From df9a79f58e25f47f7d0cb3696d59b9e896534412 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 4 Nov 2024 04:31:59 +0000 Subject: [PATCH 1/3] Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2 --- .../qiime2-III-VI-downsteam/CHANGELOG.md | 13 +++ ...hylogeny-Rarefaction-Taxonomic-Analysis.ga | 81 +++++++++++-------- ...E2-VI-diversity-metrics-and-estimations.ga | 72 ++++++++--------- 3 files changed, 97 insertions(+), 69 deletions(-) diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md index 7df9c9552..2904b2f6b 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md @@ -1,4 +1,17 @@ # Changelog +## [0.2] 2024-11-04 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2023.5.1+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2023.5.1+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0` + ## [0.1] 2024-06-22 First release. \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga index 19b3f61c9..1c6833426 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga @@ -17,7 +17,7 @@ "format-version": "0.1", "license": "MIT", "name": "QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis", - "release": "0.1", + "release": "0.2", "steps": { "0": { "annotation": "Representative sequences, e.g. from DADA2", @@ -223,7 +223,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "Phylogenetic tree for diversity analysis", + "name": "Phylogenetic tree for diversity analysis" + } + ], "label": "Phylogenetic tree for diversity analysis", "name": "QIIME2 III: Phylogenetic tree for diversity analysis", "outputs": [], @@ -307,7 +312,7 @@ }, "2": { "annotation": "qiime2 fragment-insertion sepp\nInsert fragment sequences using SEPP into reference phylogenies.", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 2, "input_connections": { @@ -358,15 +363,15 @@ "output_name": "tree" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "2fa85eae206e", + "changeset_revision": "a74f06287b8c", "name": "qiime2__fragment_insertion__sepp", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"alignment_subset_size\": \"1000\", \"placement_subset_size\": \"5000\", \"threads\": \"1\", \"debug\": false}, \"reference_database\": {\"__class__\": \"ConnectedValue\"}, \"representative_sequences\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"alignment_subset_size\": \"1000\", \"placement_subset_size\": \"5000\", \"debug\": false}, \"reference_database\": {\"__class__\": \"ConnectedValue\"}, \"representative_sequences\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "f6aa969f-1bdf-4d74-8b0a-af93a0640040", "when": null, @@ -379,8 +384,8 @@ ] } }, - "tags": "", - "uuid": "4a96a5b2-f8cc-41a3-9f16-a84e47e05afe" + "tags": [], + "uuid": "ea7b99e7-ee7b-4fd5-bda8-cd00ddfe6ade" }, "tool_id": null, "type": "subworkflow", @@ -419,7 +424,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "Taxonomic analysis", + "name": "Taxonomic analysis" + } + ], "label": "Taxonomic analysis", "name": "QIIME2 V: Taxonomic analysis", "outputs": [], @@ -557,7 +567,7 @@ }, "4": { "annotation": "qiime2 feature-classifier classify-sklearn\nPre-fitted sklearn-based taxonomy classifier", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 4, "input_connections": { @@ -592,15 +602,15 @@ "output_name": "classification" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "8aa82af30760", + "changeset_revision": "771d8be25d7a", "name": "qiime2__feature_classifier__classify_sklearn", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"__q2galaxy__GUI__conditional__reads_per_batch__\": {\"__q2galaxy__GUI__select__\": \"auto\", \"__current_case__\": 0, \"reads_per_batch\": \"auto\"}, \"n_jobs\": \"1\", \"pre_dispatch\": \"2*n_jobs\", \"__q2galaxy__GUI__conditional__confidence__\": {\"__q2galaxy__GUI__select__\": \"__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)\", \"__current_case__\": 1, \"confidence\": \"0.7\"}, \"read_orientation\": \"auto\"}, \"classifier\": {\"__class__\": \"ConnectedValue\"}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"__q2galaxy__GUI__conditional__reads_per_batch__\": {\"__q2galaxy__GUI__select__\": \"auto\", \"__current_case__\": 0, \"reads_per_batch\": \"auto\"}, \"pre_dispatch\": \"2*n_jobs\", \"__q2galaxy__GUI__conditional__confidence__\": {\"__q2galaxy__GUI__select__\": \"__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)\", \"__current_case__\": 1, \"confidence\": \"0.7\"}, \"read_orientation\": \"auto\"}, \"classifier\": {\"__class__\": \"ConnectedValue\"}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "cf9e003e-bcd4-4819-88cf-98d3bc8bf531", "when": null, @@ -614,7 +624,7 @@ }, "5": { "annotation": "qiime2 taxa barplot\nVisualize taxonomy with an interactive bar plot", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 5, "input_connections": { @@ -658,15 +668,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "124673b2e9e7", + "changeset_revision": "3da2f87501ee", "name": "qiime2__taxa__barplot", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"taxonomy\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__q2galaxy__GUI__conditional__level_delimiter__\": {\"__q2galaxy__GUI__select__\": \"__q2galaxy__::control::default\", \"__current_case__\": 0, \"level_delimiter\": \"__q2galaxy__::literal::None\"}}, \"table\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "a2146130-d5a3-4f0d-814f-61677f57709b", "when": null, @@ -680,7 +690,7 @@ }, "6": { "annotation": "qiime2 metadata tabulate\nInteractively explore Metadata in an HTML table", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 6, "input_connections": { @@ -711,15 +721,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "d6e1b976c373", + "changeset_revision": "9857be21dcaf", "name": "qiime2__metadata__tabulate", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"page_size\": \"100\"}, \"input\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__input__\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "380548c3-b9b6-4ebd-ae68-e3fbb891f7e5", "when": null, @@ -732,8 +742,8 @@ ] } }, - "tags": "", - "uuid": "41bae731-2f27-4e57-b94d-683e0ab94b43" + "tags": [], + "uuid": "d0309a9d-66d8-46e2-b103-674377fa0de8" }, "tool_id": null, "type": "subworkflow", @@ -787,7 +797,12 @@ "output_name": "Rooted tree" } }, - "inputs": [], + "inputs": [ + { + "description": "Rarefaction", + "name": "Rarefaction" + } + ], "label": "Rarefaction", "name": "QIIME2 IV: Rarefaction", "outputs": [], @@ -964,7 +979,7 @@ }, "5": { "annotation": "qiime2 diversity alpha-rarefaction\nAlpha rarefaction curves\n(Galaxy Version 2023.5.1+q2galaxy.2023.5.0.2)", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2023.5.1+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 5, "input_connections": { @@ -1020,15 +1035,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2023.5.1+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "97cb20f77d50", + "changeset_revision": "22bfda174157", "name": "qiime2__diversity__alpha_rarefaction", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"phylogeny\": {\"__class__\": \"ConnectedValue\"}, \"metrics\": [], \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"min_depth\": {\"__class__\": \"ConnectedValue\"}, \"steps\": \"10\", \"iterations\": \"10\"}, \"max_depth\": {\"__class__\": \"ConnectedValue\"}, \"table\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.1+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "489f6ea1-d13a-48ae-b71d-40c413f3b45e", "when": null, @@ -1041,8 +1056,8 @@ ] } }, - "tags": "", - "uuid": "3c96b4fd-c67a-4c79-9e78-6f77e72b4bdf" + "tags": [], + "uuid": "28382e50-9000-48f1-ae97-d468934f4962" }, "tool_id": null, "type": "subworkflow", @@ -1060,4 +1075,4 @@ "tags": [], "uuid": "3163175d-7673-42d9-8aae-505afbd74946", "version": 30 -} +} \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga index bac0948ff..d8b9ff406 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga @@ -121,7 +121,7 @@ "format-version": "0.1", "license": "MIT", "name": "QIIME2 VI: Diversity metrics and estimations", - "release": "0.1", + "release": "0.2", "steps": { "0": { "annotation": "This value is based on the DADA2 table features.\nNote: the choice of the value is prioritising either the inclusion of all the samples or a higher feature retention.", @@ -260,7 +260,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27", "errors": null, "id": 5, "input_connections": { @@ -289,15 +289,15 @@ "output_name": "imported_data" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27", "tool_shed_repository": { - "changeset_revision": "10447a4b0cc3", + "changeset_revision": "8a0db69428c7", "name": "qiime2_core__tools__import", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 29, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"ImmutableMetadataFormat\", \"__current_case__\": 0, \"import\": {\"name\": \"__q2galaxy__::literal::None\", \"data\": {\"__class__\": \"RuntimeValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+dist.h193f7cc9.3", + "tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 58, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"ImmutableMetadataFormat\", \"__current_case__\": 0, \"import\": {\"name\": \"__q2galaxy__::literal::None\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2024.10.0+dist.h3d8a7e27", "type": "tool", "uuid": "be1fae33-1b8d-4756-854f-a0587934da09", "when": null, @@ -305,7 +305,7 @@ }, "6": { "annotation": "QIIME 2\u2019s diversity analyses are available through the q2-diversity plugin, which supports computing alpha and beta diversity metrics, applying related statistical tests, and generating interactive visualizations. We\u2019ll first apply the core-metrics-phylogenetic method, which rarefies a FeatureTable[Frequency] to a user-specified depth, computes several alpha and beta diversity metrics, and generates principle coordinates analysis (PCoA) plots using Emperor for each of the beta diversity metrics.", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2023.5.1+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 6, "input_connections": { @@ -490,15 +490,15 @@ "output_name": "weighted_unifrac_pcoa_results" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2023.5.1+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "9d29f6a334e5", + "changeset_revision": "7fc930fc43cf", "name": "qiime2__diversity__core_metrics_phylogenetic", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"with_replacement\": false, \"__q2galaxy__GUI__conditional__n_jobs_or_threads__\": {\"__q2galaxy__GUI__select__\": \"__q2galaxy__::control::Int X Range(1__comma__ None)\", \"__current_case__\": 1, \"n_jobs_or_threads\": \"1\"}}, \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"phylogeny\": {\"__class__\": \"ConnectedValue\"}, \"sampling_depth\": {\"__class__\": \"ConnectedValue\"}, \"table\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.1+q2galaxy.2023.5.0.2", + "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"with_replacement\": false, \"ignore_missing_samples\": false}, \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"phylogeny\": {\"__class__\": \"ConnectedValue\"}, \"sampling_depth\": {\"__class__\": \"ConnectedValue\"}, \"table\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "cd47d601-3186-40c0-bd1a-1564728a776d", "when": null, @@ -506,7 +506,7 @@ }, "7": { "annotation": "qiime2 diversity alpha-group-significance\nAlpha diversity comparisons", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 7, "input_connections": { @@ -541,15 +541,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "b7b5dc5a067b", + "changeset_revision": "96988c25ca01", "name": "qiime2__diversity__alpha_group_significance", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"alpha_diversity\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.1+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "b1e9c678-9093-4e47-a860-89a0ce54e658", "when": null, @@ -563,7 +563,7 @@ }, "8": { "annotation": "qiime2 diversity alpha-group-significance\nAlpha diversity comparisons", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 8, "input_connections": { @@ -598,15 +598,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "b7b5dc5a067b", + "changeset_revision": "96988c25ca01", "name": "qiime2__diversity__alpha_group_significance", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"alpha_diversity\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.1+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "867c60b4-2a64-4b17-82ce-524dcd8b3362", "when": null, @@ -620,7 +620,7 @@ }, "9": { "annotation": "qiime2 diversity alpha-group-significance\nAlpha diversity comparisons", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 9, "input_connections": { @@ -655,15 +655,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "b7b5dc5a067b", + "changeset_revision": "96988c25ca01", "name": "qiime2__diversity__alpha_group_significance", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"alpha_diversity\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.1+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "6b2cd5b5-982b-42a2-b8c3-67d768219937", "when": null, @@ -677,7 +677,7 @@ }, "10": { "annotation": "qiime2 diversity beta-group-significance\nBeta diversity group", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 10, "input_connections": { @@ -725,15 +725,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "2df83b20af3f", + "changeset_revision": "a0d20b8b681e", "name": "qiime2__diversity__beta_group_significance", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"method\": \"permanova\", \"pairwise\": false, \"permutations\": \"999\"}, \"distance_matrix\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}, \"column\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.1+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "df0800f4-d40f-4245-b15f-e7c35e434f41", "when": null, @@ -747,7 +747,7 @@ }, "11": { "annotation": "qiime2 diversity beta-group-significance\nBeta diversity group", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 11, "input_connections": { @@ -795,15 +795,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "2df83b20af3f", + "changeset_revision": "a0d20b8b681e", "name": "qiime2__diversity__beta_group_significance", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"method\": \"permanova\", \"pairwise\": false, \"permutations\": \"999\"}, \"distance_matrix\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}, \"column\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.1+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "7ca4a86e-7a49-4d04-b52e-10c375d856dc", "when": null, @@ -876,7 +876,7 @@ }, "13": { "annotation": "qiime2 diversity beta-group-significance\nBeta diversity group", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 13, "input_connections": { @@ -924,15 +924,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "2df83b20af3f", + "changeset_revision": "a0d20b8b681e", "name": "qiime2__diversity__beta_group_significance", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"method\": \"permanova\", \"pairwise\": false, \"permutations\": \"999\"}, \"distance_matrix\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}, \"column\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.1+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "e16130db-b499-4d24-8950-b3779969258d", "when": null, @@ -1129,4 +1129,4 @@ "tags": [], "uuid": "300b5a7d-f763-486a-a8ea-87ea84571f19", "version": 2 -} +} \ No newline at end of file From 542ee0c2c1574213beba0dcf8c28ed8c2458aa6a Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sat, 23 Nov 2024 19:54:07 +0100 Subject: [PATCH 2/3] Update classifier --- ...2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml index b5cf8d512..bfd6737cb 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml @@ -16,7 +16,7 @@ Maximum depth: 2019 Taxonomic classifier: class: File - location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza + location: https://docs.qiime2.org/2024.10/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza filetype: qza SEPP fragment insertion reference: class: File @@ -105,4 +105,4 @@ n: 1 asserts: - has_n_lines: - n: 289 \ No newline at end of file + n: 289 From f387426f7f594f825dd2cf7d83da939684329d24 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sat, 23 Nov 2024 20:31:04 +0100 Subject: [PATCH 3/3] Update QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml --- ...ME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml index bfd6737cb..bdfd66562 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml @@ -66,7 +66,7 @@ ftype: qza asserts: - has_size: - min: 70k + min: 40k max: 80k - has_archive_member: path: "^[^/]*/metadata.yaml"