From caa51fb03b8df1de2753f124fabaaf8e826dc137 Mon Sep 17 00:00:00 2001 From: Debjyoti Ghosh Date: Wed, 27 Mar 2024 16:31:30 +0100 Subject: [PATCH 01/18] initial commit of downstream workflows --- ...etic-tree-for-diversity-analysis-tests.yml | 13 + ...hylogenetic-tree-for-diversity-analysis.ga | 152 +++++++++ .../QIIME2-IV:-Rarefaction-tests.yml | 19 ++ .../downsteam/QIIME2-IV:-Rarefaction.ga | 250 ++++++++++++++ .../QIIME2-V:-Taxonomic-analysis-tests.yml | 25 ++ .../downsteam/QIIME2-V:-Taxonomic-analysis.ga | 309 ++++++++++++++++++ 6 files changed, 768 insertions(+) create mode 100644 workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis-tests.yml create mode 100644 workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis.ga create mode 100644 workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction-tests.yml create mode 100644 workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction.ga create mode 100644 workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis-tests.yml create mode 100644 workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis.ga diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis-tests.yml b/workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis-tests.yml new file mode 100644 index 000000000..8cf6658dd --- /dev/null +++ b/workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis-tests.yml @@ -0,0 +1,13 @@ +- doc: Test outline for QIIME2-III:-Phylogenetic-tree-for-diversity-analysis + job: + Import DADA2 representative sequences: + class: File + path: test-data/Import DADA2 representative sequences.qza + filetype: qza + SEPP fragment insertion source file: + class: File + path: test-data/SEPP fragment insertion source file.qza + filetype: qza + outputs: + Rooted tree: + path: test-data/Rooted tree.qza diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis.ga b/workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis.ga new file mode 100644 index 000000000..04923a7f2 --- /dev/null +++ b/workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis.ga @@ -0,0 +1,152 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "QIIME 2 analysis allows the use of phylogenetic trees for diversity metrics such as Faith\u2019s Phylogenetic Diversity and UniFrac distance. The tree provides an inherent structure to the data, allowing us to consider an evolutionary relationship between organisms.", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "0009-0008-1496-1677", + "name": "Debjyoti Ghosh" + }, + { + "address": "Permoserstra\u00dfe 15, 04318 Leipzig", + "class": "Organization", + "name": "Helmholtz-Zentrum f\u00fcr Umweltforschung - UFZ" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "QIIME2 III: Phylogenetic tree for diversity analysis", + "steps": { + "0": { + "annotation": "Import the DADA2 denoising output for the representative sequences", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Import the DADA2 denoising output for the representative sequences", + "name": "Import DADA2 representative sequences" + } + ], + "label": "Import DADA2 representative sequences", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + 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"2023.5.0+q2galaxy.2023.5.0.2", + "type": "tool", + "uuid": "f6aa969f-1bdf-4d74-8b0a-af93a0640040", + "when": null, + "workflow_outputs": [ + { + "label": "Rooted tree", + "output_name": "tree", + "uuid": "e572bf3b-64aa-4bd5-a629-f53ba6a383be" + } + ] + } + }, + "tags": [], + "uuid": "4a96a5b2-f8cc-41a3-9f16-a84e47e05afe", + "version": 10 +} \ No newline at end of file diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction-tests.yml b/workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction-tests.yml new file mode 100644 index 000000000..5a5e1a942 --- /dev/null +++ b/workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction-tests.yml @@ -0,0 +1,19 @@ +- doc: Test outline for QIIME2-IV:-Rarefaction + job: + Metadata: + class: File + path: test-data/Metadata.qiime2.tabular + filetype: qiime2.tabular + Import DADA2 table output: + class: File + path: test-data/Import DADA2 table output.qza + filetype: qza + Rooted tree: + class: File + path: test-data/Rooted tree.qza + filetype: qza + Minimum depth: '1' + Maximum depth: '2019' + outputs: + Rarefaction curve: + path: test-data/Rarefaction curve.qzv diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction.ga b/workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction.ga new file mode 100644 index 000000000..65a399528 --- /dev/null +++ b/workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction.ga @@ -0,0 +1,250 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Rarefaction is a method for normalization via sub-sampling without replacement and is commonly used as a workaround for the issue of uneven sequencing depth. Rarefaction occurs in two steps: first, samples which are below the rarefaction depth are filtered out of the feature table. Then, all remaining samples are subsampled without replacement to get to the specified sequencing depth.", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "0009-0008-1496-1677", + "name": "Debjyoti Ghosh" + }, + { + "address": "Permoserstra\u00dfe 15, 04318 Leipzig", + "class": "Organization", + "name": "Helmholtz-Zentrum f\u00fcr Umweltforschung - UFZ" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "QIIME2 IV: Rarefaction", + "steps": { + "0": { + "annotation": "The tab separated file for the metadata", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "The tab separated file for the metadata", + "name": "Metadata" + } + ], + "label": "Metadata", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 0 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "8dde0c69-40f1-415a-a866-5d1115e80cdf", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "Import of the dada2_table file from DADA2 outputs", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Import of the dada2_table file from DADA2 outputs", + "name": "Import DADA2 table output" + } + ], + "label": "Import DADA2 table output", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 2.3167686199511115, + "top": 140.50124094027063 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"qza\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "92e667de-c04f-420c-9747-ffedf77041fa", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "Import rooted_tree output from phylogenetic tree generation step", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + 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barplot: + path: test-data/Taxa barplot.qzv + Taxonomy classification table: + path: test-data/Taxonomy classification table.qzv diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis.ga b/workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis.ga new file mode 100644 index 000000000..c91056e9a --- /dev/null +++ b/workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis.ga @@ -0,0 +1,309 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "The first step in this process is to assign taxonomy to the sequences in our FeatureData[Sequence] QIIME 2 artifact. We\u2019ll do that using a pre-trained Naive Bayes classifier and the q2-feature-classifier plugin.", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "0009-0008-1496-1677", + "name": "Debjyoti Ghosh" + }, + { + "address": "Permoserstra\u00dfe 15, 04318 Leipzig", + "class": "Organization", + "name": "Helmholtz-Zentrum f\u00fcr Umweltforschung - UFZ" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "QIIME2 V: Taxonomic analysis", + "steps": { + "0": { + "annotation": "The tab separated file for the metadata", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "The tab separated file for the metadata", + "name": "Metadata" + } + ], + "label": "Metadata", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0.791015625, + "top": 2.6916668368741092 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": 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{}, + "inputs": [ + { + "description": "This file can be from the Greengenes or the SILVA database for the taxonomy determination", + "name": "Taxonomic classifier" + } + ], + "label": "Taxonomic classifier", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0.451446533203125, + "top": 241.0041668368741 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"qza\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "ac0cdf1d-2a29-481c-aaa3-21f1b8f9b97d", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "Import of the dada2_table file from DADA2 outputs", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "Import of the dada2_table file from DADA2 outputs", + "name": "Import DADA2 table output" + } + ], + "label": "Import DADA2 table output", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 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"__q2galaxy__GUI__section__extra_opts__|taxonomy": { + "id": 4, + "output_name": "classification" + }, + "table": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool qiime2 taxa barplot", + "name": "__q2galaxy__GUI__section__extra_opts__" + } + ], + "label": "Taxonomy barplot", + "name": "qiime2 taxa barplot", + "outputs": [ + { + "name": "visualization", + "type": "qzv" + } + ], + "position": { + "left": 645.4988052205106, + "top": 0 + }, + "post_job_actions": { + "RenameDatasetActionvisualization": { + "action_arguments": { + "newname": "taxa_barplot" + }, + "action_type": "RenameDatasetAction", + "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_shed_repository": { + "changeset_revision": "124673b2e9e7", + "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", + "type": "tool", + "uuid": "a2146130-d5a3-4f0d-814f-61677f57709b", + "when": null, + "workflow_outputs": [ + { + "label": "Taxa barplot", + "output_name": "visualization", + "uuid": "cef83374-d99f-4a8c-98ec-90afd3a37da3" + } + ] + }, + "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", + "errors": null, + "id": 6, + "input_connections": { + "input_0|__q2galaxy__GUI__conditional__input__|source": { + "id": 4, + "output_name": "classification" + } + }, + "inputs": [], + "label": "Tabulate taxonomy classification", + "name": "qiime2 metadata tabulate", + "outputs": [ + { + "name": "visualization", + "type": "qzv" + } + ], + "position": { + "left": 646.2365246851235, + "top": 304.22497686132425 + }, + "post_job_actions": { + "RenameDatasetActionvisualization": { + "action_arguments": { + "newname": "taxonomy_classification_visualisation" + }, + "action_type": "RenameDatasetAction", + "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_shed_repository": { + "changeset_revision": "d6e1b976c373", + "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", + "type": "tool", + "uuid": "380548c3-b9b6-4ebd-ae68-e3fbb891f7e5", + "when": null, + "workflow_outputs": [ + { + "label": "Taxonomy classification table", + "output_name": "visualization", + "uuid": "9b1b4f66-d7a7-42cd-ac81-00c417300f47" + } + ] + } + }, + "tags": [], + "uuid": "41bae731-2f27-4e57-b94d-683e0ab94b43", + "version": 8 +} \ No newline at end of file From 43854f1ebc163c787e4159b7b11a2d372df655d4 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Mon, 8 Apr 2024 15:35:12 +0200 Subject: [PATCH 02/18] add dockstore and workflowhub files --- .../qiime2-III-V-downsteam/.dockstore.yml | 35 +++++++++++++++++++ .../qiime2-III-V-downsteam/.workflowhub.yml | 5 +++ ...tic-tree-for-diversity-analysis-tests.yml} | 0 ...ylogenetic-tree-for-diversity-analysis.ga} | 0 .../QIIME2-IV-rarefaction-tests.yml} | 0 .../QIIME2-IV-rarefaction.ga} | 0 .../QIIME2-V-taxonomic-analysis-tests.yml} | 0 .../QIIME2-V-taxonomic-analysis.ga} | 0 8 files changed, 40 insertions(+) create mode 100644 workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml create mode 100644 workflows/amplicon/qiime2/qiime2-III-V-downsteam/.workflowhub.yml rename workflows/amplicon/qiime2/{downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis-tests.yml => qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml} (100%) rename workflows/amplicon/qiime2/{downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis.ga => qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga} (100%) rename workflows/amplicon/qiime2/{downsteam/QIIME2-IV:-Rarefaction-tests.yml => qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml} (100%) rename workflows/amplicon/qiime2/{downsteam/QIIME2-IV:-Rarefaction.ga => qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga} (100%) rename workflows/amplicon/qiime2/{downsteam/QIIME2-V:-Taxonomic-analysis-tests.yml => qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml} (100%) rename workflows/amplicon/qiime2/{downsteam/QIIME2-V:-Taxonomic-analysis.ga => qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga} (100%) diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml new file mode 100644 index 000000000..7cd9575c1 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml @@ -0,0 +1,35 @@ +version: 1.2 +workflows: +- name: QIIME2-III Phylogenetic tree for diversity analysis test + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga + testParameterFiles: + - /QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" +- name: QIIME2-IV rarefaction + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-IV-rarefaction.ga + testParameterFiles: + - /QIIME2-IV-rarefaction-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" +- name: QIIME2-V-taxonomic-analysis + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-V-taxonomic-analysis.ga + testParameterFiles: + - /QIIME2-V-taxonomic-analysis-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.workflowhub.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.workflowhub.yml new file mode 100644 index 000000000..2a1023efd --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.workflowhub.yml @@ -0,0 +1,5 @@ +version: '0.1' +registries: +- url: https://workflowhub.eu + project: iwc + workflow: qiime2/main diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml similarity index 100% rename from workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis-tests.yml rename to workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga similarity index 100% rename from workflows/amplicon/qiime2/downsteam/QIIME2-III:-Phylogenetic-tree-for-diversity-analysis.ga rename to workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction-tests.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml similarity index 100% rename from workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction-tests.yml rename to workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga similarity index 100% rename from workflows/amplicon/qiime2/downsteam/QIIME2-IV:-Rarefaction.ga rename to workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml similarity index 100% rename from workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis-tests.yml rename to workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml diff --git a/workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga similarity index 100% rename from workflows/amplicon/qiime2/downsteam/QIIME2-V:-Taxonomic-analysis.ga rename to workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga From 167f0c44a91923265c7693b72c0ed62a2e847567 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 10 Apr 2024 16:27:20 +0200 Subject: [PATCH 03/18] fix and finish downstream tests --- ...etic-tree-for-diversity-analysis-tests.yml | 26 +++++++-- ...hylogenetic-tree-for-diversity-analysis.ga | 10 ++-- .../QIIME2-IV-rarefaction-tests.yml | 27 +++++++-- .../QIIME2-IV-rarefaction.ga | 12 ++-- .../QIIME2-V-taxonomic-analysis-tests.yml | 58 +++++++++++++++---- .../QIIME2-V-taxonomic-analysis.ga | 18 +++--- 6 files changed, 111 insertions(+), 40 deletions(-) diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml index 8cf6658dd..3d7c6283c 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml @@ -1,13 +1,31 @@ - doc: Test outline for QIIME2-III:-Phylogenetic-tree-for-diversity-analysis job: - Import DADA2 representative sequences: + DADA2 representative sequences: class: File - path: test-data/Import DADA2 representative sequences.qza + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_rep_set.qza filetype: qza SEPP fragment insertion source file: class: File - path: test-data/SEPP fragment insertion source file.qza + location: https://data.qiime2.org/2024.2/common/sepp-refs-gg-13-8.qza filetype: qza outputs: Rooted tree: - path: test-data/Rooted tree.qza + ftype: qza + asserts: + - has_size: + min: 2M + max: 3M + - has_archive_member: + path: "^[^/]*/data/tree.nwk" + n: 1 + asserts: + - has_text_matching: + expression: "k__Bacteria" + - has_archive_member: + path: "^[^/]*/metadata.yaml" + n: 1 + asserts: + - has_line: + line: "type: Phylogeny[Rooted]" + - has_line: + line: "format: NewickDirectoryFormat" \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga index 04923a7f2..8169044a5 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga @@ -19,18 +19,18 @@ "name": "QIIME2 III: Phylogenetic tree for diversity analysis", "steps": { "0": { - "annotation": "Import the DADA2 denoising output for the representative sequences", + "annotation": "DADA2 representative sequences", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "Import the DADA2 denoising output for the representative sequences", + "description": "DADA2 representative sequences", "name": "Import DADA2 representative sequences" } ], - "label": "Import DADA2 representative sequences", + "label": "DADA2 representative sequences", "name": "Input dataset", "outputs": [], "position": { @@ -46,14 +46,14 @@ "workflow_outputs": [] }, "1": { - "annotation": "This file is for the SEPP fragmentation for the phylogenetic tree generation", + "annotation": "Reference data for the SEPP fragmentation insertion phylogenetic tree generation", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "This file is for the SEPP fragmentation for the phylogenetic tree generation", + "description": "Reference data for the SEPP fragmentation insertion phylogenetic tree generatio", "name": "SEPP fragment insertion source file" } ], diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml index 5a5e1a942..ed5372cf9 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml @@ -2,18 +2,33 @@ job: Metadata: class: File - path: test-data/Metadata.qiime2.tabular - filetype: qiime2.tabular - Import DADA2 table output: + location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv + filetype: tabular + DADA2 feature table: class: File - path: test-data/Import DADA2 table output.qza + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza filetype: qza Rooted tree: class: File - path: test-data/Rooted tree.qza + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/tree.qza filetype: qza Minimum depth: '1' Maximum depth: '2019' outputs: Rarefaction curve: - path: test-data/Rarefaction curve.qzv + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/index.html" + n: 1 + # data per measure + - has_archive_member: + path: "^[^/]*/data/.*\\.csv" + n: 3 + # data for each measure and metadata variable (*7) + - has_archive_member: + path: "^[^/]*/data/.*\\.jsonp" + n: 21 \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga index 65a399528..c102853c8 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga @@ -19,14 +19,14 @@ "name": "QIIME2 IV: Rarefaction", "steps": { "0": { - "annotation": "The tab separated file for the metadata", + "annotation": "Tab separated metadata file", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "The tab separated file for the metadata", + "description": "Tab separated metadata file", "name": "Metadata" } ], @@ -46,18 +46,18 @@ "workflow_outputs": [] }, "1": { - "annotation": "Import of the dada2_table file from DADA2 outputs", + "annotation": "DADA2 feature table", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Import of the dada2_table file from DADA2 outputs", - "name": "Import DADA2 table output" + "description": "DADA2 feature table", + "name": "DADA2 feature table" } ], - "label": "Import DADA2 table output", + "label": "DADA2 feature table", "name": "Input dataset", "outputs": [], "position": { diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml index da4c89d94..9c3015dc8 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml @@ -2,24 +2,62 @@ job: Metadata: class: File - path: test-data/Metadata.qiime2.tabular - filetype: qiime2.tabular - Import DADA2 representative sequences: + location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv + filetype: tabular + DADA2 representative sequences: class: File - path: test-data/Import DADA2 representative sequences.qza + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_rep_set.qza filetype: qza Taxonomic classifier: class: File - path: test-data/Taxonomic classifier.qza + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza filetype: qza - Import DADA2 table output: + DADA2 feature table: class: File - path: test-data/Import DADA2 table output.qza + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza filetype: qza outputs: Taxonomy classification: - path: test-data/Taxonomy classification.qza + ftype: qza + asserts: + - has_size: + min: 70k + max: 80k + - has_archive_member: + path: "^[^/]*/metadata.yaml" + n: 1 + asserts: + - has_line: + line: "type: FeatureData[Taxonomy]" + - has_line: + line: "format: TSVTaxonomyDirectoryFormat" + - has_archive_member: + path: "^[^/]*/data/taxonomy.tsv" + n: 1 + asserts: + - has_n_lines: + n: 288 Taxa barplot: - path: test-data/Taxa barplot.qzv + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/.*\\.csv" + n: 7 + - has_archive_member: + path: "^[^/]*/data/.*\\.jsonp" + n: 7 Taxonomy classification table: - path: test-data/Taxonomy classification table.qzv + ftype: qza + asserts: + - has_size: + min: 1M + max: 2M + - has_archive_member: + path: "^[^/]*/data/metadata.tsv" + n: 1 + asserts: + - has_n_lines: + n: 289 \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga index c91056e9a..3aa9c4473 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "The first step in this process is to assign taxonomy to the sequences in our FeatureData[Sequence] QIIME 2 artifact. We\u2019ll do that using a pre-trained Naive Bayes classifier and the q2-feature-classifier plugin.", + "annotation": "Assign taxonomy to the sequences in FeatureData using a pre-trained Naive Bayes classifier with the q2-feature-classifier plugin.", "comments": [], "creator": [ { @@ -19,14 +19,14 @@ "name": "QIIME2 V: Taxonomic analysis", "steps": { "0": { - "annotation": "The tab separated file for the metadata", + "annotation": "Tab separated metadata file", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "The tab separated file for the metadata", + "description": "Tab separated metadata file", "name": "Metadata" } ], @@ -73,14 +73,14 @@ "workflow_outputs": [] }, "2": { - "annotation": "This file can be from the Greengenes or the SILVA database for the taxonomy determination", + "annotation": "Taxonomic classifier (e.g. Greengenes or SILVA)", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "This file can be from the Greengenes or the SILVA database for the taxonomy determination", + "description": "Taxonomic classifier (e.g. Greengenes or SILVA)", "name": "Taxonomic classifier" } ], @@ -100,18 +100,18 @@ "workflow_outputs": [] }, "3": { - "annotation": "Import of the dada2_table file from DADA2 outputs", + "annotation": "DADA2 feature table", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "Import of the dada2_table file from DADA2 outputs", - "name": "Import DADA2 table output" + "description": "DADA2 feature table", + "name": "DADA2 feature table" } ], - "label": "Import DADA2 table output", + "label": "DADA2 feature table", "name": "Input dataset", "outputs": [], "position": { From 77e64c189e40f81644b72c87cd9f1ea7e8d43e42 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 11 Apr 2024 12:01:17 +0200 Subject: [PATCH 04/18] fix input name --- .../qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga index 3aa9c4473..a482b8b2e 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga @@ -54,10 +54,10 @@ "inputs": [ { "description": "Demultiplexed sequences in qza format", - "name": "Import DADA2 representative sequences" + "name": "DADA2 representative sequences" } ], - "label": "Import DADA2 representative sequences", + "label": "DADA2 representative sequences", "name": "Input dataset", "outputs": [], "position": { From 375c95ef97e3c73bec32cde3148e64fd2eb604fc Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 12 Apr 2024 09:50:00 +0200 Subject: [PATCH 05/18] add joint workflow --- ...y-Rarefaction-Taxonomic-Analysis-tests.yml | 108 ++ ...hylogeny-Rarefaction-Taxonomic-Analysis.ga | 1046 +++++++++++++++++ 2 files changed, 1154 insertions(+) create mode 100644 workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml create mode 100644 workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml new file mode 100644 index 000000000..d0b065a86 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml @@ -0,0 +1,108 @@ +- doc: Test outline for QIIME2-III:-Phylogenetic-tree-for-diversity-analysis + job: + Metadata: + class: File + location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv + filetype: tabular + Representative sequences: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_rep_set.qza + filetype: qza + Feature table: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza + filetype: qza + Minimum depth: '1' + 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 + filetype: qza + SEPP fragment insertion reference: + class: File + location: https://data.qiime2.org/2024.2/common/sepp-refs-gg-13-8.qza + filetype: qza + outputs: + Rooted tree: + ftype: qza + asserts: + - has_size: + min: 2M + max: 3M + - has_archive_member: + path: "^[^/]*/data/tree.nwk" + n: 1 + asserts: + - has_text_matching: + expression: "k__Bacteria" + - has_archive_member: + path: "^[^/]*/metadata.yaml" + n: 1 + asserts: + - has_line: + line: "type: Phylogeny[Rooted]" + - has_line: + line: "format: NewickDirectoryFormat" + + Rarefaction curve: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/index.html" + n: 1 + # data per measure + - has_archive_member: + path: "^[^/]*/data/.*\\.csv" + n: 3 + # data for each measure and metadata variable (*7) + - has_archive_member: + path: "^[^/]*/data/.*\\.jsonp" + n: 21 + + Taxonomy classification: + ftype: qza + asserts: + - has_size: + min: 70k + max: 80k + - has_archive_member: + path: "^[^/]*/metadata.yaml" + n: 1 + asserts: + - has_line: + line: "type: FeatureData[Taxonomy]" + - has_line: + line: "format: TSVTaxonomyDirectoryFormat" + - has_archive_member: + path: "^[^/]*/data/taxonomy.tsv" + n: 1 + asserts: + - has_n_lines: + n: 288 + Taxa barplot: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/.*\\.csv" + n: 7 + - has_archive_member: + path: "^[^/]*/data/.*\\.jsonp" + n: 7 + Taxonomy classification table: + ftype: qza + asserts: + - has_size: + min: 1M + max: 2M + - has_archive_member: + path: "^[^/]*/data/metadata.tsv" + n: 1 + asserts: + - has_n_lines: + n: 289 \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga new file mode 100644 index 000000000..c8825404a --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga @@ -0,0 +1,1046 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "This workflow \n- Reconstruct phylogeny (insert fragments in a reference)\n- Alpha rarefaction analysis\n- Taxonomic analysis", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "0009-0008-1496-1677", + "name": "Debjyoti Ghosh" + }, + { + "address": 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a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga index c8825404a..70541e67e 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga @@ -224,7 +224,7 @@ }, "inputs": [], "label": null, - "name": "QIIME2 III: Phylogenetic tree for diversity analysis (imported from uploaded file)", + "name": "QIIME2 III: Phylogenetic tree for diversity analysis", "outputs": [], "position": { "left": 457.7998825174995, @@ -248,7 +248,7 @@ ], "format-version": "0.1", "license": "MIT", - "name": "QIIME2 III: Phylogenetic tree for diversity analysis (imported from uploaded file)", + "name": "QIIME2 III: Phylogenetic tree for diversity analysis", "steps": { "0": { "annotation": "DADA2 representative sequences", @@ -420,7 +420,7 @@ }, "inputs": [], "label": null, - "name": "QIIME2 V: Taxonomic analysis (imported from uploaded file)", + "name": "QIIME2 V: Taxonomic analysis", "outputs": [], "position": { "left": 484.1197712977931, @@ -444,7 +444,7 @@ ], "format-version": "0.1", "license": "MIT", - "name": "QIIME2 V: Taxonomic analysis (imported from uploaded file)", + "name": "QIIME2 V: Taxonomic analysis", "steps": { "0": { "annotation": "Tab separated metadata file", @@ -743,6 +743,16 @@ "label": "Taxonomy classification", "output_name": "Taxonomy classification", "uuid": "622c6287-2cea-4b85-82cc-26a2d3abfb3d" + }, + { + "label": "Taxa barplot", + "output_name": "Taxa barplot", + "uuid": "1857691f-3d38-45be-a6e5-4dca9a0d836a" + }, + { + "label": "Taxonomy classification table", + "output_name": "Taxonomy classification table", + "uuid": "8a273aca-d2bc-4038-a13c-63cea1666839" } ] }, @@ -778,7 +788,7 @@ }, "inputs": [], "label": null, - "name": "QIIME2 IV: Rarefaction (imported from uploaded file)", + "name": "QIIME2 IV: Rarefaction", "outputs": [], "position": { "left": 766.4972916356149, @@ -802,7 +812,7 @@ ], "format-version": "0.1", "license": "MIT", - "name": "QIIME2 IV: Rarefaction (imported from uploaded file)", + "name": "QIIME2 IV: Rarefaction", "steps": { "0": { "annotation": "Tab separated metadata file", @@ -1037,10 +1047,16 @@ "type": "subworkflow", "uuid": "ba53440b-8543-44d1-9f96-16845342c339", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "Rarefaction curve", + "output_name": "Rarefaction curve", + "uuid": "12394a5b-15fc-44f2-80cd-2b38de92517a" + } + ] } }, "tags": [], "uuid": "3163175d-7673-42d9-8aae-505afbd74946", "version": 30 -} \ No newline at end of file +} From 32291f40e006f8e480b14a21155612d5e72ee545 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 12 Apr 2024 11:45:41 +0200 Subject: [PATCH 07/18] add III-V to dockstore --- .../qiime2/qiime2-III-V-downsteam/.dockstore.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml index 7cd9575c1..1a9195175 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml +++ b/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml @@ -1,5 +1,16 @@ version: 1.2 workflows: +- name: QIIME2-III-V Phylogeny Rarefaction Taxonomic-Analysis + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga + testParameterFiles: + - /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" - name: QIIME2-III Phylogenetic tree for diversity analysis test subclass: Galaxy publish: true From 0b0e12cf3b6be4fac292b52146d542b945258521 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 30 May 2024 19:30:11 +0200 Subject: [PATCH 08/18] add diversity metric workflow --- .../.dockstore.yml | 12 + .../.workflowhub.yml | 0 ...y-Rarefaction-Taxonomic-Analysis-tests.yml | 0 ...hylogeny-Rarefaction-Taxonomic-Analysis.ga | 0 ...etic-tree-for-diversity-analysis-tests.yml | 0 ...hylogenetic-tree-for-diversity-analysis.ga | 0 .../QIIME2-IV-rarefaction-tests.yml | 0 .../QIIME2-IV-rarefaction.ga | 0 .../QIIME2-V-taxonomic-analysis-tests.yml | 0 .../QIIME2-V-taxonomic-analysis.ga | 0 ...iversity-metrics-and-estimations-tests.yml | 140 ++ ...E2-VI-diversity-metrics-and-estimations.ga | 1131 +++++++++++++++++ 12 files changed, 1283 insertions(+) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/.dockstore.yml (80%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/.workflowhub.yml (100%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml (100%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga (100%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml (100%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga (100%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/QIIME2-IV-rarefaction-tests.yml (100%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/QIIME2-IV-rarefaction.ga (100%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/QIIME2-V-taxonomic-analysis-tests.yml (100%) rename workflows/amplicon/qiime2/{qiime2-III-V-downsteam => qiime2-III-VI-downsteam}/QIIME2-V-taxonomic-analysis.ga (100%) create mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations-tests.yml create mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml similarity index 80% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml index 1a9195175..4cd5e75ad 100644 --- a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.dockstore.yml +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml @@ -44,3 +44,15 @@ workflows: orcid: 0009-0008-1496-1677 - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" address: "Permoserstraße 15, 04318 Leipzig" + +- name: QIIME2-VI-diversity-metrics-and-estimations + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-VI-Diversity-metrics-and-estimations.ga + testParameterFiles: + - /QIIME2-V-taxonomic-analysis-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/.workflowhub.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/.workflowhub.yml rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml diff --git a/workflows/amplicon/qiime2/qiime2-III-V-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 similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml diff --git a/workflows/amplicon/qiime2/qiime2-III-V-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 similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction-tests.yml similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction-tests.yml rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction-tests.yml diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction.ga similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-IV-rarefaction.ga rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction.ga diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis-tests.yml similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis-tests.yml rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis-tests.yml diff --git a/workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis.ga similarity index 100% rename from workflows/amplicon/qiime2/qiime2-III-V-downsteam/QIIME2-V-taxonomic-analysis.ga rename to workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis.ga diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations-tests.yml new file mode 100644 index 000000000..470ebe471 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations-tests.yml @@ -0,0 +1,140 @@ +- doc: Test outline for QIIME2-VI:-Diversity-metrics-and-estimations + job: + Metadata: + class: File + location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv + filetype: qiime2.tabular + Import DADA2 table output: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza + filetype: qza + Import rooted tree: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/tree.qza + filetype: qza + Sampling depth: '2000' + Target metadata parameter (for beta diversity): cage_id + outputs: + Alpha diversity - Pielou's evenness: + ftype: qzv + asserts: + - has_size: + min: 300k + max: 400k + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.csv" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.jsonp" + n: 6 + Alpha diversity - Shannon's diversity index: + ftype: qzv + asserts: + - has_size: + min: 300k + max: 400k + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.csv" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.jsonp" + n: 6 + Alpha diversity - Observed features: + ftype: qzv + asserts: + - has_size: + min: 300k + max: 400k + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.csv" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.jsonp" + n: 6 + Beta diversity - Bray-Curtis distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Beta diversity - Jaccard distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Beta diversity - weighted UniFrac distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Emperor plot collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + Distance matrix collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + PCoA collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + Richness and evenness collection: + element_tests: + 'rarefied_table': + ftype: qzv + 'faith_pd_vector': + ftype: qzv + 'observed_features_vector': + ftype: qzv + 'shannon_vector': + ftype: qzv + 'eveness_vector': + ftype: qzv \ 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 new file mode 100644 index 000000000..e2e9410c8 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga @@ -0,0 +1,1131 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "The first step in hypothesis testing in microbial ecology is typically to look at within- (alpha) and between-sample (beta) diversity. We can calculate diversity metrics, apply appropriate statistical tests, and visualize the data using the q2-diversity plugin.", + "comments": [ + { + "color": "none", + "data": { + "size": 1, + "text": "From DADA2 table output or rarefaction" + }, + "id": 1, + "position": [ + 0, + 221.8 + ], + "size": [ + 152, + 76 + ], + "type": "text" + }, + { + "color": "none", + "data": { + "text": "Input files" + }, + "id": 0, + "position": [ + 136.6, + 3.8000000000000114 + ], + "size": [ + 101, + 40 + ], + "type": "markdown" + }, + { + "color": "none", + "data": { + "text": "Alpha diversity" + }, + "id": 3, + "position": [ + 844.9, + 0.7000000000000028 + ], + "size": [ + 134, + 40 + ], + "type": "markdown" + }, + { + "color": "none", + "data": { + "text": "Diversity metrics" + }, + "id": 2, + "position": [ + 513, + 1.8000000000000114 + ], + "size": [ + 139, + 39 + ], + "type": "markdown" + }, + { + "color": "none", + "data": { + "text": "Beta diversity" + }, + "id": 4, + "position": [ + 1184.8999999999999, + 0 + ], + "size": [ + 120, + 39 + ], + "type": "markdown" + }, + { + "child_steps": [ + 12, + 14, + 15, + 16 + ], + "color": "none", + "data": { + "title": "Collections" + }, + "id": 5, + "position": [ + 794.4, + 1062.3 + ], + "size": [ + 1263, + 352 + ], + "type": "frame" + } + ], + "creator": [ + { + "class": "Person", + "identifier": "0009-0008-1496-1677", + "name": "Debjyoti Ghosh" + }, + { + "address": "Permoserstra\u00dfe 15, 04318 Leipzig", + "class": "Organization", + "name": "Helmholtz-Zentrum f\u00fcr Umweltforschung - UFZ" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "QIIME2 VI: Diversity metrics and estimations", + "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.", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "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.", + "name": "Sampling depth" + } + ], + "label": "Sampling depth", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 134.6, + "top": 224.1206788736988 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "a926d4ba-b238-4499-a12b-a95840970cef", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "The tab separated file for the metadata", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "The tab separated file for the metadata", + "name": "Metadata" + } + ], + "label": "Metadata", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 125.04715373257632, + "top": 312.2417148460719 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"qiime2.tabular\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "8546caa2-9723-4c36-b693-988d43717ccf", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "Import of the dada2_table file from DADA2 outputs", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Import of the dada2_table file from DADA2 outputs", + "name": "Import DADA2 table output" + } + ], + "label": "Import DADA2 table output", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 131.65948794697385, + "top": 519.9723458836958 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"qza\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "f8b970d0-8396-4793-8131-36cc24fcc630", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "Import of the phylogenetic rooted 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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 70541e67e..87e734bf3 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 @@ -208,7 +208,7 @@ "workflow_outputs": [] }, "7": { - "annotation": "", + "annotation": "Phylogenetic tree for diversity analysis", "id": 7, "input_connections": { "DADA2 representative sequences": { @@ -223,7 +223,7 @@ } }, "inputs": [], - "label": null, + "label": "Phylogenetic tree for diversity analysis", "name": "QIIME2 III: Phylogenetic tree for diversity analysis", "outputs": [], "position": { @@ -394,7 +394,7 @@ ] }, "8": { - "annotation": "", + "annotation": "Taxonomic analysis", "id": 8, "input_connections": { "DADA2 feature table": { @@ -419,7 +419,7 @@ } }, "inputs": [], - "label": null, + "label": "Taxonomic analysis", "name": "QIIME2 V: Taxonomic analysis", "outputs": [], "position": { @@ -757,7 +757,7 @@ ] }, "9": { - "annotation": "", + "annotation": "Rarefaction", "id": 9, "input_connections": { "DADA2 feature table": { @@ -787,7 +787,7 @@ } }, "inputs": [], - "label": null, + "label": "Rarefaction", "name": "QIIME2 IV: Rarefaction", "outputs": [], "position": { From 8d0d55310dbeb3dfa329f33ae057bdc2a659bee1 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 22 Jun 2024 11:04:17 +0200 Subject: [PATCH 10/18] remove spaces in dockstore.yaml --- .../amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml index 4cd5e75ad..ff1554b97 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml @@ -1,6 +1,6 @@ version: 1.2 workflows: -- name: QIIME2-III-V Phylogeny Rarefaction Taxonomic-Analysis +- name: QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis subclass: Galaxy publish: true primaryDescriptorPath: /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga @@ -11,7 +11,7 @@ workflows: orcid: 0009-0008-1496-1677 - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" address: "Permoserstraße 15, 04318 Leipzig" -- name: QIIME2-III Phylogenetic tree for diversity analysis test +- name: QIIME2-III-Phylogenetic-tree-for-diversity-analysis-test subclass: Galaxy publish: true primaryDescriptorPath: /QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga @@ -22,7 +22,7 @@ workflows: orcid: 0009-0008-1496-1677 - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" address: "Permoserstraße 15, 04318 Leipzig" -- name: QIIME2-IV rarefaction +- name: QIIME2-IV-rarefaction subclass: Galaxy publish: true primaryDescriptorPath: /QIIME2-IV-rarefaction.ga From b40d9183260ad49a53f4993cda7a7562cf5f6736 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 22 Jun 2024 11:09:21 +0200 Subject: [PATCH 11/18] add changelog --- .../amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md new file mode 100644 index 000000000..7df9c9552 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md @@ -0,0 +1,4 @@ +# Changelog + +## [0.1] 2024-06-22 +First release. \ No newline at end of file From b77ab5f52c19adaf10b3b87be2c497201668f9b0 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 22 Jun 2024 12:41:20 +0200 Subject: [PATCH 12/18] Rename inputs --- ...diversity-metrics-and-estimations-tests.yml | 4 ++-- ...ME2-VI-diversity-metrics-and-estimations.ga | 18 +++++++++--------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations-tests.yml index 470ebe471..5ef46fed7 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations-tests.yml +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations-tests.yml @@ -4,11 +4,11 @@ class: File location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv filetype: qiime2.tabular - Import DADA2 table output: + Feature table: class: File location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza filetype: qza - Import rooted tree: + Rooted tree: class: File location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/tree.qza filetype: qza 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 e2e9410c8..776f4b7f0 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 @@ -177,19 +177,19 @@ "workflow_outputs": [] }, "2": { - "annotation": "Import of the dada2_table file from DADA2 outputs", + "annotation": "For instance the dada2_table from DADA2", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Import of the dada2_table file from DADA2 outputs", - "name": "Import DADA2 table output" + "description": "For instance the dada2_table from DADA2", + "name": "Feature table" } ], - "label": "Import DADA2 table output", - "name": "Input dataset", + "label": "Feature table", + "name": "Feature table", "outputs": [], "position": { "left": 131.65948794697385, @@ -204,18 +204,18 @@ "workflow_outputs": [] }, "3": { - "annotation": "Import of the phylogenetic rooted tree", + "annotation": "Rooted phylogenetic tree", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "Import of the phylogenetic rooted tree", - "name": "Import rooted tree" + "description": "Rooted phylogenetic tree", + "name": "Rooted tree" } ], - "label": "Import rooted tree", + "label": "Rooted tree", "name": "Input dataset", "outputs": [], "position": { From 841af533594c3c6cf2988ebc24c668663c632972 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 22 Jun 2024 13:20:37 +0200 Subject: [PATCH 13/18] add README --- .../qiime2/qiime2-III-VI-downsteam/README.md | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/README.md diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/README.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/README.md new file mode 100644 index 000000000..55a291454 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/README.md @@ -0,0 +1,70 @@ +# QIIME2 workflows + +## Available workflows + +- III-V Downstream analyses: III) reconstruct a taxonomy for diversity analysis, IV) rarefaction analysis, V) taxonomic analysis. +- VI: Computation of diversity metrics and estimations + +Analogous to the procedures described in the Parkinson’s Mouse Tutorial: https://docs.qiime2.org/2024.5/tutorials/pd-mice/ + +## Inputs + +The two workflows have two inputs in common + +- Feature table: Count data +- Metadata: Metadata table + +and the following extra inputs + +III-V + +- Representative sequences: Representative (ASV) sequences +- Minimum depth: Lower limit of the sampling depth for the alpha rarefaction analysis +- Maximum depth: Upper limit of the sampling depth for the alpha rarefaction analysis +- SEPP fragment insertion reference: used for the reconstruction of the phylogenetic tree +- Taxonomic classifier: The classifier to assign taxonomic information to the ASVs + +VI: + +Sampling depth: For the metric calculation (should be based on the rarefaction analysis done in IV) +Target metadata parameter: that should be used for beta diversity calculations +Rooted Tree: for instance the tree computed in III + +## Processing + +III-V + +- Phylogenetic tree generation using `qiime2 fragment-insertion sepp` +- Alpha rarefaction analysis using `qiime2 diversity alpha-rarefaction` +- Taxonomic classification using `qiime2 feature-classifier classify-sklearn` and compute barplot and tabular output + +VI: + +- compute alpha and beta diversity metrics using `qiime2 diversity core-metrics-phylogenetic` +- organize these metrics in 4 collections: + 1. Distance matrix collection (weighted and unweighted unifrac, jaccard and bray curtis) + 2. PCoA collection (same as the distance matrices) + 3. Emperor plot collection (same as the distance matrices) + 4. Richness and evenness collection (rarefied table, faith pd vector observed features vector, shannon vector, evenness vector) +- get visualization for alpha diversity: + - Pielou's eveness + - Observed features + - Shannons diversity index +- get visualization for beta diversity + - Jaccard distance matrix + - Bray curtis distance matrix + - Unifrac distance metrix + +## Outputs + +III-V: + +- Phylogenetic tree +- Rarefaction curve +- Taxonomic classification (as qza, barplot and table) + +VI: + +- Four collections containing: distance matrix, PCoA, Emperor plots, Richness and evenness +- Visualization for alpha diversity: Pielou's eveness, Observed features, Shannons diversity index +- Visualization for beta diversity: Jaccard, Bray curtis, Unifrac \ No newline at end of file From 30ef4f0570826606cd49a2c8f232d7782a7cfd77 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 22 Jun 2024 13:22:22 +0200 Subject: [PATCH 14/18] remove redundant workflows --- .../qiime2-III-VI-downsteam/.dockstore.yml | 33 -- ...etic-tree-for-diversity-analysis-tests.yml | 31 -- ...hylogenetic-tree-for-diversity-analysis.ga | 152 --------- .../QIIME2-IV-rarefaction-tests.yml | 34 -- .../QIIME2-IV-rarefaction.ga | 250 -------------- .../QIIME2-V-taxonomic-analysis-tests.yml | 63 ---- .../QIIME2-V-taxonomic-analysis.ga | 309 ------------------ 7 files changed, 872 deletions(-) delete mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml delete mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga delete mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction-tests.yml delete mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction.ga delete mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis-tests.yml delete mode 100644 workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis.ga diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml index ff1554b97..e62e3c556 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml @@ -11,39 +11,6 @@ workflows: orcid: 0009-0008-1496-1677 - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" address: "Permoserstraße 15, 04318 Leipzig" -- name: QIIME2-III-Phylogenetic-tree-for-diversity-analysis-test - subclass: Galaxy - publish: true - primaryDescriptorPath: /QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga - testParameterFiles: - - /QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml - authors: - - name: Debjyoti Ghosh - orcid: 0009-0008-1496-1677 - - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" - address: "Permoserstraße 15, 04318 Leipzig" -- name: QIIME2-IV-rarefaction - subclass: Galaxy - publish: true - primaryDescriptorPath: /QIIME2-IV-rarefaction.ga - testParameterFiles: - - /QIIME2-IV-rarefaction-tests.yml - authors: - - name: Debjyoti Ghosh - orcid: 0009-0008-1496-1677 - - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" - address: "Permoserstraße 15, 04318 Leipzig" -- name: QIIME2-V-taxonomic-analysis - subclass: Galaxy - publish: true - primaryDescriptorPath: /QIIME2-V-taxonomic-analysis.ga - testParameterFiles: - - /QIIME2-V-taxonomic-analysis-tests.yml - authors: - - name: Debjyoti Ghosh - orcid: 0009-0008-1496-1677 - - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" - address: "Permoserstraße 15, 04318 Leipzig" - name: QIIME2-VI-diversity-metrics-and-estimations subclass: Galaxy diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml deleted file mode 100644 index 3d7c6283c..000000000 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis-tests.yml +++ /dev/null @@ -1,31 +0,0 @@ -- doc: Test outline for QIIME2-III:-Phylogenetic-tree-for-diversity-analysis - job: - DADA2 representative sequences: - class: File - location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_rep_set.qza - filetype: qza - SEPP fragment insertion source file: - class: File - location: https://data.qiime2.org/2024.2/common/sepp-refs-gg-13-8.qza - filetype: qza - outputs: - Rooted tree: - ftype: qza - asserts: - - has_size: - min: 2M - max: 3M - - has_archive_member: - path: "^[^/]*/data/tree.nwk" - n: 1 - asserts: - - has_text_matching: - expression: "k__Bacteria" - - has_archive_member: - path: "^[^/]*/metadata.yaml" - n: 1 - asserts: - - has_line: - line: "type: Phylogeny[Rooted]" - - has_line: - line: "format: NewickDirectoryFormat" \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga deleted file mode 100644 index 8169044a5..000000000 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-phylogenetic-tree-for-diversity-analysis.ga +++ /dev/null @@ -1,152 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "QIIME 2 analysis allows the use of phylogenetic trees for diversity metrics such as Faith\u2019s Phylogenetic Diversity and UniFrac distance. The tree provides an inherent structure to the data, allowing us to consider an evolutionary relationship between organisms.", - "comments": [], - "creator": [ - { - "class": "Person", - "identifier": "0009-0008-1496-1677", - "name": "Debjyoti Ghosh" - }, - { - "address": "Permoserstra\u00dfe 15, 04318 Leipzig", - "class": "Organization", - "name": "Helmholtz-Zentrum f\u00fcr Umweltforschung - UFZ" - } - ], - "format-version": "0.1", - "license": "MIT", - "name": "QIIME2 III: Phylogenetic tree for diversity analysis", - "steps": { - "0": { - "annotation": "DADA2 representative sequences", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "DADA2 representative sequences", - "name": "Import DADA2 representative sequences" - } - ], - "label": "DADA2 representative sequences", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 0, - "top": 19.497570176200952 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"qza\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "71e6440a-8aa6-4899-bd11-901dffae36a5", - "when": null, - "workflow_outputs": [] - }, - "1": { - "annotation": "Reference data for the SEPP fragmentation insertion phylogenetic tree generation", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "Reference data for the SEPP fragmentation insertion phylogenetic tree generatio", - "name": "SEPP fragment insertion source file" - } - ], - "label": "SEPP fragment insertion source file", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 0.34857177734375, - "top": 144.6569787455369 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"qza\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "2bf4a3e7-51d9-4323-ab9a-f6a85c3b0cd7", - "when": null, - "workflow_outputs": [] - }, - "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", - "errors": null, - "id": 2, - "input_connections": { - "reference_database": { - "id": 1, - "output_name": "output" - }, - "representative_sequences": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": "Phylogenetic tree generation", - "name": "qiime2 fragment-insertion sepp", - "outputs": [ - { - "name": "tree", - "type": "qza" - }, - { - "name": "placements", - "type": "qza" - } - ], - "position": { - "left": 310.42930324654003, - "top": 0 - }, - "post_job_actions": { - "HideDatasetActionplacements": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "placements" - }, - "RenameDatasetActionplacements": { - "action_arguments": { - "newname": "rooted_tree_placements" - }, - "action_type": "RenameDatasetAction", - "output_name": "placements" - }, - "RenameDatasetActiontree": { - "action_arguments": { - "newname": "rooted_tree" - }, - "action_type": "RenameDatasetAction", - "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_shed_repository": { - "changeset_revision": "2fa85eae206e", - "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", - "type": "tool", - "uuid": "f6aa969f-1bdf-4d74-8b0a-af93a0640040", - "when": null, - "workflow_outputs": [ - { - "label": "Rooted tree", - "output_name": "tree", - "uuid": "e572bf3b-64aa-4bd5-a629-f53ba6a383be" - } - ] - } - }, - "tags": [], - "uuid": "4a96a5b2-f8cc-41a3-9f16-a84e47e05afe", - "version": 10 -} \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction-tests.yml deleted file mode 100644 index ed5372cf9..000000000 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction-tests.yml +++ /dev/null @@ -1,34 +0,0 @@ -- doc: Test outline for QIIME2-IV:-Rarefaction - job: - Metadata: - class: File - location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv - filetype: tabular - DADA2 feature table: - class: File - location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza - filetype: qza - Rooted tree: - class: File - location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/tree.qza - filetype: qza - Minimum depth: '1' - Maximum depth: '2019' - outputs: - Rarefaction curve: - ftype: qzv - asserts: - - has_size: - min: 400k - max: 500k - - has_archive_member: - path: "^[^/]*/data/index.html" - n: 1 - # data per measure - - has_archive_member: - path: "^[^/]*/data/.*\\.csv" - n: 3 - # data for each measure and metadata variable (*7) - - has_archive_member: - path: "^[^/]*/data/.*\\.jsonp" - n: 21 \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction.ga deleted file mode 100644 index c102853c8..000000000 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-IV-rarefaction.ga +++ /dev/null @@ -1,250 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "Rarefaction is a method for normalization via sub-sampling without replacement and is commonly used as a workaround for the issue of uneven sequencing depth. Rarefaction occurs in two steps: first, samples which are below the rarefaction depth are filtered out of the feature table. Then, all remaining samples are subsampled without replacement to get to the specified sequencing depth.", - "comments": [], - "creator": [ - { - "class": "Person", - "identifier": "0009-0008-1496-1677", - "name": "Debjyoti Ghosh" - }, - { - "address": "Permoserstra\u00dfe 15, 04318 Leipzig", - "class": "Organization", - "name": "Helmholtz-Zentrum f\u00fcr Umweltforschung - UFZ" - } - ], - "format-version": "0.1", - "license": "MIT", - "name": "QIIME2 IV: Rarefaction", - "steps": { - "0": { - "annotation": "Tab separated metadata file", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "Tab separated metadata file", - "name": "Metadata" - } - ], - "label": "Metadata", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 0, - "top": 0 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "8dde0c69-40f1-415a-a866-5d1115e80cdf", - 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"uuid": "b4075e2a-6d99-4102-a396-05ef3f4b3cca" - } - ] - }, - "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", - "errors": null, - "id": 5, - "input_connections": { - "__q2galaxy__GUI__section__extra_opts__|metadata_0|__q2galaxy__GUI__conditional__metadata__|source": { - "id": 0, - "output_name": "output" - }, - "__q2galaxy__GUI__section__extra_opts__|min_depth": { - "id": 3, - "output_name": "output" - }, - "__q2galaxy__GUI__section__extra_opts__|phylogeny": { - "id": 2, - "output_name": "output" - }, - "max_depth": { - "id": 4, - "output_name": "output" - }, - "table": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool qiime2 diversity alpha-rarefaction", - "name": "__q2galaxy__GUI__section__extra_opts__" - }, - { - "description": "runtime parameter for tool qiime2 diversity alpha-rarefaction", - "name": "__q2galaxy__GUI__section__extra_opts__" - } - ], - "label": "Alpha rarefaction", - "name": "qiime2 diversity alpha-rarefaction", - "outputs": [ - { - "name": "visualization", - "type": "qzv" - } - ], - "position": { - "left": 348.86456298828125, - "top": 75.385009765625 - }, - "post_job_actions": { - "RenameDatasetActionvisualization": { - "action_arguments": { - "newname": "alpha_rarefaction" - }, - "action_type": "RenameDatasetAction", - "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_shed_repository": { - "changeset_revision": "97cb20f77d50", - "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", - "type": "tool", - "uuid": "489f6ea1-d13a-48ae-b71d-40c413f3b45e", - "when": null, - "workflow_outputs": [ - { - "label": "Rarefaction curve", - "output_name": "visualization", - "uuid": "5675c59e-7e5e-4b0f-a7e7-263a0fa42f1d" - } - ] - } - }, - "tags": [], - "uuid": "3c96b4fd-c67a-4c79-9e78-6f77e72b4bdf", - "version": 9 -} \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis-tests.yml deleted file mode 100644 index 9c3015dc8..000000000 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis-tests.yml +++ /dev/null @@ -1,63 +0,0 @@ -- doc: Test outline for QIIME2-V:-Taxonomic-analysis - job: - Metadata: - class: File - location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv - filetype: tabular - DADA2 representative sequences: - class: File - location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_rep_set.qza - filetype: qza - Taxonomic classifier: - class: File - location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza - filetype: qza - DADA2 feature table: - class: File - location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza - filetype: qza - outputs: - Taxonomy classification: - ftype: qza - asserts: - - has_size: - min: 70k - max: 80k - - has_archive_member: - path: "^[^/]*/metadata.yaml" - n: 1 - asserts: - - has_line: - line: "type: FeatureData[Taxonomy]" - - has_line: - line: "format: TSVTaxonomyDirectoryFormat" - - has_archive_member: - path: "^[^/]*/data/taxonomy.tsv" - n: 1 - asserts: - - has_n_lines: - n: 288 - Taxa barplot: - ftype: qzv - asserts: - - has_size: - min: 400k - max: 500k - - has_archive_member: - path: "^[^/]*/data/.*\\.csv" - n: 7 - - has_archive_member: - path: "^[^/]*/data/.*\\.jsonp" - n: 7 - Taxonomy classification table: - ftype: qza - asserts: - - has_size: - min: 1M - max: 2M - - has_archive_member: - path: "^[^/]*/data/metadata.tsv" - n: 1 - asserts: - - has_n_lines: - n: 289 \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis.ga b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis.ga deleted file mode 100644 index a482b8b2e..000000000 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-V-taxonomic-analysis.ga +++ /dev/null @@ -1,309 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "Assign taxonomy to the sequences in FeatureData using a pre-trained Naive Bayes classifier with the q2-feature-classifier plugin.", - "comments": [], - "creator": [ - { - "class": "Person", - "identifier": "0009-0008-1496-1677", - "name": "Debjyoti Ghosh" - }, - { - "address": "Permoserstra\u00dfe 15, 04318 Leipzig", - "class": "Organization", - "name": "Helmholtz-Zentrum f\u00fcr Umweltforschung - UFZ" - } - ], - "format-version": "0.1", - "license": "MIT", - "name": "QIIME2 V: Taxonomic analysis", - "steps": { - "0": { - "annotation": "Tab separated metadata file", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "Tab separated metadata file", - "name": "Metadata" - } - ], - "label": "Metadata", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 0.791015625, - "top": 2.6916668368741092 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "c2deedc3-713c-4030-9fb8-5734c016ad5c", - "when": null, - "workflow_outputs": [] - }, - "1": { - "annotation": "Demultiplexed sequences in qza format", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "Demultiplexed sequences in qza format", - "name": "DADA2 representative sequences" - } - ], - "label": "DADA2 representative sequences", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 1.8453224170332305, - "top": 111.47987345989156 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"qza\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "e250ddc1-f567-40ca-9f2b-e07bbf84cdec", - "when": null, - "workflow_outputs": [] - }, - "2": { - "annotation": "Taxonomic classifier (e.g. Greengenes or SILVA)", - "content_id": null, - "errors": null, - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "Taxonomic classifier (e.g. Greengenes or SILVA)", - "name": "Taxonomic classifier" - } - ], - "label": "Taxonomic classifier", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 0.451446533203125, - "top": 241.0041668368741 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"qza\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "ac0cdf1d-2a29-481c-aaa3-21f1b8f9b97d", - "when": null, - "workflow_outputs": [] - }, - "3": { - "annotation": "DADA2 feature table", - "content_id": null, - "errors": null, - "id": 3, - "input_connections": {}, - "inputs": [ - { - "description": "DADA2 feature table", - "name": "DADA2 feature table" - } - ], - "label": "DADA2 feature table", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 0, - "top": 365.0612957431241 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"qza\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "81495001-5b55-4676-8d7f-cb0659d6acc3", - "when": null, - "workflow_outputs": [] - }, - "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", - "errors": null, - "id": 4, - "input_connections": { - "classifier": { - "id": 2, - 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} - ], - "label": "Taxonomy barplot", - "name": "qiime2 taxa barplot", - "outputs": [ - { - "name": "visualization", - "type": "qzv" - } - ], - "position": { - "left": 645.4988052205106, - "top": 0 - }, - "post_job_actions": { - "RenameDatasetActionvisualization": { - "action_arguments": { - "newname": "taxa_barplot" - }, - "action_type": "RenameDatasetAction", - "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_shed_repository": { - "changeset_revision": "124673b2e9e7", - "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}", - 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"action_arguments": { - "newname": "taxonomy_classification_visualisation" - }, - "action_type": "RenameDatasetAction", - "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_shed_repository": { - "changeset_revision": "d6e1b976c373", - "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", - "type": "tool", - "uuid": "380548c3-b9b6-4ebd-ae68-e3fbb891f7e5", - "when": null, - "workflow_outputs": [ - { - "label": "Taxonomy classification table", - "output_name": "visualization", - "uuid": "9b1b4f66-d7a7-42cd-ac81-00c417300f47" - } - ] - } - }, - "tags": [], - "uuid": "41bae731-2f27-4e57-b94d-683e0ab94b43", - "version": 8 -} \ No newline at end of file From aa968232ec9aac45448d2c7295f301f6400d4862 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 22 Jun 2024 15:47:33 +0200 Subject: [PATCH 15/18] fix --- .../QIIME2-VI-diversity-metrics-and-estimations.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 776f4b7f0..738e53912 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 @@ -189,7 +189,7 @@ } ], "label": "Feature table", - "name": "Feature table", + "name": "Input dataset", "outputs": [], "position": { "left": 131.65948794697385, From 631267d033c4da7c7e3a4c6abbb3e8abf5652742 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 22 Jun 2024 16:24:57 +0200 Subject: [PATCH 16/18] use same version of the import tool --- ...ME2-VI-diversity-metrics-and-estimations.ga | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) 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 738e53912..9767ccd7b 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 @@ -259,7 +259,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.2.1+dist.he188c3c2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3", "errors": null, "id": 5, "input_connections": { @@ -288,15 +288,15 @@ "output_name": "imported_data" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.2.1+dist.he188c3c2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3", "tool_shed_repository": { - "changeset_revision": "9dbdf05beaa9", + "changeset_revision": "10447a4b0cc3", "name": "qiime2_core__tools__import", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 37, \"__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": "2024.2.1+dist.he188c3c2", + "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", "type": "tool", "uuid": "be1fae33-1b8d-4756-854f-a0587934da09", "when": null, @@ -989,7 +989,7 @@ } }, "tool_id": "__BUILD_LIST__", - "tool_state": "{\"datasets\": [{\"__index__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"unweighted_unifrac\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"weighted_unifrac\"}}, {\"__index__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"jaccard\"}}, {\"__index__\": 3, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"bray_curtis\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"datasets\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"unweighted_unifrac\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"weighted_unifrac\"}}, {\"__index__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"jaccard\"}}, {\"__index__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"bray_curtis\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.2.0", "type": "tool", "uuid": "ecfc4438-5355-436b-8508-8bd4bfcb03ba", @@ -1048,7 +1048,7 @@ } }, "tool_id": "__BUILD_LIST__", - "tool_state": "{\"datasets\": [{\"__index__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"unweighted_unifrac\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"weighted_unifrac\"}}, {\"__index__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"jaccard\"}}, {\"__index__\": 3, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"bray_curtis\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"datasets\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"unweighted_unifrac\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"weighted_unifrac\"}}, {\"__index__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"jaccard\"}}, {\"__index__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"bray_curtis\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.2.0", "type": "tool", "uuid": "9a17d575-227f-4f98-a949-d5d90e733a41", @@ -1111,7 +1111,7 @@ } }, "tool_id": "__BUILD_LIST__", - "tool_state": "{\"datasets\": [{\"__index__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"rarefied_table\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"faith_pd_vector\"}}, {\"__index__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"observed_features_vector\"}}, {\"__index__\": 3, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"shannon_vector\"}}, {\"__index__\": 4, \"input\": {\"__class__\": \"RuntimeValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"eveness_vector\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"datasets\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"rarefied_table\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"faith_pd_vector\"}}, {\"__index__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"observed_features_vector\"}}, {\"__index__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"shannon_vector\"}}, {\"__index__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"id_cond\": {\"id_select\": \"manual\", \"__current_case__\": 2, \"identifier\": \"eveness_vector\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.2.0", "type": "tool", "uuid": "032f5d65-2ed6-47b2-8837-25aa360fd355", @@ -1128,4 +1128,4 @@ "tags": [], "uuid": "300b5a7d-f763-486a-a8ea-87ea84571f19", "version": 2 -} \ No newline at end of file +} From 63edeb968015a08191b74bae262a67d888deea4c Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Mon, 5 Aug 2024 10:06:00 +0200 Subject: [PATCH 17/18] fix dockstore.yml --- .../amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml index e62e3c556..2031035d2 100644 --- a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml @@ -15,9 +15,9 @@ workflows: - name: QIIME2-VI-diversity-metrics-and-estimations subclass: Galaxy publish: true - primaryDescriptorPath: /QIIME2-VI-Diversity-metrics-and-estimations.ga + primaryDescriptorPath: /QIIME2-VI-diversity-metrics-and-estimations.ga testParameterFiles: - - /QIIME2-V-taxonomic-analysis-tests.yml + - /QIIME2-VI-diversity-metrics-and-estimations-tests.yml authors: - name: Debjyoti Ghosh orcid: 0009-0008-1496-1677 From 0914c963b3aca769272a85492546f54eeff193aa Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 6 Aug 2024 14:08:24 +0200 Subject: [PATCH 18/18] Apply suggestions from code review Co-authored-by: Marius van den Beek --- ...2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml | 4 ++-- .../QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga | 1 + .../QIIME2-VI-diversity-metrics-and-estimations.ga | 1 + 3 files changed, 4 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 d0b065a86..b5cf8d512 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 @@ -12,8 +12,8 @@ class: File location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza filetype: qza - Minimum depth: '1' - Maximum depth: '2019' + Minimum depth: 1 + 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 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 87e734bf3..19b3f61c9 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 @@ -17,6 +17,7 @@ "format-version": "0.1", "license": "MIT", "name": "QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis", + "release": "0.1", "steps": { "0": { "annotation": "Representative sequences, e.g. from DADA2", 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 9767ccd7b..bac0948ff 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 @@ -121,6 +121,7 @@ "format-version": "0.1", "license": "MIT", "name": "QIIME2 VI: Diversity metrics and estimations", + "release": "0.1", "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.",