t$(\'#details-csv-export\').datatableExport({\n \t\t\t\t\t\'table_id\': "details-table"\n \t\t\t\t});\n-\t\t\t});\n+\n+\t\t\t\tclusters_ditrib_load( "sequence-distrib" );\n+\n+\n+\t\t\t\tHighcharts.chart(\'container_scatter\', {\n+\t\t\t\tchart: {\n+\t\t\t\t\ttype: \'scatter\',\n+\t\t\t\t\tzoomType: \'xy\'\n+\t\t\t\t},\n+\t\t\t\ttitle: {\n+\t\t\t\t\ttext: \'\'\n+\t\t\t\t},\n+\t\t\t\txAxis: {\n+\t\t\t\t\ttitle: {\n+\t\t\t\t\t\tenabled: true,\n+\t\t\t\t\t\ttext: \'NSTI value\'\n+\t\t\t\t\t},\n+\t\t\t\t\tstartOnTick: true,\n+\t\t\t\t\tendOnTick: true,\n+\t\t\t\t\tshowLastLabel: true\n+\t\t\t\t},\n+\t\t\t\tyAxis: {\n+\t\t\t\t\ttitle: {\n+\t\t\t\t\t\ttext: \'alignment metrics (%)\'\n+\t\t\t\t\t}\n+\t\t\t\t},\n+\t\t\t\tlegend: {\n+\t\t\t\t\tbackgroundColor: Highcharts.defaultOptions.chart.backgroundColor,\n+\t\t\t\t},\n+\t\t\t\tplotOptions: {\n+\t\t\t\t\tseries : {\n+\t\t\t\t\t\tturboThreshold: 0\n+\t\t\t\t\t},\n+\t\t\t\t\tscatter: {\n+\t\t\t\t\t\tmarker: {\n+\t\t\t\t\t\t\tradius: 5,\n+\t\t\t\t\t\t\tstates: {\n+\t\t\t\t\t\t\t\thover: {\n+\t\t\t\t\t\t\t\t\tenabled: true,\n+\t\t\t\t\t\t\t\t\tlineColor: \'rgb(100,100,100)\'\n+\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\tstates: {\n+\t\t\t\t\t\t\thover: {\n+\t\t\t\t\t\t\t\tmarker: {\n+\t\t\t\t\t\t\t\t\tenabled: false\n+\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\ttooltip: {\n+\t\t\t\t\t\t\theaderFormat: \'<b>{point.key}</b><br>\',\n+\t\t\t\t\t\t\tpointFormat: \'{point.x}, {point.y}%\'\n+\t\t\t\t\t\t}\n+\t\t\t\t\t}, \n+\t\t\t\t\t\tdataLabels: {\n+ \t\tformat: "{point.key}",\n+ \t\tenabled: true\n+ \t},\n+\t\t\t\t\tenableMouseTracking: false\n+\t\t\t\t},\n+\t\t\t\tseries: [{\n+\t\t\t\t\tname: \'% identity\',\n+\t\t\t\t\tcolor: \'rgba(134, 165, 164, .5)\',\n+\t\t\t\t\tdata: alignment_series\n+\t\t\t\t\t}, {\n+\t\t\t\t\tname: \'% coverage\',\n+\t\t\t\t\tcolor: \'rgba(211, 148, 104, .5)\',\n+\t\t\t\t\tdata: coverage_series\t\t\t\t\n+\t\t\t\t\t}]\n+\t\t\t\t})\n+\t\t\t})\n \t\t</script>\n \t</head>\n \t<body>\n@@ -382,8 +637,15 @@\n \t\t</div>\n \t\t\t</div>\n \t\t\t<div id="filter-log">\n-\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Closest reference sequences by cluster</h2>\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Closest reference sequences by ASV</h2>\n \t\t\t</div>\n+\t\t\t<div class="tab-content">\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">ASV number according to NSTI threshold</h2>\n+\t\t\t\t<div id="sequence-distrib" role="tabpanel" class="tab-pane active">\n+\t\t\t\t</div>\n+\t\t\t</div>\n+\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom"> %identity and coverage vs NSTI between kept ASV and closest PICRUSt2 reference sequence</h2>\n+\t\t\t<div id="container_scatter"></div>\n \t\t</div>\n \t</body>\n </html>\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/25-frogsfunc_placeseqs_tree.nwk --- a/test-data/references/25-frogsfunc_placeseqs_tree.nwk Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/25-frogsfunc_placeseqs_tree.nwk Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,1 +1,1 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|
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/26-frogsfunc_copynumbers_marker.tsv --- a/test-data/references/26-frogsfunc_copynumbers_marker.tsv Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -sequence 16S_rRNA_Count metadata_NSTI -Cluster_1 1 0.030822000000000002 -Cluster_10 1 0.112249 -Cluster_11 1 0.045592 -Cluster_12 1 1.6e-05 -Cluster_2 4 7.000000000000001e-06 -Cluster_3 1 0.200207 -Cluster_4 2 0.790411 -Cluster_5 1 0.854059 -Cluster_6 1 0.06408 -Cluster_7 1 0.013637 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/26-frogsfunc_copynumbers_predicted_functions.tsv --- a/test-data/references/26-frogsfunc_copynumbers_predicted_functions.tsv Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,11 +0,0 @@\n-sequence\tEC:1.1.1.1\tEC:1.1.1.10\tEC:1.1.1.100\tEC:1.1.1.101\tEC:1.1.1.102\tEC:1.1.1.103\tEC:1.1.1.105\tEC:1.1.1.107\tEC:1.1.1.108\tEC:1.1.1.11\tEC:1.1.1.116\tEC:1.1.1.117\tEC:1.1.1.122\tEC:1.1.1.125\tEC:1.1.1.130\tEC:1.1.1.132\tEC:1.1.1.133\tEC:1.1.1.136\tEC:1.1.1.137\tEC:1.1.1.14\tEC:1.1.1.140\tEC:1.1.1.141\tEC:1.1.1.144\tEC:1.1.1.145\tEC:1.1.1.156\tEC:1.1.1.157\tEC:1.1.1.159\tEC:1.1.1.163\tEC:1.1.1.169\tEC:1.1.1.17\tEC:1.1.1.170\tEC:1.1.1.173\tEC:1.1.1.178\tEC:1.1.1.179\tEC:1.1.1.18\tEC:1.1.1.181\tEC:1.1.1.184\tEC:1.1.1.189\tEC:1.1.1.193\tEC:1.1.1.195\tEC:1.1.1.197\tEC:1.1.1.2\tEC:1.1.1.202\tEC:1.1.1.203\tEC:1.1.1.205\tEC:1.1.1.206\tEC:1.1.1.208\tEC:1.1.1.21\tEC:1.1.1.211\tEC:1.1.1.215\tEC:1.1.1.216\tEC:1.1.1.218\tEC:1.1.1.219\tEC:1.1.1.22\tEC:1.1.1.220\tEC:1.1.1.23\tEC:1.1.1.234\tEC:1.1.1.237\tEC:1.1.1.239\tEC:1.1.1.243\tEC:1.1.1.244\tEC:1.1.1.25\tEC:1.1.1.251\tEC:1.1.1.252\tEC:1.1.1.257\tEC:1.1.1.26\tEC:1.1.1.261\tEC:1.1.1.262\tEC:1.1.1.264\tEC:1.1.1.267\tEC:1.1.1.27\tEC:1.1.1.271\tEC:1.1.1.272\tEC:1.1.1.275\tEC:1.1.1.276\tEC:1.1.1.28\tEC:1.1.1.281\tEC:1.1.1.282\tEC:1.1.1.284\tEC:1.1.1.286\tEC:1.1.1.287\tEC:1.1.1.288\tEC:1.1.1.289\tEC:1.1.1.29\tEC:1.1.1.290\tEC:1.1.1.291\tEC:1.1.1.292\tEC:1.1.1.294\tEC:1.1.1.298\tEC:1.1.1.3\tEC:1.1.1.30\tEC:1.1.1.300\tEC:1.1.1.301\tEC:1.1.1.302\tEC:1.1.1.303\tEC:1.1.1.304\tEC:1.1.1.305\tEC:1.1.1.306\tEC:1.1.1.307\tEC:1.1.1.308\tEC:1.1.1.309\tEC:1.1.1.31\tEC:1.1.1.310\tEC:1.1.1.311\tEC:1.1.1.312\tEC:1.1.1.313\tEC:1.1.1.315\tEC:1.1.1.316\tEC:1.1.1.320\tEC:1.1.1.325\tEC:1.1.1.327\tEC:1.1.1.328\tEC:1.1.1.329\tEC:1.1.1.330\tEC:1.1.1.333\tEC:1.1.1.335\tEC:1.1.1.336\tEC:1.1.1.337\tEC:1.1.1.338\tEC:1.1.1.339\tEC:1.1.1.34\tEC:1.1.1.340\tEC:1.1.1.341\tEC:1.1.1.342\tEC:1.1.1.343\tEC:1.1.1.344\tEC:1.1.1.346\tEC:1.1.1.347\tEC:1.1.1.35\tEC:1.1.1.350\tEC:1.1.1.359\tEC:1.1.1.36\tEC:1.1.1.360\tEC:1.1.1.361\tEC:1.1.1.362\tEC:1.1.1.363\tEC:1.1.1.364\tEC:1.1.1.367\tEC:1.1.1.368\tEC:1.1.1.369\tEC:1.1.1.37\tEC:1.1.1.370\tEC:1.1.1.371\tEC:1.1.1.373\tEC:1.1.1.374\tEC:1.1.1.376\tEC:1.1.1.377\tEC:1.1.1.378\tEC:1.1.1.38\tEC:1.1.1.380\tEC:1.1.1.381\tEC:1.1.1.385\tEC:1.1.1.387\tEC:1.1.1.388\tEC:1.1.1.39\tEC:1.1.1.4\tEC:1.1.1.40\tEC:1.1.1.41\tEC:1.1.1.42\tEC:1.1.1.43\tEC:1.1.1.44\tEC:1.1.1.45\tEC:1.1.1.47\tEC:1.1.1.48\tEC:1.1.1.49\tEC:1.1.1.51\tEC:1.1.1.53\tEC:1.1.1.56\tEC:1.1.1.57\tEC:1.1.1.58\tEC:1.1.1.6\tEC:1.1.1.60\tEC:1.1.1.61\tEC:1.1.1.62\tEC:1.1.1.64\tEC:1.1.1.65\tEC:1.1.1.67\tEC:1.1.1.69\tEC:1.1.1.76\tEC:1.1.1.77\tEC:1.1.1.79\tEC:1.1.1.8\tEC:1.1.1.81\tEC:1.1.1.82\tEC:1.1.1.83\tEC:1.1.1.85\tEC:1.1.1.86\tEC:1.1.1.87\tEC:1.1.1.88\tEC:1.1.1.9\tEC:1.1.1.90\tEC:1.1.1.91\tEC:1.1.1.93\tEC:1.1.1.94\tEC:1.1.1.95\tEC:1.1.2.3\tEC:1.1.2.4\tEC:1.1.2.6\tEC:1.1.2.7\tEC:1.1.2.8\tEC:1.1.3.12\tEC:1.1.3.15\tEC:1.1.3.17\tEC:1.1.3.20\tEC:1.1.3.21\tEC:1.1.3.37\tEC:1.1.3.41\tEC:1.1.3.43\tEC:1.1.3.44\tEC:1.1.3.45\tEC:1.1.3.46\tEC:1.1.3.47\tEC:1.1.3.48\tEC:1.1.3.6\tEC:1.1.3.8\tEC:1.1.3.9\tEC:1.1.5.2\tEC:1.1.5.3\tEC:1.1.5.4\tEC:1.1.5.6\tEC:1.1.5.8\tEC:1.1.5.9\tEC:1.1.9.1\tEC:1.1.98.2\tEC:1.1.98.3\tEC:1.1.99.1\tEC:1.1.99.18\tEC:1.1.99.2\tEC:1.1.99.21\tEC:1.1.99.24\tEC:1.1.99.28\tEC:1.1.99.3\tEC:1.1.99.31\tEC:1.1.99.38\tEC:1.10.2.2\tEC:1.10.3.1\tEC:1.10.3.11\tEC:1.10.3.12\tEC:1.10.3.2\tEC:1.10.3.3\tEC:1.10.5.1\tEC:1.10.9.1\tEC:1.11.1.1\tEC:1.11.1.10\tEC:1.11.1.15\tEC:1.11.1.19\tEC:1.11.1.20\tEC:1.11.1.21\tEC:1.11.1.23\tEC:1.11.1.5\tEC:1.11.1.6\tEC:1.11.1.7\tEC:1.11.1.9\tEC:1.11.2.3\tEC:1.11.2.4\tEC:1.12.1.2\tEC:1.12.1.3\tEC:1.12.1.4\tEC:1.12.1.5\tEC:1.12.2.1\tEC:1.12.5.1\tEC:1.12.7.2\tEC:1.12.98.1\tEC:1.12.98.2\tEC:1.12.98.4\tEC:1.12.99.6\tEC:1.13.11.1\tEC:1.13.11.11\tEC:1.13.11.12\tEC:1.13.11.14\tEC:1.13.11.15\tEC:1.13.11.16\tEC:1.13.11.18\tEC:1.13.11.19\tEC:1.13.11.2\tEC:1.13.11.20\tEC:1.13.11.24\tEC:1.13.11.25\tEC:1.13.11.27\tEC:1.13.11.3\tEC:1.13.11.33\tEC:1.13.11.34\tEC:1.13.11.37\tEC:1.13.11.38\tEC:1.13.11.39\tEC:1.13.11.4\tEC:1.13.11.41\tEC:1.13.11.46\tEC:1.13.11.49\tEC:1.13.11.5\tEC:1.13.11.52\tEC:1.13.11.53\tEC:1.13.11.54\tEC:1.13.11.55\tEC:1.13.11.56\tEC:1.13.11.57\tEC:1.13.11.58\tEC:1.13.11.59\tEC:1.13.11.6\tEC:1.13.11.61\tEC:1.13.11.63\tEC:1.13.11.66\tEC:1.13.11.71\tEC:1.13.11.72\tEC:1.13.11.73\tEC:1.13.11.74\tEC:1.13.11.75\tEC:1.13.11.76\tEC:1.13.11.79\tEC:1.13.11.8\tEC:1.13.11.80\tEC:1.13.11.9\tEC:1.13.12.16\tEC:'..b'0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t4\t0\t1\t0\t1\t0\t0\t0\t0\t0\t1\t0\t1\t0\t1\t1\t0\t2\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t2\t1\t0\t0\t1\t2\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t2\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t1\t0\t1\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t1\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t0\t2\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\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| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/26-frogsfunc_copynumbers_report.html --- a/test-data/references/26-frogsfunc_copynumbers_report.html Tue Jul 19 11:11:16 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,417 +0,0 @@\n-<!DOCTYPE html>\n-<!--\n-# Copyright (C) 2022 INRAE\n-#\n-# This program is free software: you can redistribute it and/or modify\n-# it under the terms of the GNU General Public License as published by\n-# the Free Software Foundation, either version 3 of the License, or\n-# (at your option) any later version.\n-#\n-# This program is distributed in the hope that it will be useful,\n-# but WITHOUT ANY WARRANTY; without even the implied warranty of\n-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n-# GNU General Public License for more details.\n-#\n-# You should have received a copy of the GNU General Public License\n-# along with this program. If not, see <http://www.gnu.org/licenses/>.\n--->\n-<html>\n-\t<head>\n-\t\t<title>FrogsFunc copy numbers (Step2)</title>\n-\t\t<meta charset="UTF-8">\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-\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n-\t\t<style type="text/css">\n-\t\t\t#js-alert {\n-\t\t\t\twidth: 90%;\n-\t\t\t\tmargin-right: auto;\n-\t\t\t\tmargin-left: auto;\n-\t\t\t}\n-\t\t\t#content {\n-\t\t\t\twidth: 90%;\n-\t\t\t\tmargin-right: auto;\n-\t\t\t\tmargin-left: auto;\n-\t\t\t}\n-\t\t\t.clear {\n-\t\t\t\tclear: both;\n-\t\t\t\theight: 0px;\n-\t\t\t\twidth: 100%;\n-\t\t\t\tfloat: none !important;\n-\t\t\t}\n-\t\t\tul.nav-tabs {\n-\t\t\t\tmargin-bottom: 30px;\n-\t\t\t}\n-\t\t\t#hc-graph {\n-\t\t\t\theight: 500px;\n-\t\t\t\toverflow: auto;\n-\t\t\t}\n-\t\t\t#hc-warning {\n-\t\t\t\tmargin-top: 8px;\n-\t\t\t}\n-\t\t\t#hc-newick {\n-\t\t\t\twidth: 90%;\n-\t\t\t\tposition: absolute;\n-\t\t\t\tbackground-color: white;\n-\t\t\t\tborder: 1px solid lightgrey;\n-\t\t\t\tborder-radius:5px;\n-\t\t\t\tpadding: 5px 5px 5px 5px;\n-\t\t\t\tmargin-top: 10px;\n-\t\t\t}\n-\t\t\t#dispersion {\n-\t\t\t\theight: 1000px;\n-\t\t\t}\n-\t\t\t#twofigs{\n-\t\t\t\theight: 600px;\n-\t\t\t}\n-\t\t\t.label-badge {\n-\t\t\t\tposition: absolute;\n-\t\t\t\ttop: -10px;\n-\t\t\t\tleft: -10px;\n-\t\t\t}\n-\t\t\t.badge-primary{\n-\t\t\t\tbackground-color:#8EADAC;\n-\t\t\t}\n-\t\t\t.graph-nb {\n-\t\t\t\tcolor: #95959C;\n-\t\t\t\tfont-style: italic;\n-\t\t\t\ttext-align: center;\n-\t\t\t}\n-\t\t\t.circle {\n-\t\t\t\tborder-style: solid;\n-\t\t\t\tborder-width: 3px;\n-\t\t\t\tborder-radius: 50px;\n-\t\t\t\tbox-shadow: 2px 2px 2px #555;\n-\t\t\t\tborder-color: 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#8EADAC;\n-\t\t\t\tborder-color: #8EADAC;\n-\t\t\t}\n-\t\t\t.btn {\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tborder:#8EADAC;\n-\t\t\t\tbackground-color: #8EADAC;\n-\t\t\t}\n-\t\t\t.btn:focus, .btn:active {\n-\t\t\t\toutline: none !important;\n-\t\t\t\tbox-shadow: none !important;\n-\t\t\t}\n-\t\t\t.btn:hover{\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tborder:#648a89;\n-\t\t\t\tbackground-color: #648a89;\n-\t\t\t}\n-\t\t\t.pb-2, .py-2 {\n-\t\t\t\tpadding-bottom: 1.5rem !important;\n-\t\t\t\tmargin-bottom: 2rem !important;\n-\t\t\t\tmargin-top: 4rem !important;\n-\t\t\t}\n-\t\t\t.pb-2-first{\n-\t\t\t\tpadding-bottom: 1.5rem !important;\n-\t\t\t\tmargin-bottom: 2rem !important;\n-\t\t\t\tmargin-top: 1rem !important;\n-\t\t\t}\n-\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tbackground-color: #8EADAF;\n-\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n-\t\t\t}\n-\t\t\ta {\n-\t\t\t\tcolor: #8EAEAF;\n-\t\t\t}\n-\t\t\ta:hover{\n-\t\t\t\tcolor:#648a89;\n-\t\t\t}\n-\t\t\t.page-'..b'-\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n-\n-\t\t\tvar clusters_ditrib_load = function( container_id ) {\n-\n-\t\t\t\tvar cluster_by_nsti = lineplot_param("", "NSTI value", "Nb kept sequences", "Nb kept clusters", nsti_threshold, series);\n-\t\t\t\t\t$(\'#\' + container_id).append(\'<div></div>\');\n-\t\t\t\t\t$(\'#\' + container_id).highcharts( cluster_by_nsti );\n-\t\t\t\t\t$(\'#\' + container_id).append(\'<p class="graph-nb">N.B.: Select area to zoom in.</p>\');\n-\t\t\t}\n-\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n-\t\t\t//\n-\t\t\t// Data\n-\t\t\t//\n-\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n-\t\t\tvar nsti_threshold = [0.0, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12, 0.14, 0.16, 0.18, 0.2, 0.22, 0.24, 0.26, 0.28, 0.3, 0.32, 0.34, 0.36, 0.38, 0.4, 0.42, 0.44, 0.46, 0.48, 0.5, 0.52, 0.54, 0.56, 0.58, 0.6, 0.62, 0.64, 0.66, 0.68, 0.7, 0.72, 0.74, 0.76, 0.78, 0.8, 0.82, 0.84, 0.86, 0.88, 0.9, 0.92, 0.94, 0.96, 0.98, 1.0, 1.02, 1.04, 1.06, 1.08, 1.1, 1.12, 1.14, 1.16, 1.18, 1.2, 1.22, 1.24, 1.26, 1.28, 1.3, 1.32, 1.34, 1.36, 1.38, 1.4, 1.42, 1.44, 1.46, 1.48, 1.5, 1.52, 1.54, 1.56, 1.58, 1.6, 1.62, 1.64, 1.66, 1.68, 1.7, 1.72, 1.74, 1.76, 1.78, 1.8, 1.82, 1.84, 1.86, 1.88, 1.9, 1.92, 1.94, 1.96, 1.98, 2.0] ;\n-\t\t\tvar series = [{\n-\t\t\t\t\'name\': "Nb clusters",\n-\t\t\t\t\'data\': [0, 3, 4, 5, 6, 6, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10],\n-\t\t\t\t\'yAxis\': 1,\n-\t\t\t}, {\n-\t\t\t\t\'name\': "Nb sequences (cluster abundance)",\n-\t\t\t\t\'data\': [0, 371162, 614635, 663777, 766425, 766425, 818838, 818838, 818838, 818838, 818838, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1004066, 1117153, 1117153, 1117153, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250, 1221250]\n-\t\t\t}];\n-\t\t\tvar sum_series = new Array() ;\n-\n-\n-\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n-\t\t\t//\n-\t\t\t// Main\n-\t\t\t//\n-\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n-\t\t\t$(function() {\t\t\t\n-\t\t\t\t// Remove alert\n-\t\t\t\t$(\'#js-alert\').remove();\n-\t\t\t\t$(\'#content\').removeClass("hidden");\n-\n-\t\t\t\t// Load active tab\n-\t\t\t\tclusters_ditrib_load( "sequence-distrib" );\n-\t\t\t\t\n-\t\t\t\t// Add tab listener\n-\t\t\t});\n-\t\t</script>\n-\t</head>\n-\t<body>\n-\t\t<p id="js-alert" class="alert alert-warning">\n-\t\t\tjavascript is needed to display data.<br />\n-\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n-\t\t</p>\n-\t\t\n-\t\t<div id="content" class="hidden">\n-\t\t\t<div class="tab-content">\n-\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Cluster/sequence number according to NSTI threshold</h2>\n-\t\t\t\t<div id="sequence-distrib" role="tabpanel" class="tab-pane active">\n-\t\t\t\t</div>\n-\t\t\t</div>\n-\t\t</div>\n-\t</body>\n-</html>\n\\ No newline at end of file\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/27-frogsfunc_functions_excluded.txt --- a/test-data/references/27-frogsfunc_functions_excluded.txt Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/27-frogsfunc_functions_excluded.txt Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,1 +1,1 @@ -#No excluded OTUs. +#No excluded ASV. |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/27-frogsfunc_functions_marker_norm.tsv --- a/test-data/references/27-frogsfunc_functions_marker_norm.tsv Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/27-frogsfunc_functions_marker_norm.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -3,9 +3,9 @@ Cluster_10 2.0 4.0 7.0 19.0 4.0 7.0 7.0 290.0 369.0 3062.0 948.0 1596.0 231.0 1769.0 824.0 152.0 165.0 190.0 350.0 57.0 344.0 1.0 0.0 1.0 9.0 0.0 0.0 0.0 1634.0 963.0 3978.0 1161.0 398.0 15.0 1884.0 278.0 2075.0 333.0 629.0 1036.0 1579.0 4682.0 26.0 0.0 0.0 0.0 1.0 0.0 1.0 717.0 1213.0 4106.0 167.0 1136.0 1806.0 513.0 58.0 995.0 5041.0 610.0 160.0 3817.0 993.0 Cluster_11 762.0 2421.0 812.0 1403.0 859.0 973.0 2543.0 107.0 152.0 233.0 186.0 639.0 85.0 364.0 177.0 222.0 525.0 249.0 311.0 947.0 411.0 355.0 114.0 736.0 720.0 257.0 940.0 314.0 358.0 720.0 41.0 22.0 727.0 348.0 205.0 49.0 18.0 176.0 152.0 31.0 48.0 376.0 1781.0 6486.0 2989.0 4222.0 3170.0 3299.0 2726.0 167.0 434.0 198.0 453.0 281.0 304.0 295.0 266.0 269.0 274.0 179.0 61.0 134.0 66.0 Cluster_12 175.0 168.0 505.0 260.0 140.0 338.0 316.0 1055.0 491.0 4500.0 1006.0 448.0 1647.0 1191.0 323.0 682.0 771.0 510.0 839.0 1232.0 708.0 11.0 198.0 26.0 224.0 32.0 50.0 11.0 559.0 263.0 281.0 2647.0 71.0 526.0 875.0 1022.0 612.0 103.0 269.0 371.0 382.0 271.0 358.0 869.0 296.0 348.0 586.0 368.0 627.0 1384.0 1800.0 613.0 3138.0 1499.0 978.0 3175.0 1861.0 1951.0 1888.0 1655.0 1355.0 911.0 1416.0 -Cluster_2 99.5 339.75 680.0 925.0 541.5 137.0 696.5 178.25 712.75 827.25 851.25 718.75 386.75 1007.75 2445.25 1030.75 496.5 297.5 474.25 980.0 1263.25 179.75 545.75 70.0 246.5 242.5 267.25 41.25 1387.75 951.5 2478.25 1969.0 934.5 2855.25 1419.5 578.25 996.5 2363.5 402.25 540.75 409.75 189.0 352.0 891.5 484.5 258.75 684.75 903.5 426.25 1241.0 1399.25 874.25 1711.0 1531.5 891.25 777.0 224.0 1221.25 798.0 2001.25 1133.5 1331.5 966.25 +Cluster_2 132.67 453.0 906.67 1233.33 722.0 182.67 928.67 237.67 950.33 1103.0 1135.0 958.33 515.67 1343.67 3260.33 1374.33 662.0 396.67 632.33 1306.67 1684.33 239.67 727.67 93.33 328.67 323.33 356.33 55.0 1850.33 1268.67 3304.33 2625.33 1246.0 3807.0 1892.67 771.0 1328.67 3151.33 536.33 721.0 546.33 252.0 469.33 1188.67 646.0 345.0 913.0 1204.67 568.33 1654.67 1865.67 1165.67 2281.33 2042.0 1188.33 1036.0 298.67 1628.33 1064.0 2668.33 1511.33 1775.33 1288.33 Cluster_3 842.0 1141.0 1162.0 1488.0 659.0 566.0 1822.0 1699.0 2709.0 2202.0 2769.0 1114.0 1806.0 2064.0 6555.0 5217.0 5265.0 20805.0 2725.0 6685.0 7949.0 4948.0 88.0 1572.0 3705.0 1466.0 1032.0 723.0 1617.0 1202.0 1266.0 2912.0 2020.0 842.0 2817.0 1706.0 4674.0 1892.0 1659.0 937.0 1226.0 2938.0 160.0 89.0 824.0 87.0 186.0 326.0 1490.0 2422.0 756.0 1769.0 1907.0 2959.0 1271.0 1191.0 5254.0 7123.0 12594.0 4108.0 7510.0 8390.0 6326.0 -Cluster_4 1140.0 338.0 517.5 1366.5 918.5 349.0 559.0 8.5 15.0 3.5 14.0 5.0 3.5 2.5 1472.0 546.0 897.5 295.0 1517.0 456.5 853.5 655.5 866.5 300.0 506.0 196.5 599.5 1001.5 2.5 0.5 2.0 20.5 3.0 4.5 9.0 3411.5 164.5 1131.0 3898.0 6164.0 3665.5 3855.0 1200.5 904.5 885.0 665.5 4085.0 535.5 422.5 4.5 5.0 5.0 15.0 9.0 6.0 8.5 1964.0 1724.5 923.5 2200.5 1038.5 1268.0 938.0 +Cluster_4 2280.0 676.0 1035.0 2733.0 1837.0 698.0 1118.0 17.0 30.0 7.0 28.0 10.0 7.0 5.0 2944.0 1092.0 1795.0 590.0 3034.0 913.0 1707.0 1311.0 1733.0 600.0 1012.0 393.0 1199.0 2003.0 5.0 1.0 4.0 41.0 6.0 9.0 18.0 6823.0 329.0 2262.0 7796.0 12328.0 7331.0 7710.0 2401.0 1809.0 1770.0 1331.0 8170.0 1071.0 845.0 9.0 10.0 10.0 30.0 18.0 12.0 17.0 3928.0 3449.0 1847.0 4401.0 2077.0 2536.0 1876.0 Cluster_5 14.0 16.0 18.0 11.0 49.0 60.0 44.0 227.0 7500.0 22187.0 17526.0 19048.0 11102.0 20612.0 0.0 0.0 94.0 77.0 0.0 2.0 39.0 1.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 0.0 0.0 1.0 2.0 1.0 5369.0 1.0 3.0 2.0 33.0 2.0 2.0 3.0 27.0 8.0 10.0 Cluster_6 3028.0 7155.0 7405.0 9799.0 4656.0 1759.0 2455.0 51.0 39.0 37.0 78.0 47.0 13.0 19.0 2668.0 2347.0 288.0 558.0 432.0 900.0 5393.0 1507.0 2756.0 3386.0 3607.0 2661.0 4604.0 2104.0 5.0 7.0 3.0 4.0 4.0 2.0 11.0 108.0 5.0 4.0 21.0 13.0 87.0 16.0 5819.0 610.0 1198.0 5003.0 6177.0 2239.0 5907.0 38.0 596.0 27.0 86.0 18.0 35.0 18.0 224.0 1154.0 2566.0 389.0 83.0 163.0 256.0 Cluster_7 1148.0 1468.0 1044.0 1396.0 552.0 612.0 1846.0 13.0 13.0 15.0 35.0 9.0 24.0 21.0 2666.0 728.0 4407.0 3321.0 9514.0 1597.0 2373.0 969.0 372.0 97.0 697.0 42.0 836.0 399.0 1.0 2.0 6.0 8.0 6.0 7.0 4.0 5184.0 1406.0 2379.0 1471.0 4165.0 2616.0 473.0 1876.0 1757.0 3013.0 1270.0 2225.0 1771.0 3610.0 41.0 20.0 32.0 76.0 34.0 22.0 11.0 15266.0 4545.0 2580.0 2981.0 1403.0 638.0 3822.0 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/27-frogsfunc_functions_report.html --- a/test-data/references/27-frogsfunc_functions_report.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/27-frogsfunc_functions_report.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -17,9 +17,9 @@\n -->\n <html>\n \t<head>\n-\t\t<title>FrogsFunc functions (Step3)</title>\n+\t\t<title>FrogsFunc functions (Step2)</title>\n \t\t<meta charset="UTF-8">\n-\t\t<meta name="version" content="4.0.1">\n+\t\t<meta name="version" content="4.1.0">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -135,6 +135,7 @@\n \t\t<script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script>\n \t\t<script type="text/javascript" src="https://code.highcharts.com/8.2.0/highcharts.js"></script>\n \t\t<script type="text/javascript" src="https://code.highcharts.com/8.2.0/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://code.highcharts.com/8.2.0/highcharts-more.js"></script>\n \t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>\n \t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script>\n \t\t<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/js/bootstrap.min.js" integrity="sha384-smHYKdLADwkXOn1EmN1qk/HfnUcbVRZyYmZ4qpPea6sjB/pTJ0euyQp0Mk8ck+5T" crossorigin="anonymous"></script>\n@@ -302,6 +303,9 @@\n \t\t\t\tvar series = [{\n \t type: \'pie\',\n \t name: unity,\n+\t\t\tcredits: {\n+\t\t\t \t \tenabled: false\n+\t\t\t \t },\n \t data: pData\n \t}]\n \t\t\t\tvar plot = chartplot( pTitle, null, null, null, series );\n@@ -468,9 +472,10 @@\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'..b'\\"55\\": 6350, \\"56\\": 3722, \\"57\\": 3902, \\"58\\": 3776, \\"59\\": 3310, \\"60\\": 2710, \\"61\\": 1822, \\"62\\": 2832},\\"Cobaltochelatase\\":{\\"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+\n \t\t\t$(function() {\n \n \t\t\t\t// Remove alert\n@@ -526,7 +532,7 @@\n \t\t\t\t\t[\'Kept\', remove_info[\'nb_kept\']],\n \t\t\t\t\t[\'Removed\', remove_info[\'nb_removed\']]\n \t\t\t\t];\n-\t\t\t\t$(\'#nb-filtered\').highcharts( pie_param(\'Clusters\', nb_filtered_data, \'Clusters\') );\n+\t\t\t\t$(\'#nb-filtered\').highcharts( pie_param(\'ASVs\', nb_filtered_data, \'ASVs\') );\n \t\t\t\tvar abundance_filtered_data = [\n \t\t\t\t\t[\'Kept\', remove_info[\'abundance_kept\']],\n \t\t\t\t\t[\'Removed\', remove_info[\'abundance_removed\']]\n@@ -543,6 +549,90 @@\n \t\t\t\t\ttable_series.push( nb_by_step );\n \t\t\t\t};\n \n+\t\t\t\tHighcharts.chart(\'starplot_container\', {\n+\n+\t\t\t\t\tchart: {\n+\t\t\t\t\t\tpolar: true,\n+\t\t\t\t\t\ttype: \'line\'\n+\t\t\t\t\t},\n+\n+\t\t\t\t\ttitle: {\n+\t\t\t\t\t\ttext: \'\',\n+\t\t\t\t\t\tx: -80\n+\t\t\t\t\t},\n+\n+\t\t\t\t\tpane: {\n+\t\t\t\t\t\tsize: \'80%\'\n+\t\t\t\t\t},\n+\n+\t\t\t\t\txAxis: {\n+\t\t\t\t\t\tcategories: [\'Kingdom\', \'Phylum\', \'Class\', \'Order\',\n+\t\t\t\t\t\t\t\'Family\', \'Genus\', \'Species\'],\n+\t\t\t\t\t\ttickmarkPlacement: \'on\',\n+\t\t\t\t\t\tlineWidth: 0\n+\t\t\t\t\t},\n+\n+\t\t\t\t\tyAxis: {\n+\t\t\t\t\t\tlabels: {\n+\t\t\t\t\t\t\tenabled: false\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\ttype: \'logarithmic\',\n+\t\t\t\t\t\tgridLineInterpolation: \'polygon\',\n+\t\t\t\t\t\tlineWidth: 0,\n+\t\t\t\t\t\tmin: 0.1\n+\t\t\t\t\t},\n+\n+\t\t\t\t\ttooltip: {\n+\t\t\t\t\t\tshared: true,\n+\t\t\t\t\t\tpointFormat: \'<span style="color:{series.color}">{series.name}: <b>{point.y:,.0f}</b><br/>\'\n+\t\t\t\t\t},\n+\n+\t\t\t\t\tcredits: {\n+\t\t\t \t \tenabled: false\n+\t\t\t \t },\n+\n+\t\t\t\t\tlegend: {\n+\t\t\t\t\t\talign: \'center\',\n+\t\t\t\t\t\tverticalAlign: \'bottom\',\n+\t\t\t\t\t\tlayout: \'vertical\',\n+\t\t\t\t\t\ttitle: {\n+\t\t\t\t\t\t\ttext: \'Number of different taxonomic observations per rank before and after applying NSTI or alignments thresholds\',\n+\t\t\t\t\t\t\tstyle: {\n+\t\t\t\t\t\t\t\tfontStyle: \'italic\'\n+\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t}\n+\t\t\t\t\t},\n+\n+\t\t\t\t\tseries: [{\n+\t\t\t\t\t\tname: \'Before\',\n+\t\t\t\t\t\tdata: starplot_series[\'before_series\'],\n+\t\t\t\t\t\tpointPlacement: \'on\'\n+\t\t\t\t\t}, {\n+\t\t\t\t\t\tname: \'After\',\n+\t\t\t\t\t\tdata: starplot_series[\'after_series\'],\n+\t\t\t\t\t\tpointPlacement: \'on\'\n+\t\t\t\t\t}],\n+\n+\t\t\t\t\tresponsive: {\n+\t\t\t\t\t\trules: [{\n+\t\t\t\t\t\t\tcondition: {\n+\t\t\t\t\t\t\t\tmaxWidth: 500\n+\t\t\t\t\t\t\t},\n+\t\t\t\t\t\t\tchartOptions: {\n+\t\t\t\t\t\t\t\tlegend: {\n+\t\t\t\t\t\t\t\t\talign: \'center\',\n+\t\t\t\t\t\t\t\t\tverticalAlign: \'bottom\',\n+\t\t\t\t\t\t\t\t\tlayout: \'horizontal\'\n+\t\t\t\t\t\t\t\t},\n+\t\t\t\t\t\t\t\tpane: {\n+\t\t\t\t\t\t\t\t\tsize: \'70%\'\n+\t\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t\t}\n+\t\t\t\t\t\t}]\n+\t\t\t\t\t}\n+\n+\t\t\t\t});\n+\n \n \t\t\t\t// Load active tab\n \t\t\t\ttaxBySample_load( "tax-distrib" );\n@@ -581,6 +671,8 @@\n \t\t \t\t<div id="abundance-filtered" class="col-md-6"></div>\n \t \t\t</div>\n \t\t\t\t</div>\n+\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Remaining diversity after filtering for functional inference</h2>\n+\t\t\t\t<div id="starplot_container"></div>\n \t\t\t\t<div id="tax-distrib" role="tabpanel" class="tab-pane active">\n \t\t\t\t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Function abundances per sample \n \n@@ -625,4 +717,4 @@\n \t\t\t</div>\n \t\t</div>\n \t</body>\n-</html>\n\\ No newline at end of file\n+</html>\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/27-frogsfunc_functions_unstrat.tsv --- a/test-data/references/27-frogsfunc_functions_unstrat.tsv Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/27-frogsfunc_functions_unstrat.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,1167 +1,1108 @@\n-classification\tdb_link\tobservation_name\tSC1703-104_TTGCCC-B6TML_L001_R\tSC1703-105_CAGTCT-B6TML_L001_R\tSC1703-106_TTAAAT-B6TML_L001_R\tSC1703-107_AATTGC-B6TML_L001_R\tSC1703-108_ACTCGA-B6TML_L001_R\tSC1703-109_GTTACC-B6TML_L001_R\tSC1703-110_CAGATG-B6TML_L001_R\tSC1703-125_TCGCGC-B6TML_L001_R\tSC1703-126_TAACTT-B6TML_L001_R\tSC1703-127_CTGTAA-B6TML_L001_R\tSC1703-128_CCATTG-B6TML_L001_R\tSC1703-129_TAGGCT-B6TML_L001_R\tSC1703-130_TTCTTG-B6TML_L001_R\tSC1703-131_CCGACC-B6TML_L001_R\tSC1703-132_TTAGCT-B6TML_L001_R\tSC1703-133_CAGAGC-B6TML_L001_R\tSC1703-134_AATATG-B6TML_L001_R\tSC1703-135_TGAGCA-B6TML_L001_R\tSC1703-136_AATCAC-B6TML_L001_R\tSC1703-137_GGTAGC-B6TML_L001_R\tSC1703-138_CTCTCG-B6TML_L001_R\tSC1703-145_AGCGAC-B6TML_L001_R\tSC1703-146_GCCAAG-B6TML_L001_R\tSC1703-147_AGGTTC-B6TML_L001_R\tSC1703-148_TTTTTC-B6TML_L001_R\tSC1703-149_GTCGTG-B6TML_L001_R\tSC1703-150_GCTATC-B6TML_L001_R\tSC1703-151_TATGCG-B6TML_L001_R\tSC1703-41_TCGTTC-B6TML_L001_R\tSC1703-42_GCGATG-B6TML_L001_R\tSC1703-43_ATATAA-B6TML_L001_R\tSC1703-44_ATACTG-B6TML_L001_R\tSC1703-45_GGAGAG-B6TML_L001_R\tSC1703-46_ACGAGA-B6TML_L001_R\tSC1703-47_ATTACA-B6TML_L001_R\tSC1703-48_TGATTT-B6TML_L001_R\tSC1703-49_GGGGTG-B6TML_L001_R\tSC1703-50_ACAAAA-B6TML_L001_R\tSC1703-51_CTCCAG-B6TML_L001_R\tSC1703-52_GGTGTT-B6TML_L001_R\tSC1703-53_CGGGAG-B6TML_L001_R\tSC1703-54_TGGTAG-B6TML_L001_R\tSC1703-62_TGCGGG-B6TML_L001_R\tSC1703-63_TCTATG-B6TML_L001_R\tSC1703-64_GGACGG-B6TML_L001_R\tSC1703-65_AGAGGG-B6TML_L001_R\tSC1703-66_ATGAAC-B6TML_L001_R\tSC1703-67_TACCTG-B6TML_L001_R\tSC1703-68_CTAGAG-B6TML_L001_R\tSC1703-83_CTTGCA-B6TML_L001_R\tSC1703-84_CATGTT-B6TML_L001_R\tSC1703-85_TGGATT-B6TML_L001_R\tSC1703-86_AACGCA-B6TML_L001_R\tSC1703-87_TTCGAG-B6TML_L001_R\tSC1703-88_AAGCTA-B6TML_L001_R\tSC1703-89_AGTTTG-B6TML_L001_R\tSC1703-90_TCCCCA-B6TML_L001_R\tSC1703-91_AACTAG-B6TML_L001_R\tSC1703-92_GTTCGC-B6TML_L001_R\tSC1703-93_TGCCTT-B6TML_L001_R\tSC1703-94_ATAAGA-B6TML_L001_R\tSC1703-95_CACACT-B6TML_L001_R\tSC1703-96_ACAGTT-B6TML_L001_R\n-Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.1\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.1\tEC:1.1.1.1\t10937\t21568\t22912\t30967\t15764\t7394\t14257\t8139\t21831\t40099\t33944\t36207\t18113\t37099\t29436\t19640\t15087\t28286\t18217\t20304\t32524\t10460\t10795\t10171\t14299\t8535\t13752\t7508\t14924\t7729\t18573\t18865\t13270\t15035\t21741\t20772\t16731\t15853\t19760\t23086\t16225\t22163\t18355\t16365\t10974\t17803\t28371\t13969\t20106\t14717\t16212\t22396\t21263\t26409\t13764\t16760\t23047\t35566\t37117\t35318\t26832\t33037\t24795\n-Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.100\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.100\tEC:1.1.1.100\t19088\t40567\t38318\t50204\t24510\t14219\t27066\t22529\t55798\t76863\t78641\t88958\t35444\t81237\t51887\t40345\t41090\t83814\t56914\t48196\t69476\t23294\t15391\t18587\t27786\t14210\t23046\t12200\t31362\t11706\t26710\t29946\t35204\t13957\t55274\t52190\t41080\t20386\t46839\t46825\t32982\t49318\t30293\t35316\t23344\t33890\t44339\t24590\t38844\t30516\t30049\t63704\t32959\t71044\t32393\t40039\t78044\t95183\t90201\t86953\t71718\t84572\t67538\n-Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.103\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.103\tEC:1.1.1.103\t332\t1645\t2018\t2420\t1140\t485\t1092\t3052\t7873\t852\t7765\t10654\t402\t6842\t5618\t3807\t3636\t3346\t7832\t4496\t6082\t269\t1314\t228\t452\t306\t471\t113\t6019\t1448\t5281\t3520\t7166\t4199\t10786\t7921\t5412\t3886\t7737\t6364\t3874\t5316\t577\t2348\t950\t684\t1263\t1348\t697\t4834\t4807\t12409\t1756\t14386\t5668\t6025\t8666\t13854\t6057\t15925\t10720\t12010\t9281\n-Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptor;EC:1.1.1.108\thttps://www.genome.jp/dbget-bin/www_bget?EC:1.1.1.108\tEC:1.1.1.108\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-Oxidoreductases;Acting o'..b"45.34\t5560.66\t9577.66\t5737.0\t14144.66\t7155.34\t18968.66\t14757.66\t12353.0\t10722.0\t20850.34\t24333.0\t18266.34\t15306.66\t21033.66\t27182.0\t19404.66\t26779.0\t13610.66\t15454.34\t11847.0\t13377.0\t22921.0\t11928.34\t16614.66\t12398.34\t13183.34\t24728.34\t16000.66\t24020.0\t13390.66\t13055.0\t35987.34\t36372.66\t39220.0\t34196.66\t25445.66\t34642.66\t26649.66\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);RNA ligase (ATP)\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.3\tEC:6.5.1.3\t72347.32\t132.67\t453.0\t906.67\t1233.33\t722.0\t182.67\t928.67\t237.67\t950.33\t1103.0\t1135.0\t958.33\t515.67\t1343.67\t3260.33\t1374.33\t662.0\t396.67\t632.33\t1306.67\t1684.33\t239.67\t727.67\t93.33\t328.67\t323.33\t356.33\t55.0\t1850.33\t1268.67\t3304.33\t2625.33\t1246.0\t3807.0\t1892.67\t771.0\t1328.67\t3151.33\t536.33\t721.0\t546.33\t252.0\t469.33\t1188.67\t646.0\t345.0\t913.0\t1204.67\t568.33\t1654.67\t1865.67\t1165.67\t2281.33\t2042.0\t1188.33\t1036.0\t298.67\t1628.33\t1064.0\t2668.33\t1511.33\t1775.33\t1288.33\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);RNA 3'-terminal-phosphate cyclase (ATP)\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.4\tEC:6.5.1.4\t72347.32\t132.67\t453.0\t906.67\t1233.33\t722.0\t182.67\t928.67\t237.67\t950.33\t1103.0\t1135.0\t958.33\t515.67\t1343.67\t3260.33\t1374.33\t662.0\t396.67\t632.33\t1306.67\t1684.33\t239.67\t727.67\t93.33\t328.67\t323.33\t356.33\t55.0\t1850.33\t1268.67\t3304.33\t2625.33\t1246.0\t3807.0\t1892.67\t771.0\t1328.67\t3151.33\t536.33\t721.0\t546.33\t252.0\t469.33\t1188.67\t646.0\t345.0\t913.0\t1204.67\t568.33\t1654.67\t1865.67\t1165.67\t2281.33\t2042.0\t1188.33\t1036.0\t298.67\t1628.33\t1064.0\t2668.33\t1511.33\t1775.33\t1288.33\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);DNA ligase (ATP or NAD(+))\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.6\tEC:6.5.1.6\t100935.0\t1148.0\t1468.0\t1044.0\t1396.0\t552.0\t612.0\t1846.0\t13.0\t13.0\t15.0\t35.0\t9.0\t24.0\t21.0\t2666.0\t728.0\t4407.0\t3321.0\t9514.0\t1597.0\t2373.0\t969.0\t372.0\t97.0\t697.0\t42.0\t836.0\t399.0\t1.0\t2.0\t6.0\t8.0\t6.0\t7.0\t4.0\t5184.0\t1406.0\t2379.0\t1471.0\t4165.0\t2616.0\t473.0\t1876.0\t1757.0\t3013.0\t1270.0\t2225.0\t1771.0\t3610.0\t41.0\t20.0\t32.0\t76.0\t34.0\t22.0\t11.0\t15266.0\t4545.0\t2580.0\t2981.0\t1403.0\t638.0\t3822.0\n+Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date);DNA ligase (ATP, ADP or GTP)\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.5.1.7\tEC:6.5.1.7\t100935.0\t1148.0\t1468.0\t1044.0\t1396.0\t552.0\t612.0\t1846.0\t13.0\t13.0\t15.0\t35.0\t9.0\t24.0\t21.0\t2666.0\t728.0\t4407.0\t3321.0\t9514.0\t1597.0\t2373.0\t969.0\t372.0\t97.0\t697.0\t42.0\t836.0\t399.0\t1.0\t2.0\t6.0\t8.0\t6.0\t7.0\t4.0\t5184.0\t1406.0\t2379.0\t1471.0\t4165.0\t2616.0\t473.0\t1876.0\t1757.0\t3013.0\t1270.0\t2225.0\t1771.0\t3610.0\t41.0\t20.0\t32.0\t76.0\t34.0\t22.0\t11.0\t15266.0\t4545.0\t2580.0\t2981.0\t1403.0\t638.0\t3822.0\n+Ligases;Forming nitrogen-D-metal bonds;Forming coordination complexes;Magnesium chelatase\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.6.1.1\tEC:6.6.1.1\t106370.0\t350.0\t336.0\t1010.0\t520.0\t280.0\t676.0\t632.0\t2110.0\t982.0\t9000.0\t2012.0\t896.0\t3294.0\t2382.0\t646.0\t1364.0\t1542.0\t1020.0\t1678.0\t2464.0\t1416.0\t22.0\t396.0\t52.0\t448.0\t64.0\t100.0\t22.0\t1118.0\t526.0\t562.0\t5294.0\t142.0\t1052.0\t1750.0\t2044.0\t1224.0\t206.0\t538.0\t742.0\t764.0\t542.0\t716.0\t1738.0\t592.0\t696.0\t1172.0\t736.0\t1254.0\t2768.0\t3600.0\t1226.0\t6276.0\t2998.0\t1956.0\t6350.0\t3722.0\t3902.0\t3776.0\t3310.0\t2710.0\t1822.0\t2832.0\n+Ligases;Forming nitrogen-D-metal bonds;Forming coordination complexes;Cobaltochelatase\thttps://www.genome.jp/dbget-bin/www_bget?EC:6.6.1.2\tEC:6.6.1.2\t53185.0\t175.0\t168.0\t505.0\t260.0\t140.0\t338.0\t316.0\t1055.0\t491.0\t4500.0\t1006.0\t448.0\t1647.0\t1191.0\t323.0\t682.0\t771.0\t510.0\t839.0\t1232.0\t708.0\t11.0\t198.0\t26.0\t224.0\t32.0\t50.0\t11.0\t559.0\t263.0\t281.0\t2647.0\t71.0\t526.0\t875.0\t1022.0\t612.0\t103.0\t269.0\t371.0\t382.0\t271.0\t358.0\t869.0\t296.0\t348.0\t586.0\t368.0\t627.0\t1384.0\t1800.0\t613.0\t3138.0\t1499.0\t978.0\t3175.0\t1861.0\t1951.0\t1888.0\t1655.0\t1355.0\t911.0\t1416.0\n" |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/27-frogsfunc_functions_weighted_nsti.tsv --- a/test-data/references/27-frogsfunc_functions_weighted_nsti.tsv Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/27-frogsfunc_functions_weighted_nsti.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,64 +1,64 @@ sample weighted_NSTI -SC1703-104_TTGCCC-B6TML_L001_R 0.17914150607912946 -SC1703-105_CAGTCT-B6TML_L001_R 0.07932894967173432 -SC1703-106_TTAAAT-B6TML_L001_R 0.09080771320013344 -SC1703-107_AATTGC-B6TML_L001_R 0.11818550863041984 -SC1703-108_ACTCGA-B6TML_L001_R 0.14077219806171326 -SC1703-109_GTTACC-B6TML_L001_R 0.11989821072052824 -SC1703-110_CAGATG-B6TML_L001_R 0.10816648303458604 -SC1703-125_TCGCGC-B6TML_L001_R 0.10306686405751414 -SC1703-126_TAACTT-B6TML_L001_R 0.37740610671555136 -SC1703-127_CTGTAA-B6TML_L001_R 0.5968370519918107 -SC1703-128_CCATTG-B6TML_L001_R 0.5231984447238046 -SC1703-129_TAGGCT-B6TML_L001_R 0.5069389503571987 -SC1703-130_TTCTTG-B6TML_L001_R 0.6450335398919236 -SC1703-131_CCGACC-B6TML_L001_R 0.5600120698434661 -SC1703-132_TTAGCT-B6TML_L001_R 0.1419254065112728 -SC1703-133_CAGAGC-B6TML_L001_R 0.1276668132948926 -SC1703-134_AATATG-B6TML_L001_R 0.12846096254985043 -SC1703-135_TGAGCA-B6TML_L001_R 0.15917250493160484 -SC1703-136_AATCAC-B6TML_L001_R 0.09278446537558062 -SC1703-137_GGTAGC-B6TML_L001_R 0.11838970007634753 -SC1703-138_CTCTCG-B6TML_L001_R 0.11937427126310667 -SC1703-145_AGCGAC-B6TML_L001_R 0.1879727543094794 -SC1703-146_GCCAAG-B6TML_L001_R 0.1600764763760564 -SC1703-147_AGGTTC-B6TML_L001_R 0.1274322590608257 -SC1703-148_TTTTTC-B6TML_L001_R 0.1434060941075659 -SC1703-149_GTCGTG-B6TML_L001_R 0.12773588649193549 -SC1703-150_GCTATC-B6TML_L001_R 0.12141885198206909 -SC1703-151_TATGCG-B6TML_L001_R 0.23442467589864463 -SC1703-41_TCGTTC-B6TML_L001_R 0.06557337247737917 -SC1703-42_GCGATG-B6TML_L001_R 0.08653810681719495 -SC1703-43_ATATAA-B6TML_L001_R 0.07276758683489512 -SC1703-44_ATACTG-B6TML_L001_R 0.07564785035698673 -SC1703-45_GGAGAG-B6TML_L001_R 0.06513132526817066 -SC1703-46_ACGAGA-B6TML_L001_R 0.03892453152471083 -SC1703-47_ATTACA-B6TML_L001_R 0.06522837413735949 -SC1703-48_TGATTT-B6TML_L001_R 0.1715184741803122 -SC1703-49_GGGGTG-B6TML_L001_R 0.10128897243491579 -SC1703-50_ACAAAA-B6TML_L001_R 0.1411397600343313 -SC1703-51_CTCCAG-B6TML_L001_R 0.23605287190780647 -SC1703-52_GGTGTT-B6TML_L001_R 0.2837680935628841 -SC1703-53_CGGGAG-B6TML_L001_R 0.25748284180749037 -SC1703-54_TGGTAG-B6TML_L001_R 0.24228485608300326 -SC1703-62_TGCGGG-B6TML_L001_R 0.12464056160203432 -SC1703-63_TCTATG-B6TML_L001_R 0.08698956613594612 -SC1703-64_GGACGG-B6TML_L001_R 0.11157174351272835 -SC1703-65_AGAGGG-B6TML_L001_R 0.08858109336129151 -SC1703-66_ATGAAC-B6TML_L001_R 0.2179048621829742 -SC1703-67_TACCTG-B6TML_L001_R 0.0829670102154344 -SC1703-68_CTAGAG-B6TML_L001_R 0.07704852970624808 -SC1703-83_CTTGCA-B6TML_L001_R 0.07193392241244731 -SC1703-84_CATGTT-B6TML_L001_R 0.04738857817974204 -SC1703-85_TGGATT-B6TML_L001_R 0.061930723698803515 -SC1703-86_AACGCA-B6TML_L001_R 0.3876369947559189 -SC1703-87_TTCGAG-B6TML_L001_R 0.05602382962233978 -SC1703-88_AAGCTA-B6TML_L001_R 0.06223474071780647 -SC1703-89_AGTTTG-B6TML_L001_R 0.0428010915602616 -SC1703-90_TCCCCA-B6TML_L001_R 0.09329136916527744 -SC1703-91_AACTAG-B6TML_L001_R 0.10880410298803678 -SC1703-92_GTTCGC-B6TML_L001_R 0.13134141935130225 -SC1703-93_TGCCTT-B6TML_L001_R 0.11178773580920295 -SC1703-94_ATAAGA-B6TML_L001_R 0.12023295545218712 -SC1703-95_CACACT-B6TML_L001_R 0.1269879755473051 -SC1703-96_ACAGTT-B6TML_L001_R 0.10627232104335031 +SC1703-104_TTGCCC-B6TML_L001_R 0.29917236721842666 +SC1703-105_CAGTCT-B6TML_L001_R 0.1035861227122307 +SC1703-106_TTAAAT-B6TML_L001_R 0.12805555130836307 +SC1703-107_AATTGC-B6TML_L001_R 0.18553915101276228 +SC1703-108_ACTCGA-B6TML_L001_R 0.2267801279277491 +SC1703-109_GTTACC-B6TML_L001_R 0.18034293788050154 +SC1703-110_CAGATG-B6TML_L001_R 0.15454214425687188 +SC1703-125_TCGCGC-B6TML_L001_R 0.1046706706378497 +SC1703-126_TAACTT-B6TML_L001_R 0.3461641208674658 +SC1703-127_CTGTAA-B6TML_L001_R 0.5432674473345119 +SC1703-128_CCATTG-B6TML_L001_R 0.47655096734693875 +SC1703-129_TAGGCT-B6TML_L001_R 0.4621641903732451 +SC1703-130_TTCTTG-B6TML_L001_R 0.5856106278614006 +SC1703-131_CCGACC-B6TML_L001_R 0.5088300120803054 +SC1703-132_TTAGCT-B6TML_L001_R 0.2016670654461444 +SC1703-133_CAGAGC-B6TML_L001_R 0.1643572889413742 +SC1703-134_AATATG-B6TML_L001_R 0.17665652679562852 +SC1703-135_TGAGCA-B6TML_L001_R 0.17083847035350017 +SC1703-136_AATCAC-B6TML_L001_R 0.14903071928647094 +SC1703-137_GGTAGC-B6TML_L001_R 0.14468378124783238 +SC1703-138_CTCTCG-B6TML_L001_R 0.15265641534364796 +SC1703-145_AGCGAC-B6TML_L001_R 0.25200760060943606 +SC1703-146_GCCAAG-B6TML_L001_R 0.2771250054293862 +SC1703-147_AGGTTC-B6TML_L001_R 0.1738033591920028 +SC1703-148_TTTTTC-B6TML_L001_R 0.19082084348290343 +SC1703-149_GTCGTG-B6TML_L001_R 0.1660634335739776 +SC1703-150_GCTATC-B6TML_L001_R 0.18515215858883696 +SC1703-151_TATGCG-B6TML_L001_R 0.3858130579021471 +SC1703-41_TCGTTC-B6TML_L001_R 0.07000065003240988 +SC1703-42_GCGATG-B6TML_L001_R 0.08986543319109526 +SC1703-43_ATATAA-B6TML_L001_R 0.07899689265663386 +SC1703-44_ATACTG-B6TML_L001_R 0.0796495886606273 +SC1703-45_GGAGAG-B6TML_L001_R 0.0682335713885517 +SC1703-46_ACGAGA-B6TML_L001_R 0.04152046710144927 +SC1703-47_ATTACA-B6TML_L001_R 0.06973929438954837 +SC1703-48_TGATTT-B6TML_L001_R 0.30323459714825635 +SC1703-49_GGGGTG-B6TML_L001_R 0.11504408147661219 +SC1703-50_ACAAAA-B6TML_L001_R 0.22434470790106517 +SC1703-51_CTCCAG-B6TML_L001_R 0.4030133353210863 +SC1703-52_GGTGTT-B6TML_L001_R 0.4765044691445427 +SC1703-53_CGGGAG-B6TML_L001_R 0.4327752792243681 +SC1703-54_TGGTAG-B6TML_L001_R 0.39649115793087664 +SC1703-62_TGCGGG-B6TML_L001_R 0.2123704877086585 +SC1703-63_TCTATG-B6TML_L001_R 0.1495576853691414 +SC1703-64_GGACGG-B6TML_L001_R 0.18576000348183197 +SC1703-65_AGAGGG-B6TML_L001_R 0.14043836625230202 +SC1703-66_ATGAAC-B6TML_L001_R 0.3778399384286818 +SC1703-67_TACCTG-B6TML_L001_R 0.1316985475532164 +SC1703-68_CTAGAG-B6TML_L001_R 0.10275650339132945 +SC1703-83_CTTGCA-B6TML_L001_R 0.07494555006198468 +SC1703-84_CATGTT-B6TML_L001_R 0.05171908240843095 +SC1703-85_TGGATT-B6TML_L001_R 0.06820788765189521 +SC1703-86_AACGCA-B6TML_L001_R 0.34445551189795415 +SC1703-87_TTCGAG-B6TML_L001_R 0.05962196473467038 +SC1703-88_AAGCTA-B6TML_L001_R 0.06770573688599726 +SC1703-89_AGTTTG-B6TML_L001_R 0.04628026473144446 +SC1703-90_TCCCCA-B6TML_L001_R 0.1436828097658562 +SC1703-91_AACTAG-B6TML_L001_R 0.15913631795238603 +SC1703-92_GTTCGC-B6TML_L001_R 0.16228688361769592 +SC1703-93_TGCCTT-B6TML_L001_R 0.18083837256281304 +SC1703-94_ATAAGA-B6TML_L001_R 0.16339674672472368 +SC1703-95_CACACT-B6TML_L001_R 0.17264462667239922 +SC1703-96_ACAGTT-B6TML_L001_R 0.14431378397945202 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/references/28-frogsfunc_pathways_report.html --- a/test-data/references/28-frogsfunc_pathways_report.html Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/28-frogsfunc_pathways_report.html Tue May 23 07:59:04 2023 +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="4.0.1">\n+\t\t<meta name="version" content="4.1.0">\n \t\t<!-- CSS -->\n \t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n \t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n@@ -348,7 +348,7 @@\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\\": 7321, \\"1\\": 14325, \\"2\\": 13731, \\"3\\": 18401, \\"4\\": 9165, \\"5\\": 5130, \\"6\\": 10367, \\"7\\": 6498, \\"8\\": 14613, \\"9\\": 23242, \\"10\\": 21992, \\"11\\": 23517, \\"12\\": 9826, \\"13\\": 23196, \\"14\\": 19358, \\"15\\": 13471, \\"16\\": 13598, \\"17\\": 27558, \\"18\\": 17603, \\"19\\": 15737, \\"20\\": 22658, \\"21\\": 8514, \\"22\\": 5772, \\"23\\": 6614, \\"24\\": 10150, \\"25\\": 5239, \\"26\\": 8655, \\"27\\": 4718, \\"28\\": 9228, \\"29\\": 4889, \\"30\\": 10617, \\"31\\": 11911, \\"32\\": 7525, \\"33\\": 6446, \\"34\\": 13741, \\"35\\": 15330, \\"36\\": 12684, \\"37\\": 9102, \\"38\\": 12373, \\"39\\": 15912, \\"40\\": 11604, \\"41\\": 16114, \\"42\\": 11837, \\"43\\": 12584, \\"44\\": 8987, \\"45\\": 12400, \\"46\\": 17749, \\"47\\": 9635, \\"48\\": 15002, \\"49\\": 9970, \\"50\\": 10515, \\"51\\": 14576, \\"52\\": 12758, \\"53\\": 16484, \\"54\\": 9472, \\"55\\": 12386, \\"56\\": 24040, \\"57\\": 25946, \\"58\\": 30949, \\"59\\": 22210, \\"60\\": 19344, \\"61\\": 24072, \\"62\\": 19012},\\"COA-PWY\\":{\\"0\\": 7308, \\"1\\": 13391, \\"2\\": 12564, \\"3\\": 17074, \\"4\\": 8552, \\"5\\": 4956, \\"6\\": 10457, \\"7\\": 4171, \\"8\\": 13295, \\"9\\": 34093, \\"10\\": 24992, \\"11\\": 25577, \\"12\\": 15682, \\"13\\": 28520, \\"14\\": 17888, \\"15\\": 11624, \\"16\\": 13706, \\"17\\": 27110, \\"18\\": 17647, \\"19\\": 13786, \\"20\\": 20472, \\"21\\": 8652, \\"22\\": 5152, \\"23\\": 6233, \\"24\\": 9818, \\"25\\": 4920, \\"26\\": 8391, \\"27\\": 4615, \\"28\\": 6327, \\"29\\": 4277, \\"30\\": 8654, \\"31\\": 9516, \\"32\\": 4902, \\"33\\": 4958, \\"34\\": 8467, \\"35\\": 13723, \\"36\\": 10862, \\"37\\": 8736, \\"38\\": 9639, \\"39\\": 14405, \\"40\\": 10759, \\"41\\": 13825, \\"42\\": 11713, \\"43\\": 12113, \\"44\\": 9869, \\"45\\": 12039, \\"46\\": 17393, \\"47\\": 9633, \\"48\\": 15425, \\"49\\": 6784, \\"50\\": 7025, \\"51\\": 9009, \\"52\\": 13594, \\"53\\": 8938, \\"54\\": 6110, \\"55\\": 7015, \\"56\\": 27120, \\"57\\": 21298, \\"58\\": 28154, \\"59\\": 16259, \\"60\\": 14436, \\"61\\": 18564, \\"62\\": 16422},\\"FOLSYN-PWY\\":{\\"0\\": 5764, \\"1\\": 10422, \\"2\\": 9862, \\"3\\": 13279, \\"4\\": 6433, \\"5\\": 3815, \\"6\\": 9461, \\"7\\": 1699, \\"8\\": 5045, \\"9\\": 5688, \\"10\\": 6125, \\"11\\": 4841, \\"12\\": 3018, \\"13\\": 6411, \\"14\\": 17379, \\"15\\": 9460, \\"16\\": 12756, \\"17\\": 20043, \\"18\\": 17065, \\"19\\": 11761, \\"20\\": 17589, \\"21\\": 6355, \\"22\\": 4358, \\"23\\": 1847, \\"24\\": 6419, \\"25\\": 2498, \\"26\\": 6355, \\"27\\": 2894, \\"28\\": 5670, \\"29\\": 3790, \\"30\\": 7528, \\"31\\": 7523, \\"32\\": 4974, \\"33\\": 6266, \\"34\\": 7094, \\"35\\": 12078, \\"36\\": 9414, \\"37\\": 9526, \\"38\\": 6744, \\"39\\": 10454, \\"40\\": 7689, \\"41\\": 4906, \\"42\\": 9806, \\"43\\": 10459, \\"44\\": 9151, \\"45\\": 8873, \\"46\\": 13319, \\"47\\": 9096, \\"48\\": 14078, \\"49\\": 5710, \\"50\\": 5541, \\"51\\": 5187, \\"52\\": 7298, \\"53\\": 7794, \\"54\\": 4344, \\"55\\": 3909, \\"56\\": 24793, \\"57\\": 19768, \\"58\\": 19001, \\"59\\": 15774, \\"60\\": 12453, \\"61\\": 12322, \\"62\\": 15376},\\"NAD-BIOSYNTHESIS-II\\":{\\"0\\": 192, \\"1\\": 630, \\"2\\": 1205, \\"3\\": 1625, \\"4\\": 937, \\"5\\": 256, \\"6\\": 1234, \\"7\\": 324, \\"8\\": 1156, \\"9\\": 1396, \\"10\\": 1386, \\"11\\": 1123, \\"12\\": 671, \\"13\\": 1594, \\"14\\": 4003, \\"15\\": 1758, \\"16\\": 923, \\"17\\": 574, \\"18\\": 878, \\"19\\": 1725, \\"20\\": 2228, \\"21\\": 336, \\"22\\": 909, \\"23\\": 126, \\"24\\": 452, \\"25\\": 411, \\"26\\": 486, \\"27\\": 78, \\"28\\": 2052, \\"29\\": 1445, \\"30\\": 3332, \\"31\\": 2993, \\"32\\": 1449, \\"33\\": 3782, \\"34\\": 2189, \\"35\\": 1001, \\"36\\": 1678, \\"37\\": 3402, \\"38\\": 694, \\"39\\": 886, \\"40\\": 704, \\"41\\": 344, \\"42\\": 655, \\"43\\": 1566, \\"44\\": 884, \\"45\\": 485, \\"46\\": 1241, '..b'0\\": 641, \\"1\\": 2778, \\"2\\": 3181, \\"3\\": 3250, \\"4\\": 1336, \\"5\\": 1034, \\"6\\": 1106, \\"7\\": 6803, \\"8\\": 14811, \\"9\\": 4550, \\"10\\": 14834, \\"11\\": 20318, \\"12\\": 1677, \\"13\\": 12859, \\"14\\": 6669, \\"15\\": 6234, \\"16\\": 7049, \\"17\\": 6608, \\"18\\": 15555, \\"19\\": 8264, \\"20\\": 10346, \\"21\\": 189, \\"22\\": 1734, \\"23\\": 342, \\"24\\": 634, \\"25\\": 158, \\"26\\": 458, \\"27\\": 155, \\"28\\": 9821, \\"29\\": 1255, \\"30\\": 5887, \\"31\\": 5749, \\"32\\": 12533, \\"33\\": 3214, \\"34\\": 19607, \\"35\\": 15708, \\"36\\": 9442, \\"37\\": 3147, \\"38\\": 14939, \\"39\\": 12017, \\"40\\": 7310, \\"41\\": 10525, \\"42\\": 808, \\"43\\": 3783, \\"44\\": 1226, \\"45\\": 1198, \\"46\\": 1742, \\"47\\": 1258, \\"48\\": 1169, \\"49\\": 8570, \\"50\\": 8616, \\"51\\": 23683, \\"52\\": 3228, \\"53\\": 27207, \\"54\\": 10532, \\"55\\": 13671, \\"56\\": 18745, \\"57\\": 27217, \\"58\\": 12406, \\"59\\": 29503, \\"60\\": 20529, \\"61\\": 22267, \\"62\\": 18046},\\"anhydromuropeptides recycling\\":{\\"0\\": 1192, \\"1\\": 3095, \\"2\\": 5725, \\"3\\": 7215, \\"4\\": 4094, \\"5\\": 1577, \\"6\\": 5327, \\"7\\": 2328, \\"8\\": 6643, \\"9\\": 11037, \\"10\\": 8942, \\"11\\": 7166, \\"12\\": 4983, \\"13\\": 10482, \\"14\\": 15022, \\"15\\": 8005, \\"16\\": 5191, \\"17\\": 3538, \\"18\\": 5317, \\"19\\": 8692, \\"20\\": 10524, \\"21\\": 1522, \\"22\\": 3909, \\"23\\": 664, \\"24\\": 2414, \\"25\\": 1697, \\"26\\": 2199, \\"27\\": 402, \\"28\\": 8654, \\"29\\": 4898, \\"30\\": 12101, \\"31\\": 12223, \\"32\\": 6063, \\"33\\": 9542, \\"34\\": 10574, \\"35\\": 6367, \\"36\\": 7868, \\"37\\": 10869, \\"38\\": 4022, \\"39\\": 5385, \\"40\\": 4196, \\"41\\": 2259, \\"42\\": 3488, \\"43\\": 7444, \\"44\\": 4181, \\"45\\": 2722, \\"46\\": 6628, \\"47\\": 6217, \\"48\\": 4429, \\"49\\": 8709, \\"50\\": 9761, \\"51\\": 7735, \\"52\\": 13065, \\"53\\": 12346, \\"54\\": 7133, \\"55\\": 8042, \\"56\\": 3431, \\"57\\": 12471, \\"58\\": 9294, \\"59\\": 16412, \\"60\\": 10512, \\"61\\": 11763, \\"62\\": 9530})\\"Sugar Derivative Degradation\\")\\"Secondary Metabolite Degradation\\")\\"Degradation/Utilization/Assimilation\\",(((\\"queuosine biosynthesis\\":{\\"0\\": 2233, \\"1\\": 3403, \\"2\\": 3438, \\"3\\": 4647, \\"4\\": 2264, \\"5\\": 1395, \\"6\\": 4480, \\"7\\": 2185, \\"8\\": 2686, \\"9\\": 9678, \\"10\\": 4006, \\"11\\": 2701, \\"12\\": 3817, \\"13\\": 4716, \\"14\\": 9403, \\"15\\": 3685, \\"16\\": 7860, \\"17\\": 6615, \\"18\\": 14534, \\"19\\": 4991, \\"20\\": 7011, \\"21\\": 2143, \\"22\\": 1895, \\"23\\": 370, \\"24\\": 1871, \\"25\\": 683, \\"26\\": 2112, \\"27\\": 841, \\"28\\": 3948, \\"29\\": 2351, \\"30\\": 5502, \\"31\\": 7354, \\"32\\": 2346, \\"33\\": 5397, \\"34\\": 4779, \\"35\\": 9525, \\"36\\": 4634, \\"37\\": 7546, \\"38\\": 3649, \\"39\\": 8206, \\"40\\": 5355, \\"41\\": 1404, \\"42\\": 3987, \\"43\\": 4907, \\"44\\": 5534, \\"45\\": 2878, \\"46\\": 5502, \\"47\\": 4675, \\"48\\": 6656, \\"49\\": 4731, \\"50\\": 5490, \\"51\\": 3264, \\"52\\": 7956, \\"53\\": 6083, \\"54\\": 3612, \\"55\\": 6349, \\"56\\": 21830, \\"57\\": 10482, \\"58\\": 6583, \\"59\\": 9591, \\"60\\": 5208, \\"61\\": 4924, \\"62\\": 8489})\\"Queuosine Biosynthesis and Salvage\\",(\\"tRNA processing\\":{\\"0\\": 380, \\"1\\": 1200, \\"2\\": 2240, \\"3\\": 3082, \\"4\\": 1782, \\"5\\": 496, \\"6\\": 2165, \\"7\\": 660, \\"8\\": 2587, \\"9\\": 3100, \\"10\\": 3164, \\"11\\": 2719, \\"12\\": 1447, \\"13\\": 3724, \\"14\\": 7132, \\"15\\": 3287, \\"16\\": 1792, \\"17\\": 1121, \\"18\\": 1784, \\"19\\": 3247, \\"20\\": 4247, \\"21\\": 647, \\"22\\": 1722, \\"23\\": 261, \\"24\\": 865, \\"25\\": 751, \\"26\\": 924, \\"27\\": 161, \\"28\\": 4061, \\"29\\": 2381, \\"30\\": 6260, \\"31\\": 5173, \\"32\\": 2984, \\"33\\": 5284, \\"34\\": 4602, \\"35\\": 2155, \\"36\\": 3294, \\"37\\": 5859, \\"38\\": 1523, \\"39\\": 2040, \\"40\\": 1535, \\"41\\": 738, \\"42\\": 1256, \\"43\\": 2884, \\"44\\": 1631, \\"45\\": 932, \\"46\\": 2475, \\"47\\": 2650, \\"48\\": 1450, \\"49\\": 3650, \\"50\\": 4028, \\"51\\": 3113, \\"52\\": 5048, \\"53\\": 5083, \\"54\\": 2877, \\"55\\": 2619, \\"56\\": 876, \\"57\\": 4394, \\"58\\": 2946, \\"59\\": 6745, \\"60\\": 3954, \\"61\\": 4686, \\"62\\": 3434})\\"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 37e6f0c959bb -r b2967b704d6b test-data/references/28-frogsfunc_pathways_unstrat.tsv --- a/test-data/references/28-frogsfunc_pathways_unstrat.tsv Tue Jul 19 11:11:16 2022 +0000 +++ b/test-data/references/28-frogsfunc_pathways_unstrat.tsv Tue May 23 07:59:04 2023 +0000 |
| b |
| b'@@ -1,262 +1,251 @@\n-classification\tdb_link\tobservation_name\tSC1703-104_TTGCCC-B6TML_L001_R\tSC1703-105_CAGTCT-B6TML_L001_R\tSC1703-106_TTAAAT-B6TML_L001_R\tSC1703-107_AATTGC-B6TML_L001_R\tSC1703-108_ACTCGA-B6TML_L001_R\tSC1703-109_GTTACC-B6TML_L001_R\tSC1703-110_CAGATG-B6TML_L001_R\tSC1703-125_TCGCGC-B6TML_L001_R\tSC1703-126_TAACTT-B6TML_L001_R\tSC1703-127_CTGTAA-B6TML_L001_R\tSC1703-128_CCATTG-B6TML_L001_R\tSC1703-129_TAGGCT-B6TML_L001_R\tSC1703-130_TTCTTG-B6TML_L001_R\tSC1703-131_CCGACC-B6TML_L001_R\tSC1703-132_TTAGCT-B6TML_L001_R\tSC1703-133_CAGAGC-B6TML_L001_R\tSC1703-134_AATATG-B6TML_L001_R\tSC1703-135_TGAGCA-B6TML_L001_R\tSC1703-136_AATCAC-B6TML_L001_R\tSC1703-137_GGTAGC-B6TML_L001_R\tSC1703-138_CTCTCG-B6TML_L001_R\tSC1703-145_AGCGAC-B6TML_L001_R\tSC1703-146_GCCAAG-B6TML_L001_R\tSC1703-147_AGGTTC-B6TML_L001_R\tSC1703-148_TTTTTC-B6TML_L001_R\tSC1703-149_GTCGTG-B6TML_L001_R\tSC1703-150_GCTATC-B6TML_L001_R\tSC1703-151_TATGCG-B6TML_L001_R\tSC1703-41_TCGTTC-B6TML_L001_R\tSC1703-42_GCGATG-B6TML_L001_R\tSC1703-43_ATATAA-B6TML_L001_R\tSC1703-44_ATACTG-B6TML_L001_R\tSC1703-45_GGAGAG-B6TML_L001_R\tSC1703-46_ACGAGA-B6TML_L001_R\tSC1703-47_ATTACA-B6TML_L001_R\tSC1703-48_TGATTT-B6TML_L001_R\tSC1703-49_GGGGTG-B6TML_L001_R\tSC1703-50_ACAAAA-B6TML_L001_R\tSC1703-51_CTCCAG-B6TML_L001_R\tSC1703-52_GGTGTT-B6TML_L001_R\tSC1703-53_CGGGAG-B6TML_L001_R\tSC1703-54_TGGTAG-B6TML_L001_R\tSC1703-62_TGCGGG-B6TML_L001_R\tSC1703-63_TCTATG-B6TML_L001_R\tSC1703-64_GGACGG-B6TML_L001_R\tSC1703-65_AGAGGG-B6TML_L001_R\tSC1703-66_ATGAAC-B6TML_L001_R\tSC1703-67_TACCTG-B6TML_L001_R\tSC1703-68_CTAGAG-B6TML_L001_R\tSC1703-83_CTTGCA-B6TML_L001_R\tSC1703-84_CATGTT-B6TML_L001_R\tSC1703-85_TGGATT-B6TML_L001_R\tSC1703-86_AACGCA-B6TML_L001_R\tSC1703-87_TTCGAG-B6TML_L001_R\tSC1703-88_AAGCTA-B6TML_L001_R\tSC1703-89_AGTTTG-B6TML_L001_R\tSC1703-90_TCCCCA-B6TML_L001_R\tSC1703-91_AACTAG-B6TML_L001_R\tSC1703-92_GTTCGC-B6TML_L001_R\tSC1703-93_TGCCTT-B6TML_L001_R\tSC1703-94_ATAAGA-B6TML_L001_R\tSC1703-95_CACACT-B6TML_L001_R\tSC1703-96_ACAGTT-B6TML_L001_R\n-Biosynthesis;Cofactor, Carrier, and Vitamin Biosynthesis;Carrier Biosynthesis;1CMET2-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=1CMET2-PWY\t1CMET2-PWY\t7321\t14325\t13731\t18401\t9165\t5130\t10367\t6498\t14613\t23242\t21992\t23517\t9826\t23196\t19358\t13471\t13598\t27558\t17603\t15737\t22658\t8514\t5772\t6614\t10150\t5239\t8655\t4718\t9228\t4889\t10617\t11911\t7525\t6446\t13741\t15330\t12684\t9102\t12373\t15912\t11604\t16114\t11837\t12584\t8987\t12400\t17749\t9635\t15002\t9970\t10515\t14576\t12758\t16484\t9472\t12386\t24040\t25946\t30949\t22210\t19344\t24072\t19012\n-Superpathways;Superpathways;unknow;ALL-CHORISMATE-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALL-CHORISMATE-PWY\tALL-CHORISMATE-PWY\t249\t791\t1397\t1896\t1055\t319\t1508\t296\t1154\t1326\t1393\t1170\t630\t1634\t4655\t1917\t1207\t743\t1199\t2021\t2657\t426\t999\t145\t549\t405\t599\t102\t2131\t1421\t3659\t2968\t1466\t3875\t2231\t1408\t2009\t4210\t922\t1308\t978\t422\t829\t1870\t1141\t609\t1537\t1869\t1036\t1937\t2154\t1417\t2661\t2436\t1410\t1239\t584\t2779\t1808\t4054\t2279\t2420\t2206\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\t612\t1994\t3603\t4888\t2768\t794\t3485\t1005\t3739\t4473\t4586\t3888\t2141\t5281\t10205\t4984\t2801\t1851\t2781\t4982\t6612\t1070\t2467\t434\t1440\t1297\t1521\t256\t5165\t3173\t7437\t6814\t3957\t5861\t6086\t3229\t4802\t7146\t2253\t3015\t2274\t1152\t2011\t4383\t2558\t1534\t3765\t4134\t2457\t4882\t5207\t4270\t6725\t6690\t3828\t3581\t1406\t6603\t4633\t9274\t5839\t6881\t5171\n-Generation of Precursor Metabolites and Energy;Glycolysis;unknow;ANAGLYCOLYSIS-PWY\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ANAGLYCOLYSIS-PWY\tANAGLYCOLYSIS-PWY\t8721\t17059\t16472\t21957\t10866\t6182\t12610\t8479\t23260\t38198\t35622\t39116\t17645\t38117\t24992\t17258\t18824\t35069\t26178\t20414\t29879\t10360\t7065\t7632\t11994\t6072\t10119\t5495\t13044\t5778\t13613\t13602\t13218\t8007\t21190\t23105\t17707\t11926\t19215\t22098\t15751\t21531\t13717\t15373\t11353\t14240\t20715\t11628\t17918\t12585\t12666\t23822\t16157\t26147\t12900\t15071\t36152\t39095\t39005\t35068\t28351\t3422'..b'hesis (prokaryotic)\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=UBISYN-PWY\tUBISYN-PWY\t103858.1690088619\t283.8557548849694\t857.2970795672918\t1428.00671147494\t1933.5822973879115\t1055.6951674553789\t346.749906089441\t1604.9103272494349\t288.8943839261784\t1126.66296374311\t1250.0138278055124\t1352.6763149912217\t1138.2839079962312\t593.9631676031337\t1581.6698246873405\t4825.763957611481\t1918.211339708544\t1382.0521688734486\t849.0363208807887\t1416.6368513351201\t2091.8218480785467\t2766.4464531937388\t466.43374616245313\t1003.4002142043897\t144.56418551839175\t575.2255768716637\t387.8366722833915\t634.7686239480747\t115.54607556217086\t2143.0988381466377\t1438.7567516062481\t3772.72656113961\t2988.7500590323143\t1462.1963680616043\t4315.248308940894\t2217.7692399998714\t1616.2497725244123\t2079.7587226048186\t4583.913939648795\t1001.5227466875572\t1485.0154897292168\t1098.2365486353374\t443.93982932279005\t912.0770189625796\t1955.0142471356696\t1284.2867465943698\t663.3965325002138\t1637.7059942990818\t1969.172271496301\t1175.1063134585977\t1934.8767195491605\t2161.112299112384\t1395.894751669367\t2610.512427071326\t2418.3526042781864\t1399.0607103275108\t1219.447198492738\t701.250471758203\t3033.57279225788\t1929.7858215173665\t4239.384401677083\t2333.6501232288256\t2398.108049124061\t2419.2126691765907\n+Biosynthesis;Carbohydrate Biosynthesis;Sugar Biosynthesis;UDP-N-acetyl-D-glucosamine biosynthesis I\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=UDPNAGSYN-PWY\tUDPNAGSYN-PWY\t1048419.8001489481\t6766.185504471118\t8771.17856639686\t9838.869975430502\t13387.17483264015\t6965.613267497504\t4397.794425088211\t9144.41725220489\t7477.300760558702\t19856.18115016376\t38374.19163107772\t31552.329788421004\t34059.51260873622\t16946.075180330918\t34303.54705421636\t21739.28604694809\t14231.415431810892\t17678.16551755997\t30022.701373987325\t25860.874850954104\t17784.583873423988\t23562.17541791721\t8599.742818061677\t5452.131224175115\t4082.621368259923\t8474.65398358582\t3524.1465071684306\t5816.773924486878\t4396.328960374379\t11122.803115062992\t4908.896250726809\t11953.232802538503\t13198.701938812888\t10488.359217140394\t7324.001590255255\t17871.0743178017\t24240.136117777864\t15450.707038969818\t11872.529130435525\t20099.625689764853\t25782.92211487701\t17627.573699931796\t22009.10519394557\t8906.80965864585\t11264.633918349735\t9390.241208928634\t7104.597745127698\t17685.71369297843\t7963.064399862438\t11717.510669022933\t11235.358051195046\t11479.819870446734\t20009.349064343263\t16491.475983324548\t22200.452754216003\t11238.31905161429\t14997.63516144053\t37319.08720243839\t35322.406310496364\t34107.61845531864\t32391.292498843413\t25042.047369969645\t29879.379754193083\t25657.345814203323\n+Biosynthesis;Amino Acid Biosynthesis;Proteinogenic Amino Acid Biosynthesis;L-valine biosynthesis\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=VALSYN-PWY\tVALSYN-PWY\t1406181.5843505547\t10684.910156546483\t18976.923220449982\t18486.72420752998\t25290.373468875503\t12754.883404746864\t7156.599891624007\t14503.12004036198\t9094.285963847777\t25263.90262908061\t42551.78579183445\t38994.781352656624\t42285.80108355911\t19323.601876318047\t42002.79842228746\t29780.60846116226\t19703.198069940474\t22569.62039674206\t38989.61304862352\t32321.6757306435\t23335.073155163114\t33985.00912983194\t11694.978163174403\t8725.043001031105\t8335.694826572677\t13240.178673554536\t6538.382510741776\t11449.85685041585\t6930.363655053134\t14771.985665406823\t6743.192044422416\t16300.418836600396\t15653.732328803198\t14525.717183788292\t9593.72614590039\t23116.77181643358\t29660.906969471704\t20400.915099286296\t15414.24681153891\t25132.915122548573\t31632.994179303143\t21894.346102294094\t28386.107283144374\t16308.361958728472\t18609.91639148099\t14007.367568843936\t16395.507761486464\t27202.814905682022\t13608.517957005228\t20151.97585989198\t14143.581942644538\t14234.935612270985\t24860.894194913755\t18259.296360388158\t27745.870286889243\t14227.588190474917\t15995.258460700343\t45778.78628939491\t45322.76509773363\t44965.837757481444\t41081.327973799685\t32515.946190633553\t39655.429651332626\t32911.841167466635\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/taxo_affi.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxo_affi.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1935 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpv9ahn2ok/galaxy-dev\n+Clonage dans \'/tmp/tmpv9ahn2ok/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n+\n+[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n+[notice] To update, run: pip install --upgrade pip\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) ('..b'Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-2048}/1024)) && taxonomic_affiliation.py --reference \'/home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/test-data/databases/frogs_db_data/ITS1.rdp.fasta\' --taxonomy-ranks Domain Phylum Class Order Family Genus Species --input-biom \'/tmp/tmpv9ahn2ok/files/2/7/9/dataset_27937c9c-1fbc-477a-b099-678abaa23667.dat\' --input-fasta \'/tmp/tmpv9ahn2ok/files/1/4/5/dataset_1455887e-4ae8-421d-a28e-a933c5982219.dat\' --output-biom \'/tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_7b0c8ce1-2f28-4ed6-962f-312e182b344d.dat\' --summary \'/tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_e29b56ae-b50b-400d-ade8-e98564b2a375.dat\' --nb-cpus ${GALAXY_SLOTS:-1} --java-mem $GALAXY_MEMORY_GB --rdp]\n+\n+galaxy.jobs.runners DEBUG 2023-05-19 15:13:17,335 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpv9ahn2ok/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpv9ahn2ok/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmpv9ahn2ok/job_working_directory/000/3/working/affiliation.biom" ] ; then cp "/tmp/tmpv9ahn2ok/job_working_directory/000/3/working/affiliation.biom" "/tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_7b0c8ce1-2f28-4ed6-962f-312e182b344d.dat" ; fi; \n+if [ -f "/tmp/tmpv9ahn2ok/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmpv9ahn2ok/job_working_directory/000/3/working/report.html" "/tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_e29b56ae-b50b-400d-ade8-e98564b2a375.dat" ; fi; cd \'/tmp/tmpv9ahn2ok/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-19 15:13:17,349 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] (3) executing job script: /tmp/tmpv9ahn2ok/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-19 15:13:23,160 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 283405\n+galaxy.jobs.runners.local DEBUG 2023-05-19 15:13:23,162 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpv9ahn2ok/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs DEBUG 2023-05-19 15:13:23,246 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_7b0c8ce1-2f28-4ed6-962f-312e182b344d.dat to /tmp/tmpv9ahn2ok/files/7/b/0/dataset_7b0c8ce1-2f28-4ed6-962f-312e182b344d.dat\n+galaxy.jobs DEBUG 2023-05-19 15:13:23,246 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_e29b56ae-b50b-400d-ade8-e98564b2a375.dat to /tmp/tmpv9ahn2ok/files/e/2/9/dataset_e29b56ae-b50b-400d-ade8-e98564b2a375.dat\n+galaxy.model.metadata DEBUG 2023-05-19 15:13:23,399 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.model.metadata DEBUG 2023-05-19 15:13:23,437 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.jobs DEBUG 2023-05-19 15:13:23,561 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 3 executed (345.756 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_taxonomic_affiliation (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/taxo_enrichment.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxo_enrichment.tsv Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,271 @@\n+Taxonomic_rank\tDESeq2_Log2fc_sens\tTaxonomic_name\tNb_total_clusters\tNb_observ_taxonomic_name_from_total\tNb_Deseq2_differentially_abundant(OVER_or_UNDER)\tNb_observ_taxonomic_names_from_diff_abundant\tRatio_between_total_and_diff_abundant\tPvalue\tPadj\tSignificance\n+Kingdom\tunder\tBacteria\t1053\t1052\t446\t446\t1.0009505703422052\t1.0\t1.1894273127753303\t \n+Kingdom\tover\tBacteria\t1053\t1052\t539\t538\t0.9990935191912922\t1.0\t1.1894273127753303\t \n+Kingdom\tover\tArchaea\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Phylum\tunder\tFirmicutes\t1053\t924\t446\t438\t1.1191689476442839\t0.16857521467058206\t0.722465205731066\t \n+Phylum\tunder\tActinobacteriota\t1053\t17\t446\t2\t0.2777631231864943\t0.07791272826318164\t0.5685523413799741\t \n+Phylum\tunder\tProteobacteria\t1053\t19\t446\t6\t0.7455746990795374\t0.6612319979689567\t1.075497828021797\t \n+Phylum\tover\tBacteroidota\t1053\t63\t539\t60\t1.860588391200636\t0.0011351669261284913\t0.029190006671875494\t*\n+Phylum\tover\tFirmicutes\t1053\t924\t539\t424\t0.8964653157603065\t0.16781086719530242\t0.7307892603666395\t \n+Phylum\tover\tCampylobacterota\t1053\t4\t539\t4\t1.9536178107606679\t0.45541696874088\t0.956907249494456\t \n+Phylum\tover\tActinobacteriota\t1053\t17\t539\t15\t1.7237804212594128\t0.13405213838570162\t0.6765248105446624\t \n+Phylum\tover\tCyanobacteria\t1053\t11\t539\t11\t1.9536178107606679\t0.118258108369516\t0.6385937851953863\t \n+Phylum\tover\tDesulfobacterota\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n+Phylum\tover\tProteobacteria\t1053\t19\t539\t11\t1.1310418904403867\t0.8459115632544228\t1.2480662408671812\t \n+Phylum\tover\tEuryarchaeota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Phylum\tover\tVerrucomicrobiota\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n+Phylum\tover\tFusobacteriota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Phylum\tover\tSpirochaetota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Phylum\tover\tPatescibacteria\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n+Phylum\tover\tElusimicrobiota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Phylum\tover\tDeferribacterota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Class\tunder\tClostridia\t1053\t809\t446\t376\t1.0973188401780418\t0.2732172729268453\t0.8106446559367938\t \n+Class\tunder\tCoriobacteriia\t1053\t16\t446\t2\t0.2951233183856502\t0.11717288255667199\t0.6660353324273988\t \n+Class\tunder\tBacilli\t1053\t99\t446\t62\t1.4785976355483081\t0.024469955011065025\t0.3003130842267071\t \n+Class\tunder\tGammaproteobacteria\t1053\t15\t446\t6\t0.9443946188340807\t1.0\t1.1894273127753303\t \n+Class\tover\tBacteroidia\t1053\t63\t539\t60\t1.860588391200636\t0.0011351669261284913\t0.029190006671875494\t*\n+Class\tover\tClostridia\t1053\t809\t539\t377\t0.9104003889453298\t0.25364720652701717\t0.7694915254190409\t \n+Class\tover\tCampylobacteria\t1053\t4\t539\t4\t1.9536178107606679\t0.45541696874088\t0.956907249494456\t \n+Class\tover\tCoriobacteriia\t1053\t16\t539\t14\t1.7094155844155845\t0.17287093235368073\t0.7236457633409892\t \n+Class\tover\tVampirivibrionia\t1053\t11\t539\t11\t1.9536178107606679\t0.118258108369516\t0.6385937851953863\t \n+Class\tover\tDesulfovibrionia\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n+Class\tover\tBacilli\t1053\t99\t539\t31\t0.6117389104402091\t0.019927328662647383\t0.25620851137689493\t \n+Class\tover\tGammaproteobacteria\t1053\t15\t539\t7\t0.9116883116883117\t1.0\t1.1894273127753303\t \n+Class\tover\tNegativicutes\t1053\t16\t539\t16\t1.9536178107606679\t0.0616223676700078\t0.4893540962030031\t \n+Class\tover\tAlphaproteobacteria\t1053\t4\t539\t4\t1.9536178107606679\t0.45541696874088\t0.956907249494456\t \n+Class\tover\tMethanobacteria\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Class\tover\tLentisphaeria\t1053\t2\t539\t2\t1.9536178107606679\t0.6080045456777096\t1.0489535292842274\t \n+Class\tover\tFusobacteriia\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Class\tover\tSpirochaetia\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Class\tover\tActinobacteria\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+C'..b'303\t \n+Genus\tover\tMonoglobus\t1053\t14\t539\t6\t0.8372647760402863\t0.8156053043522413\t1.2302426378497495\t \n+Genus\tover\tDefluviitaleaceae UCG-011\t1053\t2\t539\t2\t1.9536178107606679\t0.6080045456777096\t1.0489535292842274\t \n+Genus\tover\tFrisingicoccus\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tSlackia\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n+Genus\tover\tCandidatus Saccharimonas\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tRomboutsia\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\t[Eubacterium] brachy group\t1053\t2\t539\t2\t1.9536178107606679\t0.6080045456777096\t1.0489535292842274\t \n+Genus\tover\tPaludicola\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tRikenella\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tAnaerofustis\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tRuminiclostridium\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tLachnospiraceae NK4A136 group\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n+Genus\tover\tRuminococcus\t1053\t4\t539\t4\t1.9536178107606679\t0.45541696874088\t0.956907249494456\t \n+Genus\tover\tOscillospira\t1053\t2\t539\t2\t1.9536178107606679\t0.6080045456777096\t1.0489535292842274\t \n+Genus\tover\tLachnospiraceae FCS020 group\t1053\t4\t539\t1\t0.48840445269016697\t0.6679746014045207\t1.0767351783834065\t \n+Genus\tover\tSubdoligranulum\t1053\t22\t539\t9\t0.7992072862202733\t0.7024005437634327\t1.1090534901527886\t \n+Genus\tover\tAnaerobiospirillum\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tShuttleworthia\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n+Genus\tover\tUC5-1-2E3\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tEisenbergiella\t1053\t9\t539\t3\t0.6512059369202227\t0.7607987197842374\t1.1771670735916568\t \n+Genus\tover\tEnorma\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tHoldemania\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tUCG-007\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tVerruc-01\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tMailhella\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tV9D2013 group\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tCollinsella\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tStreptococcus\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tIntestinimonas\t1053\t4\t539\t3\t1.465213358070501\t0.6948956697811112\t1.1069134562884957\t \n+Genus\tover\tUCG-009\t1053\t3\t539\t1\t0.6512059369202227\t1.0\t1.1894273127753303\t \n+Genus\tover\tButyricimonas\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tAnaerofilum\t1053\t7\t539\t1\t0.2790882586800954\t0.27940399260505516\t0.8155576000363772\t \n+Genus\tover\tPseudoflavonifractor\t1053\t11\t539\t1\t0.17760161916006073\t0.07043883619246838\t0.5433853077704703\t \n+Genus\tover\tButyricicoccus\t1053\t32\t539\t2\t0.12210111317254174\t0.00029765878402967713\t0.016073574337602564\t*\n+Genus\tover\t[Eubacterium] ventriosum group\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tFlavonifractor\t1053\t10\t539\t1\t0.1953617810760668\t0.1115103878662504\t0.6690623271975024\t \n+Genus\tover\tEndomicrobium\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tFournierella\t1053\t7\t539\t1\t0.2790882586800954\t0.27940399260505516\t0.8155576000363772\t \n+Genus\tover\tPrevotellaceae UCG-001\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tNegativibacillus\t1053\t4\t539\t1\t0.48840445269016697\t0.6679746014045207\t1.0767351783834065\t \n+Genus\tover\tHelicobacter\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tCoprococcus\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tMerdibacter\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n+Genus\tover\tMucispirillum\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/taxonomic_affiliation.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomic_affiliation.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,4322 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp8zb9uvoe/galaxy-dev\n+Clonage dans \'/tmp/tmp8zb9uvoe/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n+ __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n+ File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n+ if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n+ File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n+ self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n+ File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n+ return self.app.toolbox.dependency_manager.dependency_shell_commands(\n+ File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n+ self.build_cache(requirements, **kwds)\n+ File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n+ self.build_environment()\n+ File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n+ raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n+galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n+galaxy.jobs DEBUG 2023-04-25 09:01:44,478 [pN:main.1,p:115722,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp7b_u0d84/job_working_directory/000/3/outputs/galaxy_dataset_8699930c-0294-4403-a908-5f848a23c91a.dat to /tmp/tmp7b_u0d84/files/8/6/9/dataset_8699930c-0294-4403-a908-5f848a23c91a.dat\n+galaxy.jobs DEBUG 2023-04-25 09:01:44,479 [pN:main.1,p:115722,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp7b_u0d84/job_working_directory/000/3/outputs/galaxy_dataset_e879ac4e-3717-4720-94c4-4d80c890ec87.dat to /tmp/tmp7b_u0d84/files/e/8/7/dataset_e879ac4e-3717-4720-94c4-4d80c890ec87.dat\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_taxonomic_affiliation (Test #1): failed\n+Traceback (most recent call last):\n+ File "/home/vdarbot/.local/bin/planemo", line 5, in <module>\n+ from planemo.cli import planemo\n+ModuleNotFoundError: No module named \'planemo\'\n+Traceback (most recent call last):\n+ File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/bin/planemo", line 6, in <module>\n+ from planemo.cli import planemo\n+ File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/planemo/cli.py", line 14, in <module>\n+ from planemo.galaxy import profiles\n+ File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/planemo/galaxy/__init__.py", line 4, in <module>\n+ from .config import galaxy_config\n+ File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/planemo/galaxy/config.py", line 25, in <module>\n+ from planemo.galaxy.workflows import remote_runnable_to_workflow_id\n+ File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/planemo/galaxy/workflows.py", line 14, in <module>\n+ from ephemeris import (\n+ File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/ephemeris/generate_tool_list_from_ga_workflow_files.py", line 13, in <module>\n+ from .shed_tools import InstallRepoDict\n+ File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 62, in <module>\n+ from typing_extensions import (\n+ImportError: cannot import name \'NamedTuple\'\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/test/deseq2_preprocess.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/deseq2_preprocess.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,6538 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp833m4nfr/galaxy-dev\n+Clonage dans \'/tmp/tmp833m4nfr/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 60% (3720/6176)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6176)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6176)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6176)\rMise \xc3\xa0 jour des fichiers: 64% (3953/6176)\rMise \xc3\xa0 jour des fichiers: 65% (4015/6176)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6176)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6176)\rMise \xc3\xa0 jour des fichiers: 68% (4200/6176)\rMise \xc3\xa0 jour des fichiers: 69% (4262/6176)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6176)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6176)\rMise \xc3\xa0 jour des fichiers: 72% (4447/6176)\rMise \xc3\xa0 jour des fichiers: 73% (4509/6176)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6176)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6176)\rMise \xc3\xa0 jour des fichiers: 76% (4694/6176)\rMise \xc3\xa0 jour des fichiers: 77% (4756/6176)\rMise \xc3\xa0 jour des fichiers: 78% (4818/6176)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6176)\rMise \xc3\xa0 jour des fichiers: 80% (4941/6176)\rMise \xc3\xa0 jour des fichiers: 81% (5003/6176)\rMise \xc3\xa0 jour des fichiers: 82% (5065/6176)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6176)\rMise \xc3\xa0 jour des fichiers: 84% (5188/6176)\rMise \xc3\xa0 jour des fichiers: 85% (5250/6176)\rMise \xc3\xa0 jour des fichiers: 86% (5312/6176)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6176)\rMise \xc3\xa0 jour des fichiers: 88% (5435/6176)\rMise \xc3\xa0 jour des fichiers: 89% (5497/6176)\rMise \xc3\xa0 jour des fichiers: 90% (5559/6176)\rMise \xc3\xa0 jour des fichiers: 91% (5621/6176)\rMise \xc3\xa0 jour des fichiers: 92% (5682/6176)\rMise \xc3\xa0 jour des fichiers: 93% (5744/6176)\rMise \xc3\xa0 jour des fichiers: 94% (5806/6176)\rMise \xc3\xa0 jour des fichiers: 95% (5868/6176)\rMise \xc3\xa0 jour des fichiers: 96% (5929/6176)\rMise \xc3\xa0 jour des fichiers: 97% (5991/6176)\rMise \xc3\xa0 jour des fichiers: 98% (6053/6176)\rMise \xc3\xa0 jour des fichiers: 99% (6115/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: ma'..b'3b865de29fe8f6184\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; deseq2_preprocess.py --analysis \'ASV\' --data \'/tmp/tmpvxp3pnmm/files/9/6/5/dataset_9652a7ff-5a94-4a05-8bfb-5d14a84addfa.dat\' --out-Rdata \'/tmp/tmpvxp3pnmm/job_working_directory/000/2/outputs/galaxy_dataset_b36f895f-38be-49a4-a342-4c975571abee.dat\' --var \'EnvType\']\n+galaxy.jobs.runners DEBUG 2023-05-09 09:29:06,375 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpvxp3pnmm/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpvxp3pnmm/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmpvxp3pnmm/job_working_directory/000/2/working/asv_dds.Rdata" ] ; then cp "/tmp/tmpvxp3pnmm/job_working_directory/000/2/working/asv_dds.Rdata" "/tmp/tmpvxp3pnmm/job_working_directory/000/2/outputs/galaxy_dataset_b36f895f-38be-49a4-a342-4c975571abee.dat" ; fi; cd \'/tmp/tmpvxp3pnmm/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-09 09:29:06,412 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] (2) executing job script: /tmp/tmpvxp3pnmm/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 09:29:10,718 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 33253\n+galaxy.jobs.runners.local DEBUG 2023-05-09 09:29:10,718 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpvxp3pnmm/job_working_directory/000/2/galaxy_2.sh\n+galaxy.tool_util.output_checker INFO 2023-05-09 09:29:10,723 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] Job error detected, failing job. Reasons are [{\'type\': \'exit_code\', \'desc\': \'Fatal error: Exit code 127 ()\', \'exit_code\': 127, \'code_desc\': \'\', \'error_level\': 3}]\n+galaxy.jobs DEBUG 2023-05-09 09:29:10,748 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpvxp3pnmm/job_working_directory/000/2/outputs/galaxy_dataset_b36f895f-38be-49a4-a342-4c975571abee.dat to /tmp/tmpvxp3pnmm/files/b/3/6/dataset_b36f895f-38be-49a4-a342-4c975571abee.dat\n+galaxy.jobs DEBUG 2023-05-09 09:29:10,846 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] (2) setting dataset 2 state to ERROR\n+galaxy.jobs DEBUG 2023-05-09 09:29:10,992 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 2 executed (251.730 ms)\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/test/frogsfunc_function.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/frogsfunc_function.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1438 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmppl8bdhp8/galaxy-dev\n+Clonage dans \'/tmp/tmppl8bdhp8/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n+\n+[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n+[notice] To update, run: pip install --upgrade pip\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) ('..b'ctory.py", line 81, in build_command\n+ __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n+ File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n+ if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n+ File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n+ self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n+ File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n+ return self.app.toolbox.dependency_manager.dependency_shell_commands(\n+ File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n+ self.build_cache(requirements, **kwds)\n+ File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n+ [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n+ File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n+ self.build_environment()\n+ File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n+ raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n+galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n+galaxy.jobs DEBUG 2023-05-19 16:04:04,194 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_bb3e7f6f-d9c9-4d3c-b660-bc2929f6a46d.dat to /tmp/tmppl8bdhp8/files/b/b/3/dataset_bb3e7f6f-d9c9-4d3c-b660-bc2929f6a46d.dat\n+galaxy.jobs DEBUG 2023-05-19 16:04:04,196 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_99793432-3096-457e-981e-6c01776f985c.dat to /tmp/tmppl8bdhp8/files/9/9/7/dataset_99793432-3096-457e-981e-6c01776f985c.dat\n+galaxy.jobs DEBUG 2023-05-19 16:04:04,197 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_f64e4735-b301-4f8d-a533-b023e9c931ff.dat to /tmp/tmppl8bdhp8/files/f/6/4/dataset_f64e4735-b301-4f8d-a533-b023e9c931ff.dat\n+galaxy.jobs DEBUG 2023-05-19 16:04:04,198 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_9530a299-a956-452f-9dc4-64a85af59daf.dat to /tmp/tmppl8bdhp8/files/9/5/3/dataset_9530a299-a956-452f-9dc4-64a85af59daf.dat\n+galaxy.jobs DEBUG 2023-05-19 16:04:04,200 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_1c6b2c69-d5eb-4ea9-b577-646a5cf03b7c.dat to /tmp/tmppl8bdhp8/files/1/c/6/dataset_1c6b2c69-d5eb-4ea9-b577-646a5cf03b7c.dat\n+galaxy.jobs DEBUG 2023-05-19 16:04:04,201 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_b5ad6f82-05b9-4346-9e4e-cca9bb0e76c6.dat to /tmp/tmppl8bdhp8/files/b/5/a/dataset_b5ad6f82-05b9-4346-9e4e-cca9bb0e76c6.dat\n+galaxy.jobs DEBUG 2023-05-19 16:04:04,202 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_4c101ec2-bcd1-444b-ba28-6f52686c0009.dat to /tmp/tmppl8bdhp8/files/4/c/1/dataset_4c101ec2-bcd1-444b-ba28-6f52686c0009.dat\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGSFUNC_step1_placeseqs (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/test/frogsfunc_pathway.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/frogsfunc_pathway.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1058 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp13l64xd9/galaxy-dev\n+Clonage dans \'/tmp/tmp13l64xd9/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'iconda3/envs/mulled-v1-0ba21a4ae58f6e1dad373d217531ef4f6cd0ce45cfa2892e499f6ac681126382\')" ] || {\n+MAX_TRIES=3\n+COUNT=0\n+while [ $COUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0ba21a4ae58f6e1dad373d217531ef4f6cd0ce45cfa2892e499f6ac681126382\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; frogsfunc_pathways.py --input-file /tmp/tmp13l64xd9/files/5/a/5/dataset_5a556338-76d1-4220-9780-158113435cca.dat --map /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/test-data/databases/frogs_picrust2_db/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt --summary /tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_352c1def-fa51-4411-8e60-c5641dc4dc2d.dat]\n+galaxy.jobs.runners DEBUG 2023-05-09 11:56:47,840 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmp13l64xd9/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp13l64xd9/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmp13l64xd9/job_working_directory/000/2/working/report.html" ] ; then cp "/tmp/tmp13l64xd9/job_working_directory/000/2/working/report.html" "/tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_352c1def-fa51-4411-8e60-c5641dc4dc2d.dat" ; fi; \n+if [ -f "/tmp/tmp13l64xd9/job_working_directory/000/2/working/frogsfunc_pathways_unstrat.tsv" ] ; then cp "/tmp/tmp13l64xd9/job_working_directory/000/2/working/frogsfunc_pathways_unstrat.tsv" "/tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_7ffd4c72-ac4d-44c8-8707-22a80707e74d.dat" ; fi; cd \'/tmp/tmp13l64xd9/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-09 11:56:47,856 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] (2) executing job script: /tmp/tmp13l64xd9/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 11:57:58,456 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 58241\n+galaxy.jobs.runners.local DEBUG 2023-05-09 11:57:58,456 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmp13l64xd9/job_working_directory/000/2/galaxy_2.sh\n+galaxy.jobs DEBUG 2023-05-09 11:57:58,489 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_352c1def-fa51-4411-8e60-c5641dc4dc2d.dat to /tmp/tmp13l64xd9/files/3/5/2/dataset_352c1def-fa51-4411-8e60-c5641dc4dc2d.dat\n+galaxy.jobs DEBUG 2023-05-09 11:57:58,489 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_7ffd4c72-ac4d-44c8-8707-22a80707e74d.dat to /tmp/tmp13l64xd9/files/7/f/f/dataset_7ffd4c72-ac4d-44c8-8707-22a80707e74d.dat\n+galaxy.model.metadata DEBUG 2023-05-09 11:57:58,561 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 2\n+galaxy.model.metadata DEBUG 2023-05-09 11:57:58,581 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 3\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGSFUNC_step4_pathways (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/test/frogsfunc_pathways.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/frogsfunc_pathways.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1910 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpbjte8_kh/galaxy-dev\n+Clonage dans \'/tmp/tmpbjte8_kh/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 47% (2961/6177)\rMise \xc3\xa0 jour des fichiers: 48% (2965/6177)\rMise \xc3\xa0 jour des fichiers: 49% (3027/6177)\rMise \xc3\xa0 jour des fichiers: 50% (3089/6177)\rMise \xc3\xa0 jour des fichiers: 51% (3151/6177)\rMise \xc3\xa0 jour des fichiers: 52% (3213/6177)\rMise \xc3\xa0 jour des fichiers: 53% (3274/6177)\rMise \xc3\xa0 jour des fichiers: 54% (3336/6177)\rMise \xc3\xa0 jour des fichiers: 55% (3398/6177)\rMise \xc3\xa0 jour des fichiers: 56% (3460/6177)\rMise \xc3\xa0 jour des fichiers: 57% (3521/6177)\rMise \xc3\xa0 jour des fichiers: 58% (3583/6177)\rMise \xc3\xa0 jour des fichiers: 59% (3645/6177)\rMise \xc3\xa0 jour des fichiers: 60% (3707/6177)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6177)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6177)\rMise \xc3\xa0 jour des fichiers: 63% (3892/6177)\rMise \xc3\xa0 jour des fichiers: 64% (3954/6177)\rMise \xc3\xa0 jour des fichiers: 65% (4016/6177)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6177)\rMise \xc3\xa0 jour des fichiers: 67% (4139/6177)\rMise \xc3\xa0 jour des fichiers: 68% (4201/6177)\rMise \xc3\xa0 jour des fichiers: 69% (4263/6177)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6177)\rMise \xc3\xa0 jour des fichiers: 71% (4386/6177)\rMise \xc3\xa0 jour des fichiers: 72% (4448/6177)\rMise \xc3\xa0 jour des fichiers: 73% (4510/6177)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6177)\rMise \xc3\xa0 jour des fichiers: 75% (4633/6177)\rMise \xc3\xa0 jour des fichiers: 76% (4695/6177)\rMise \xc3\xa0 jour des fichiers: 77% (4757/6177)\rMise \xc3\xa0 jour des fichiers: 78% (4819/6177)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6177)\rMise \xc3\xa0 jour des fichiers: 80% (4942/6177)\rMise \xc3\xa0 jour des fichiers: 81% (5004/6177)\rMise \xc3\xa0 jour des fichiers: 82% (5066/6177)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6177)\rMise \xc3\xa0 jour des fichiers: 84% (5189/6177)\rMise \xc3\xa0 jour des fichiers: 85% (5251/6177)\rMise \xc3\xa0 jour des fichiers: 86% (5313/6177)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6177)\rMise \xc3\xa0 jour des fichiers: 88% (5436/6177)\rMise \xc3\xa0 jour des fichiers: 89% (5498/6177)\rMise \xc3\xa0 jour des fichiers: 90% (5560/6177)\rMise \xc3\xa0 jour des fichiers: 91% (5622/6177)\rMise \xc3\xa0 jour des fichiers: 92% (5683/6177)\rMise \xc3\xa0 jour des fichiers: 93% (5745/6177)\rMise \xc3\xa0 jour des fichiers: 94% (5807/6177)\rMise \xc3\xa0 jour des fichiers: 95% (5869/6177)\rMise \xc3\xa0 jour des fichiers: 96% (5930/6177)\rMise \xc3\xa0 jour des fichiers: 97% (5992/6177)\rMise \xc3\xa0 jour des fichiers: 98% (6054/6177)\rMise \xc3\xa0 jour des fichiers: 99% (6116/6177)\rMise \xc3\xa0 jour des fichiers: 100% (6177/6177)\rMise \xc3\xa0 jour des fichiers: 100% (6177/6177), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement alr'..b'MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; frogsfunc_pathways.py --input-file /tmp/tmpbjte8_kh/files/e/5/d/dataset_e5dac98d-9aff-4195-bdff-9aff88e1def9.dat --map /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/test-data/databases/frogs_picrust2_db/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt --summary /tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_75fd79d2-e1a2-4cf6-a728-006bdab8dcd6.dat]\n+galaxy.jobs.runners DEBUG 2023-05-19 16:14:01,505 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpbjte8_kh/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpbjte8_kh/job_working_directory/000/2/galaxy_2.ec; \n+if [ -f "/tmp/tmpbjte8_kh/job_working_directory/000/2/working/report.html" ] ; then cp "/tmp/tmpbjte8_kh/job_working_directory/000/2/working/report.html" "/tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_75fd79d2-e1a2-4cf6-a728-006bdab8dcd6.dat" ; fi; \n+if [ -f "/tmp/tmpbjte8_kh/job_working_directory/000/2/working/frogsfunc_pathways_unstrat.tsv" ] ; then cp "/tmp/tmpbjte8_kh/job_working_directory/000/2/working/frogsfunc_pathways_unstrat.tsv" "/tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_6747e83c-e4f3-4d4c-b0eb-0bda0b685bd2.dat" ; fi; cd \'/tmp/tmpbjte8_kh/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-19 16:14:01,537 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmpbjte8_kh/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-19 16:15:34,372 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 350452\n+galaxy.jobs.runners.local DEBUG 2023-05-19 16:15:34,380 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpbjte8_kh/job_working_directory/000/2/galaxy_2.sh\n+galaxy.tool_util.output_checker INFO 2023-05-19 16:15:34,404 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] Job error detected, failing job. Reasons are [{\'type\': \'exit_code\', \'desc\': \'Fatal error: Exit code 1 ()\', \'exit_code\': 1, \'code_desc\': \'\', \'error_level\': 3}]\n+galaxy.jobs DEBUG 2023-05-19 16:15:34,502 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_75fd79d2-e1a2-4cf6-a728-006bdab8dcd6.dat to /tmp/tmpbjte8_kh/files/7/5/f/dataset_75fd79d2-e1a2-4cf6-a728-006bdab8dcd6.dat\n+galaxy.jobs DEBUG 2023-05-19 16:15:34,510 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_6747e83c-e4f3-4d4c-b0eb-0bda0b685bd2.dat to /tmp/tmpbjte8_kh/files/6/7/4/dataset_6747e83c-e4f3-4d4c-b0eb-0bda0b685bd2.dat\n+galaxy.jobs DEBUG 2023-05-19 16:15:34,756 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] (2) setting dataset 2 state to ERROR\n+galaxy.jobs DEBUG 2023-05-19 16:15:34,772 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] (2) setting dataset 3 state to ERROR\n+galaxy.jobs DEBUG 2023-05-19 16:15:35,182 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 2 executed (719.836 ms)\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGSFUNC_step4_pathways (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/test/frogsfunc_placeseqs.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/frogsfunc_placeseqs.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,7143 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpnylvbdf7/galaxy-dev\n+Clonage dans \'/tmp/tmpnylvbdf7/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 53% (3331/6176)\rMise \xc3\xa0 jour des fichiers: 54% (3336/6176)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6176)\rMise \xc3\xa0 jour des fichiers: 56% (3459/6176)\rMise \xc3\xa0 jour des fichiers: 57% (3521/6176)\rMise \xc3\xa0 jour des fichiers: 58% (3583/6176)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6176)\rMise \xc3\xa0 jour des fichiers: 60% (3706/6176)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6176)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6176)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6176)\rMise \xc3\xa0 jour des fichiers: 64% (3953/6176)\rMise \xc3\xa0 jour des fichiers: 65% (4015/6176)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6176)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6176)\rMise \xc3\xa0 jour des fichiers: 68% (4200/6176)\rMise \xc3\xa0 jour des fichiers: 69% (4262/6176)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6176)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6176)\rMise \xc3\xa0 jour des fichiers: 72% (4447/6176)\rMise \xc3\xa0 jour des fichiers: 73% (4509/6176)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6176)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6176)\rMise \xc3\xa0 jour des fichiers: 76% (4694/6176)\rMise \xc3\xa0 jour des fichiers: 77% (4756/6176)\rMise \xc3\xa0 jour des fichiers: 78% (4818/6176)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6176)\rMise \xc3\xa0 jour des fichiers: 80% (4941/6176)\rMise \xc3\xa0 jour des fichiers: 81% (5003/6176)\rMise \xc3\xa0 jour des fichiers: 82% (5065/6176)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6176)\rMise \xc3\xa0 jour des fichiers: 84% (5188/6176)\rMise \xc3\xa0 jour des fichiers: 85% (5250/6176)\rMise \xc3\xa0 jour des fichiers: 86% (5312/6176)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6176)\rMise \xc3\xa0 jour des fichiers: 88% (5435/6176)\rMise \xc3\xa0 jour des fichiers: 89% (5497/6176)\rMise \xc3\xa0 jour des fichiers: 90% (5559/6176)\rMise \xc3\xa0 jour des fichiers: 91% (5621/6176)\rMise \xc3\xa0 jour des fichiers: 92% (5682/6176)\rMise \xc3\xa0 jour des fichiers: 93% (5744/6176)\rMise \xc3\xa0 jour des fichiers: 94% (5806/6176)\rMise \xc3\xa0 jour des fichiers: 95% (5868/6176)\rMise \xc3\xa0 jour des fichiers: 96% (5929/6176)\rMise \xc3\xa0 jour des fichiers: 97% (5991/6176)\rMise \xc3\xa0 jour des fichiers: 98% (6053/6176)\rMise \xc3\xa0 jour des fichiers: 99% (6115/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, v'..b'.handler INFO 2023-05-09 12:08:46,918 [pN:main.1,p:59716,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n+galaxy.jobs DEBUG 2023-05-09 12:08:47,030 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] Job wrapper for Job [2] prepared (104.686 ms)\n+galaxy.jobs.command_factory INFO 2023-05-09 12:08:47,047 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] Built script [/tmp/tmpqihjec1x/job_working_directory/000/2/tool_script.sh] for tool command [python \'/tmp/tmpqihjec1x/galaxy-dev/tools/data_source/upload.py\' \'/tmp/tmpqihjec1x/galaxy-dev\' \'/tmp/tmpqihjec1x/job_working_directory/000/2/registry.xml\' \'/tmp/tmpqihjec1x/tmp/upload_params_jmuygh1j\' \'2:/tmp/tmpqihjec1x/job_working_directory/000/2/working/dataset_1c58f0a1-9180-4a1c-a069-2af497d19cc7_files:/tmp/tmpqihjec1x/job_working_directory/000/2/outputs/galaxy_dataset_1c58f0a1-9180-4a1c-a069-2af497d19cc7.dat\']\n+galaxy.jobs.runners DEBUG 2023-05-09 12:08:47,195 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpqihjec1x/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpqihjec1x/job_working_directory/000/2/galaxy_2.ec; cd \'/tmp/tmpqihjec1x/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-09 12:08:47,216 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] (2) executing job script: /tmp/tmpqihjec1x/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 12:08:52,499 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 59735\n+galaxy.jobs.runners.local DEBUG 2023-05-09 12:08:52,500 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpqihjec1x/job_working_directory/000/1/galaxy_1.sh\n+galaxy.jobs DEBUG 2023-05-09 12:08:52,569 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpqihjec1x/job_working_directory/000/1/outputs/galaxy_dataset_1825cf33-e6b6-4ab5-aaec-c075b0ac7d36.dat to /tmp/tmpqihjec1x/files/1/8/2/dataset_1825cf33-e6b6-4ab5-aaec-c075b0ac7d36.dat\n+galaxy.model.metadata DEBUG 2023-05-09 12:08:52,678 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1\n+galaxy.jobs DEBUG 2023-05-09 12:08:52,768 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 1 executed (218.260 ms)\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 12:08:53,940 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 59756\n+galaxy.jobs.runners.local DEBUG 2023-05-09 12:08:53,940 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmpqihjec1x/job_working_directory/000/2/galaxy_2.sh\n+galaxy.jobs DEBUG 2023-05-09 12:08:53,975 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmpqihjec1x/job_working_directory/000/2/outputs/galaxy_dataset_1c58f0a1-9180-4a1c-a069-2af497d19cc7.dat to /tmp/tmpqihjec1x/files/1/c/5/dataset_1c58f0a1-9180-4a1c-a069-2af497d19cc7.dat\n+galaxy.model.metadata DEBUG 2023-05-09 12:08:54,077 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 2\n+galaxy.jobs DEBUG 2023-05-09 12:08:54,186 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] job_wrapper.finish for job 2 executed (220.424 ms)\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGSFUNC_step1_placeseqs (Test #1): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/test/preprocess.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/preprocess.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,2182 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp7qbuuh95/galaxy-dev\n+Clonage dans \'/tmp/tmp7qbuuh95/galaxy-dev\'...\n+fait.\n+Mise \xc3\xa0 jour des fichiers: 45% (2792/6176)\rMise \xc3\xa0 jour des fichiers: 46% (2841/6176)\rMise \xc3\xa0 jour des fichiers: 47% (2903/6176)\rMise \xc3\xa0 jour des fichiers: 48% (2965/6176)\rMise \xc3\xa0 jour des fichiers: 49% (3027/6176)\rMise \xc3\xa0 jour des fichiers: 50% (3088/6176)\rMise \xc3\xa0 jour des fichiers: 51% (3150/6176)\rMise \xc3\xa0 jour des fichiers: 52% (3212/6176)\rMise \xc3\xa0 jour des fichiers: 53% (3274/6176)\rMise \xc3\xa0 jour des fichiers: 54% (3336/6176)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6176)\rMise \xc3\xa0 jour des fichiers: 56% (3459/6176)\rMise \xc3\xa0 jour des fichiers: 57% (3521/6176)\rMise \xc3\xa0 jour des fichiers: 58% (3583/6176)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6176)\rMise \xc3\xa0 jour des fichiers: 60% (3706/6176)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6176)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6176)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6176)\rMise \xc3\xa0 jour des fichiers: 64% (3953/6176)\rMise \xc3\xa0 jour des fichiers: 65% (4015/6176)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6176)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6176)\rMise \xc3\xa0 jour des fichiers: 68% (4200/6176)\rMise \xc3\xa0 jour des fichiers: 69% (4262/6176)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6176)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6176)\rMise \xc3\xa0 jour des fichiers: 72% (4447/6176)\rMise \xc3\xa0 jour des fichiers: 73% (4509/6176)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6176)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6176)\rMise \xc3\xa0 jour des fichiers: 76% (4694/6176)\rMise \xc3\xa0 jour des fichiers: 77% (4756/6176)\rMise \xc3\xa0 jour des fichiers: 78% (4818/6176)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6176)\rMise \xc3\xa0 jour des fichiers: 80% (4941/6176)\rMise \xc3\xa0 jour des fichiers: 81% (5003/6176)\rMise \xc3\xa0 jour des fichiers: 82% (5065/6176)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6176)\rMise \xc3\xa0 jour des fichiers: 84% (5188/6176)\rMise \xc3\xa0 jour des fichiers: 85% (5250/6176)\rMise \xc3\xa0 jour des fichiers: 86% (5312/6176)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6176)\rMise \xc3\xa0 jour des fichiers: 88% (5435/6176)\rMise \xc3\xa0 jour des fichiers: 89% (5497/6176)\rMise \xc3\xa0 jour des fichiers: 90% (5559/6176)\rMise \xc3\xa0 jour des fichiers: 91% (5621/6176)\rMise \xc3\xa0 jour des fichiers: 92% (5682/6176)\rMise \xc3\xa0 jour des fichiers: 93% (5744/6176)\rMise \xc3\xa0 jour des fichiers: 94% (5806/6176)\rMise \xc3\xa0 jour des fichiers: 95% (5868/6176)\rMise \xc3\xa0 jour des fichiers: 96% (5929/6176)\rMise \xc3\xa0 jour des fichiers: 97% (5991/6176)\rMise \xc3\xa0 jour des fichiers: 98% (6053/6176)\rMise \xc3\xa0 jour des fichiers: 99% (6115/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176), fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome'..b'.1,p:159691,tN:WSGI_0] (Job[id=2,tool_id=upload1]) Handler \'_default_\' assigned using \'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED\' assignment method\n+galaxy.tools.execute DEBUG 2023-05-09 13:05:04,671 [pN:main.1,p:159691,tN:WSGI_0] Created 1 job(s) for tool upload1 request (190.789 ms)\n+galaxy.jobs.mapper DEBUG 2023-05-09 13:05:04,940 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: upload_dest\n+galaxy.jobs.handler DEBUG 2023-05-09 13:05:04,949 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner\n+galaxy.jobs DEBUG 2023-05-09 13:05:05,010 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: upload_dest)\n+galaxy.jobs DEBUG 2023-05-09 13:05:05,020 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmpkmhzemjv/job_working_directory/000/2\n+galaxy.jobs.runners DEBUG 2023-05-09 13:05:05,046 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] Job [2] queued (97.041 ms)\n+galaxy.jobs.handler INFO 2023-05-09 13:05:05,057 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n+galaxy.jobs DEBUG 2023-05-09 13:05:05,185 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] Job wrapper for Job [2] prepared (93.411 ms)\n+galaxy.jobs.command_factory INFO 2023-05-09 13:05:05,199 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] Built script [/tmp/tmpkmhzemjv/job_working_directory/000/2/tool_script.sh] for tool command [python \'/tmp/tmpkmhzemjv/galaxy-dev/tools/data_source/upload.py\' \'/tmp/tmpkmhzemjv/galaxy-dev\' \'/tmp/tmpkmhzemjv/job_working_directory/000/2/registry.xml\' \'/tmp/tmpkmhzemjv/tmp/upload_params_0b03oqzh\' \'2:/tmp/tmpkmhzemjv/job_working_directory/000/2/working/dataset_e02e3022-5cb8-4a1a-837b-97a74809bd36_files:/tmp/tmpkmhzemjv/job_working_directory/000/2/outputs/galaxy_dataset_e02e3022-5cb8-4a1a-837b-97a74809bd36.dat\']\n+galaxy.jobs.runners DEBUG 2023-05-09 13:05:05,251 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] (2) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmpkmhzemjv/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpkmhzemjv/job_working_directory/000/2/galaxy_2.ec; cd \'/tmp/tmpkmhzemjv/job_working_directory/000/2\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-09 13:05:05,272 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] (2) executing job script: /tmp/tmpkmhzemjv/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 13:05:09,889 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 159745\n+galaxy.jobs.runners.local DEBUG 2023-05-09 13:05:09,890 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpkmhzemjv/job_working_directory/000/2/galaxy_2.sh\n+\n+galaxy.jobs DEBUG 2023-05-09 13:05:12,440 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpkmhzemjv/job_working_directory/000/2/outputs/galaxy_dataset_e02e3022-5cb8-4a1a-837b-97a74809bd36.dat to /tmp/tmpkmhzemjv/files/e/0/2/dataset_e02e3022-5cb8-4a1a-837b-97a74809bd36.dat\n+galaxy.model.metadata DEBUG 2023-05-09 13:05:12,481 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 2\n+\n+Shut down\n+supervisord has terminated\n+There were problems with 2 test(s) - out of 2 test(s) executed. See tool_test_output.html for detailed breakdown.\n+FROGS_preprocess (Test #1): failed\n+FROGS_preprocess (Test #2): failed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/test/taxo_affi.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/taxo_affi.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1698 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp_1t0d9vn/galaxy-dev\n+Clonage dans \'/tmp/tmp_1t0d9vn/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-2048}/1024)) && taxonomic_affiliation.py --reference \'/home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/test-data/databases/frogs_db_data/ITS1.rdp.fasta\' --taxonomy-ranks Domain Phylum Class Order Family Genus Species --input-biom \'/tmp/tmp_1t0d9vn/files/7/6/8/dataset_7684e6bd-7410-46ed-ac32-1bc9f98e4c8a.dat\' --input-fasta \'/tmp/tmp_1t0d9vn/files/4/f/1/dataset_4f106e37-c173-4a9f-ba80-a5a8566725ab.dat\' --output-biom \'/tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_129bd961-982f-4e88-b3d9-32169c06dfbb.dat\' --summary \'/tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_59c1907c-4060-4f2c-9634-d2b7f6659ecb.dat\' --nb-cpus ${GALAXY_SLOTS:-1} --java-mem $GALAXY_MEMORY_GB --rdp]\n+galaxy.jobs.runners DEBUG 2023-05-09 11:18:01,194 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmp_1t0d9vn/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp_1t0d9vn/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmp_1t0d9vn/job_working_directory/000/3/working/affiliation.biom" ] ; then cp "/tmp/tmp_1t0d9vn/job_working_directory/000/3/working/affiliation.biom" "/tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_129bd961-982f-4e88-b3d9-32169c06dfbb.dat" ; fi; \n+if [ -f "/tmp/tmp_1t0d9vn/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmp_1t0d9vn/job_working_directory/000/3/working/report.html" "/tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_59c1907c-4060-4f2c-9634-d2b7f6659ecb.dat" ; fi; cd \'/tmp/tmp_1t0d9vn/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-09 11:18:01,206 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] (3) executing job script: /tmp/tmp_1t0d9vn/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 11:18:05,850 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 54104\n+galaxy.jobs.runners.local DEBUG 2023-05-09 11:18:05,850 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmp_1t0d9vn/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-05-09 11:18:05,899 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_129bd961-982f-4e88-b3d9-32169c06dfbb.dat to /tmp/tmp_1t0d9vn/files/1/2/9/dataset_129bd961-982f-4e88-b3d9-32169c06dfbb.dat\n+galaxy.jobs DEBUG 2023-05-09 11:18:05,899 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_59c1907c-4060-4f2c-9634-d2b7f6659ecb.dat to /tmp/tmp_1t0d9vn/files/5/9/c/dataset_59c1907c-4060-4f2c-9634-d2b7f6659ecb.dat\n+galaxy.model.metadata DEBUG 2023-05-09 11:18:05,930 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.model.metadata DEBUG 2023-05-09 11:18:05,939 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.jobs DEBUG 2023-05-09 11:18:06,016 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] job_wrapper.finish for job 3 executed (123.811 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_taxonomic_affiliation (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/tool_test_output_all.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tool_test_output_all.html Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,291 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <meta http-equiv="X-UA-Compatible" content="IE=edge">\n+ <meta name="viewport" content="width=device-width, initial-scale=1">\n+ <title>Test Results (powered by Planemo)</title>\n+\n+ <!-- Bootstrap -->\n+ <style>/*!\n+ * Bootstrap v3.3.1 (http://getbootstrap.com)\n+ * Copyright 2011-2014 Twitter, Inc.\n+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)\n+ *//*! normalize.css v3.0.2 | MIT License | git.io/normalize */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background-color:transparent}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0;font-size:2em}mark{color:#000;background:#ff0}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}pre{overflow:auto}code,kbd,pre,samp{font-family:monospace,monospace;font-size:1em}button,input,optgroup,select,textarea{margin:0;font:inherit;color:inherit}button{overflow:visible}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0}input{line-height:normal}input[type=checkbox],input[type=radio]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;padding:0}input[type=number]::-webkit-inner-spin-button,input[type=number]::-webkit-outer-spin-button{height:auto}input[type=search]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield}input[type=search]::-webkit-search-cancel-button,input[type=search]::-webkit-search-decoration{-webkit-appearance:none}fieldset{padding:.35em .625em .75em;margin:0 2px;border:1px solid silver}legend{padding:0;border:0}textarea{overflow:auto}optgroup{font-weight:700}table{border-spacing:0;border-collapse:collapse}td,th{padding:0}/*! 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format(\'svg\')}.glyphicon{position:relative;top:1px;display:inline-block;font-family:\'Glyphi'..b"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'));\n+ </script>\n+ </body>\n+</html>\n\\ No newline at end of file\n" |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/tree.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,6116 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpeb913vpo/galaxy-dev\n+Clonage dans \'/tmp/tmpeb913vpo/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'a3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-663b8adea9f89270af0e128d394b30e933a8f81efb8a32d25f7cdca23513d2c5\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; tree.py --input-sequences \'/tmp/tmptzzsg46p/files/f/6/7/dataset_f67e887f-af82-4a01-89bf-d98ea02d75f7.dat\' --biom-file \'/tmp/tmptzzsg46p/files/4/7/f/dataset_47fab374-6bc3-434c-8ace-d4be1ed43098.dat\' --nb-cpus ${GALAXY_SLOTS:-1} --out-tree \'/tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_d5f9f3dd-3929-4ff5-a24d-81dbe0035332.dat\' --html \'/tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_472c1815-c603-4fb0-9d4b-f0d2c9015184.dat\']\n+galaxy.jobs.runners DEBUG 2023-05-04 11:20:12,285 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmptzzsg46p/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmptzzsg46p/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmptzzsg46p/job_working_directory/000/3/working/tree.nwk" ] ; then cp "/tmp/tmptzzsg46p/job_working_directory/000/3/working/tree.nwk" "/tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_d5f9f3dd-3929-4ff5-a24d-81dbe0035332.dat" ; fi; \n+if [ -f "/tmp/tmptzzsg46p/job_working_directory/000/3/working/summary.html" ] ; then cp "/tmp/tmptzzsg46p/job_working_directory/000/3/working/summary.html" "/tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_472c1815-c603-4fb0-9d4b-f0d2c9015184.dat" ; fi; cd \'/tmp/tmptzzsg46p/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-05-04 11:20:12,299 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] (3) executing job script: /tmp/tmptzzsg46p/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 11:20:30,580 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 181876\n+galaxy.jobs.runners.local DEBUG 2023-05-04 11:20:30,581 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmptzzsg46p/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-05-04 11:20:30,635 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_d5f9f3dd-3929-4ff5-a24d-81dbe0035332.dat to /tmp/tmptzzsg46p/files/d/5/f/dataset_d5f9f3dd-3929-4ff5-a24d-81dbe0035332.dat\n+galaxy.jobs DEBUG 2023-05-04 11:20:30,635 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_472c1815-c603-4fb0-9d4b-f0d2c9015184.dat to /tmp/tmptzzsg46p/files/4/7/2/dataset_472c1815-c603-4fb0-9d4b-f0d2c9015184.dat\n+galaxy.model.metadata DEBUG 2023-05-04 11:20:30,688 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.model.metadata DEBUG 2023-05-04 11:20:30,703 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.jobs DEBUG 2023-05-04 11:20:30,794 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 3 executed (171.644 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_Tree (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b test-data/tsv_to_biom.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tsv_to_biom.log Tue May 23 07:59:04 2023 +0000 |
| [ |
| b'@@ -0,0 +1,1032 @@\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n+git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n+git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp983sks31/galaxy-dev\n+Clonage dans \'/tmp/tmp983sks31/galaxy-dev\'...\n+fait.\n+if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n+galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n+Activated a virtualenv for Galaxy\n+/home/vdarbot/.planemo/gx_venv_3\n+Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n+Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n+Initializing static/welcome.html from welcome.html.sample\n+Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n+Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n+Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n+WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n+You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n+Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n+Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n+Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n+Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n+Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n+Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n+Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n+Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n+Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n+Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n+Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n+Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n+Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'OUNT -lt $MAX_TRIES ]; do\n+ . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n+ if [ $? -eq 0 ];then\n+ break\n+ else\n+ let COUNT=COUNT+1\n+ if [ $COUNT -eq $MAX_TRIES ];then\n+ echo "Failed to activate conda environment! Error was:"\n+ cat conda_activate.log\n+ exit 1\n+ fi\n+ sleep 10s\n+ fi\n+done\n+} ; tsv_to_biom.py --input-tsv \'/tmp/tmp983sks31/files/5/e/a/dataset_5eadd393-2680-4ca6-9e9b-e44a65ef8e5c.dat\' --output-biom \'/tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d869dda1-1a92-4598-a1f5-1474a87202f1.dat\' --input-multi-affi \'/tmp/tmp983sks31/files/0/e/d/dataset_0ed28cc9-6a1e-4fb0-83dd-dacc95e890b5.dat\' --output-fasta \'/tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d30d4afa-9491-47be-b5b7-42236b5ec488.dat\']\n+galaxy.jobs.runners DEBUG 2023-04-26 10:47:14,358 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] (3) command is: mkdir -p working outputs configs\n+if [ -d _working ]; then\n+ rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n+else\n+ cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n+fi\n+cd working; /bin/bash /tmp/tmp983sks31/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp983sks31/job_working_directory/000/3/galaxy_3.ec; \n+if [ -f "/tmp/tmp983sks31/job_working_directory/000/3/working/abundance.biom" ] ; then cp "/tmp/tmp983sks31/job_working_directory/000/3/working/abundance.biom" "/tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d869dda1-1a92-4598-a1f5-1474a87202f1.dat" ; fi; \n+if [ -f "/tmp/tmp983sks31/job_working_directory/000/3/working/seed.fasta" ] ; then cp "/tmp/tmp983sks31/job_working_directory/000/3/working/seed.fasta" "/tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d30d4afa-9491-47be-b5b7-42236b5ec488.dat" ; fi; cd \'/tmp/tmp983sks31/job_working_directory/000/3\'; \n+[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n+galaxy.jobs.runners.local DEBUG 2023-04-26 10:47:14,408 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmp983sks31/job_working_directory/000/3/galaxy_3.sh\n+\n+galaxy.jobs.runners.util.process_groups DEBUG 2023-04-26 10:47:20,391 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 209044\n+galaxy.jobs.runners.local DEBUG 2023-04-26 10:47:20,392 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmp983sks31/job_working_directory/000/3/galaxy_3.sh\n+galaxy.jobs DEBUG 2023-04-26 10:47:20,427 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d869dda1-1a92-4598-a1f5-1474a87202f1.dat to /tmp/tmp983sks31/files/d/8/6/dataset_d869dda1-1a92-4598-a1f5-1474a87202f1.dat\n+galaxy.jobs DEBUG 2023-04-26 10:47:20,427 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d30d4afa-9491-47be-b5b7-42236b5ec488.dat to /tmp/tmp983sks31/files/d/3/0/dataset_d30d4afa-9491-47be-b5b7-42236b5ec488.dat\n+galaxy.model.metadata DEBUG 2023-04-26 10:47:20,457 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n+galaxy.model.metadata DEBUG 2023-04-26 10:47:20,466 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 4\n+galaxy.jobs DEBUG 2023-04-26 10:47:20,552 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (132.107 ms)\n+\n+Shut down\n+supervisord has terminated\n+All 1 test(s) executed passed.\n+FROGS_tsv_to_biom (Test #1): passed\n' |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b tool-data/frogs_HVL_db.loc.sample --- a/tool-data/frogs_HVL_db.loc.sample Tue Jul 19 11:11:16 2022 +0000 +++ b/tool-data/frogs_HVL_db.loc.sample Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -27,10 +27,6 @@ #<unique_database_name> <name> <file_path> # #First column will be the visible name in galaxy. -#So, for example, if you have UNITE 7.1 ITS1 (only!) stored -#in /galaxy_databanks/ITS/UNITE_7.1/UNITE_ITS1.fasta -#then the HVL_db.loc entry would look like this: -# # # # EXAMPLE FOR TEST : @@ -40,5 +36,5 @@ # # PRODUCTION FILES, with FROGS toolsheds path to adapt (Galaxy_dir and XXXXXX) # -#UNITE_7.1_ITS1 UNITE 7.1 ITS1 <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/tool-data/databases/frogs_HVL_db_data/Unite_s_7.1_20112016_ITS1.fasta -#UNITE_7.1_ITS2 UNITE 7.1 ITS2 <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/tool-data/databases/frogs_HVL_db_data/Unite_s_7.1_20112016_ITS2.fasta +#UNITE_7.1_ITS1 UNITE 7.1 ITS1 <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/tool-data/Unite_s_7.1_20112016_ITS1.fasta +#UNITE_7.1_ITS2 UNITE 7.1 ITS2 <Galaxy_dir>/database/shed_tools/toolshed.g2.bx.psu.edu/repos/frogs/frogs/XXXXXX/frogs/tool-data/Unite_s_7.1_20112016_ITS2.fasta |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b tool-data/frogs_picrust2_default_dir.loc.sample --- a/tool-data/frogs_picrust2_default_dir.loc.sample Tue Jul 19 11:11:16 2022 +0000 +++ b/tool-data/frogs_picrust2_default_dir.loc.sample Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -25,7 +25,7 @@ # #The indicated path is the one if you do not change the default galaxy config of conda directory. # -#<identifiant> <marker_gene> <path_to_default_dir> +#<identifiant> <marker_gene> <path_to_default_dir> <path_to_marker_copy_numbers> <placement_tool> # #default dir must contain these files: # @@ -36,6 +36,7 @@ #-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_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/ +#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryiotic/pro_ref/16S_counts.txt.gz epa-ng +#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryiotic/pro_ref/16S_counts.txt.gz sepp +#picrust2_default_dir_ITS ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_ITS/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryiotic/fungi/fungi_ITS/ITS_counts.txt.gz epa-ng +#picrust2_default_dir_18S 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_18S/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryiotic/fungi/fungi_18S/18S_counts.txt.gz epa-ng |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Jul 19 11:11:16 2022 +0000 +++ b/tool_data_table_conf.xml.sample Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -14,7 +14,7 @@ </table> <!-- Locations of picrust2 default directory --> <table name="frogs_picrust2_default_dir" comment_char="#"> - <columns>value, name, path</columns> + <columns>value, name, dir, path, placement_tool</columns> <file path="${__HERE__}/tool-data/frogs_picrust2_default_dir.loc" /> </table> <!-- Locations of picrust2 description files directory --> @@ -33,4 +33,4 @@ <columns>marker, path, value, name </columns> <file path="${__HERE__}/tool-data/frogs_picrust2_pathway_map.loc" /> </table> -</tables> +</tables> \ No newline at end of file |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Tue Jul 19 11:11:16 2022 +0000 +++ b/tool_data_table_conf.xml.test Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -14,7 +14,7 @@ </table> <!-- Locations of picrust2 default directory --> <table name="frogs_picrust2_default_dir" comment_char="#"> - <columns>value, name, path</columns> + <columns>value, name, dir, path, placement_tool</columns> <file path="${__HERE__}/test-data/databases/frogs_picrust2_default_dir.loc" /> </table> <!-- Locations of picrust2 marker table files --> @@ -27,4 +27,4 @@ <columns>marker, path, value, name </columns> <file path="${__HERE__}/test-data/databases/frogs_picrust2_pathway_map.loc" /> </table> -</tables> +</tables> \ No newline at end of file |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b tree.xml --- a/tree.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/tree.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGS_Tree" name="FROGS Tree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Reconstruction of phylogenetic tree </description> + <description>Reconstruction of phylogenetic tree </description> <macros> <import>macros.xml</import> </macros> @@ -40,7 +40,7 @@ <has_text_matching expression="abundance_removed.*:\s0" /> <has_text_matching expression="abundance_kept.*:\s300" /> <has_text_matching expression="otu_removed.*:\s0" /> - <has_text_matching expression="otu_kept.*:\s51" /> + <has_text_matching expression="otu_kept.*:\s50" /> </assert_contents> </output> </test> @@ -52,8 +52,8 @@ What it does -This tool creates a multiple alignment of OTUs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_. -And creates a rooted phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_ and `Phangorn R package <https://cran.r-project.org/web/packages/phangorn/index.html>`_. +This tool creates a multiple alignment of ASVs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_. +And creates a rooted phylogenetic tree with FastTree and `Phangorn R package <https://cran.r-project.org/web/packages/phangorn/index.html>`_. .. class:: infomark page-header h2 @@ -65,14 +65,14 @@ **Fasta file**: -The OTU sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). +The ASV sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). Careful: FROGS Tree works only with less than 10 000 sequences! .. image:: FROGS_tree_otufile.png **Biom file**: -The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). +The ASVs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). This file can be obtained in particular with the FROGS pipeline. .. class:: h3 @@ -87,7 +87,7 @@ **Report file** (report.html): -The report file describing which OTUs are contained or not in the phylogenetic tree. +The report file describing which ASVs are contained or not in the phylogenetic tree. .. class:: infomark page-header h2 |
| b |
| diff -r 37e6f0c959bb -r b2967b704d6b tsv_to_biom.xml --- a/tsv_to_biom.xml Tue Jul 19 11:11:16 2022 +0000 +++ b/tsv_to_biom.xml Tue May 23 07:59:04 2023 +0000 |
| b |
| @@ -1,5 +1,5 @@ <tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05"> - <description>Converts a TSV file in a BIOM file</description> + <description>Converts a TSV file in a BIOM file 1 </description> <macros> <import>macros.xml</import> </macros> @@ -11,7 +11,7 @@ #if $multi_affi_file --input-multi-affi '$multi_affi_file' #end if - #if $extract_fasta + #if $extract_fasta == "yes" --output-fasta '$sequence_file' #end if </command> @@ -20,19 +20,22 @@ <param format="tabular,tsv" name="tsv_file" type="data" label="Abundance TSV File" help="Your FROGS abundance TSV file. Take care to keep original column names." /> <param format="tabular,tsv" name="multi_affi_file" type="data" label="Multi_affiliation TSV File" help="TSV file describing multi_affiliation blast results." optional="true" /> <!-- Parameters --> - <param name="extract_fasta" type="boolean" label="Extract seeds in FASTA file" help="If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file." /> + <param name="extract_fasta" type="select" display="radio" label="Extract seeds in FASTA file" help="If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file." > + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> </inputs> <outputs> <data format="biom1" name="biom_file" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" /> <data format="fasta" name="sequence_file" label="${tool.name}: sequences.fasta" from_work_dir="seed.fasta"> - <filter>extract_fasta</filter> + <filter>extract_fasta == "yes"</filter> </data> </outputs> <tests> <test> <param name="tsv_file" value="references/12-biom2tsv.tsv" /> <param name="multi_affi_file" value="references/12-biom2tsv-affiliation_multihit.tsv" /> - <param name="extract_fasta" value="true" /> + <param name="extract_fasta" value="yes" /> <output name="biom_file" file="references/14-tsv2biom.biom" compare="sim_size" delta="0" /> <output name="sequence_file" file="references/14-tsv2biom.fasta" compare="diff" lines_diff="0" /> </test> @@ -94,11 +97,11 @@ If you modify your abundance TSV file - * -do not modify column names - * -do not remove columns - * -take care to choose a taxonomy available in your multi_affiliation TSV file - * -if you delete lines of the multi_affiliation file, take care to not remove a complete cluster whithout removing all "multi tags" in you abundance TSV file. - * -if you want to rename a taxon level (ex : genus "Ruminiclostridium 5;" to genus "Ruminiclostridium;"), do not forget to modify also your multi_affiliation TSV file. + * do not modify column names + * do not remove columns + * take care to choose a taxonomy available in your multi_affiliation TSV file + * if you delete lines of the multi_affiliation file, take care to not remove a complete cluster whithout removing all "multi tags" in you abundance TSV file. + * if you want to rename a taxon level (ex : genus "Ruminiclostridium 5;" to genus "Ruminiclostridium;"), do not forget to modify also your multi_affiliation TSV file. |
