From c6f5fa53538c65e06375e82eb8cbfc0c065c43cf Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 4 Nov 2024 04:30:17 +0000 Subject: [PATCH] Updating workflows/amplicon/qiime2/qiime2-II-denoising from 0.2 to 0.3 --- .../qiime2/qiime2-II-denoising/CHANGELOG.md | 9 ++++ ...g-and-feature-table-creation-single-end.ga | 45 ++++++++++--------- ...g-and-feature-table-creation-paired-end.ga | 45 ++++++++++--------- 3 files changed, 59 insertions(+), 40 deletions(-) diff --git a/workflows/amplicon/qiime2/qiime2-II-denoising/CHANGELOG.md b/workflows/amplicon/qiime2/qiime2-II-denoising/CHANGELOG.md index e0e5441b4..0e0572df0 100644 --- a/workflows/amplicon/qiime2/qiime2-II-denoising/CHANGELOG.md +++ b/workflows/amplicon/qiime2/qiime2-II-denoising/CHANGELOG.md @@ -1,5 +1,14 @@ # Changelog +## [0.3] 2024-11-04 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2024.10.0+q2galaxy.2024.10.0` +- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2024.10.0+q2galaxy.2024.10.0` + ## [0.1] 2024-04-08 First release. ## [0.2] 2024-05-23 diff --git a/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga b/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga index 8c0b2479c..48e2874bb 100644 --- a/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga +++ b/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga @@ -15,7 +15,7 @@ } ], "format-version": "0.1", - "release": "0.2", + "release": "0.3", "license": "MIT", "name": "QIIME2 IIa: Denoising (sequence quality control) and feature table creation (single-end)", "steps": { @@ -129,7 +129,7 @@ }, "4": { "annotation": "qiime2 dada2 denoise-paired\nDenoise and dereplicate paired-end sequences\nSmall insight: if the denoising percentage is lower or poorer, reduce 'trunc_q: Int' from 2 to 1.", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 4, "input_connections": { @@ -173,15 +173,15 @@ "top": 133.89925462837766 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "e7812ca89033", + "changeset_revision": "354f63459d37", "name": "qiime2__dada2__denoise_single", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"trim_left\": {\"__class__\": \"ConnectedValue\"}, \"max_ee\": \"2.0\", \"trunc_q\": \"2\", \"pooling_method\": \"independent\", \"chimera_method\": \"consensus\", \"min_fold_parent_over_abundance\": \"1.0\", \"allow_one_off\": false, \"n_threads\": \"1\", \"n_reads_learn\": \"1000000\", \"hashed_feature_ids\": true}, \"demultiplexed_seqs\": {\"__class__\": \"ConnectedValue\"}, \"trunc_len\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"trim_left\": {\"__class__\": \"ConnectedValue\"}, \"max_ee\": \"2.0\", \"trunc_q\": \"2\", \"pooling_method\": \"independent\", \"chimera_method\": \"consensus\", \"min_fold_parent_over_abundance\": \"1.0\", \"allow_one_off\": false, \"n_reads_learn\": \"1000000\", \"hashed_feature_ids\": true, \"retain_all_samples\": true}, \"demultiplexed_seqs\": {\"__class__\": \"ConnectedValue\"}, \"trunc_len\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "a6369693-372e-4258-9e81-b7085746e441", "when": null, @@ -205,7 +205,7 @@ }, "5": { "annotation": "qiime2 feature-table tabulate-seqs\nView sequence associated with each feature", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 5, "input_connections": { @@ -214,7 +214,12 @@ "output_name": "representative_sequences" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool qiime2 feature-table tabulate-seqs", + "name": "__q2galaxy__GUI__section__extra_opts__" + } + ], "label": "Tabulate DADA2 denoised representative sequences", "name": "qiime2 feature-table tabulate-seqs", "outputs": [ @@ -236,15 +241,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "6d5cd7bcc0d0", + "changeset_revision": "c4570ced1d88", "name": "qiime2__feature_table__tabulate_seqs", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"taxonomy\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [], \"merge_method\": \"strict\"}, \"data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "221fe314-49e9-48bd-979e-1b6d0c2f4192", "when": null, @@ -258,7 +263,7 @@ }, "6": { "annotation": "qiime2 metadata tabulate\nInteractively explore Metadata in a table", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 6, "input_connections": { @@ -289,15 +294,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "d6e1b976c373", + "changeset_revision": "9857be21dcaf", "name": "qiime2__metadata__tabulate", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"page_size\": \"100\"}, \"input\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__input__\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "082c2df8-422c-4661-b39d-181ef7ff3072", "when": null, @@ -311,7 +316,7 @@ }, "7": { "annotation": "qiime2 feature-table summarize\nSummarize table\n", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 7, "input_connections": { @@ -346,15 +351,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "365ce7a8e641", + "changeset_revision": "d0f2249afe30", "name": "qiime2__feature_table__summarize", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"sample_metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__sample_metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}]}, \"table\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "f6376403-1be3-4bc0-af85-d5e2e04984b2", "when": null, diff --git a/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga b/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga index 1ee508999..ccd671a82 100644 --- a/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga +++ b/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga @@ -15,7 +15,7 @@ } ], "format-version": "0.1", - "release": "0.2", + "release": "0.3", "license": "MIT", "name": "QIIME2 IIb: Denoising (sequence quality control) and feature table creation (paired-end)", "steps": { @@ -183,7 +183,7 @@ }, "6": { "annotation": "qiime2 dada2 denoise-paired\nDenoise and dereplicate paired-end sequences\nSmall insight: if the denoising percentage is lower or poorer, reduce 'trunc_q: Int' from 2 to 1.", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 6, "input_connections": { @@ -239,15 +239,15 @@ "top": 186.09945678710938 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "06bacd08bb47", + "changeset_revision": "933b92011b91", "name": "qiime2__dada2__denoise_paired", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"trim_left_f\": {\"__class__\": \"ConnectedValue\"}, \"trim_left_r\": {\"__class__\": \"ConnectedValue\"}, \"max_ee_f\": \"2.0\", \"max_ee_r\": \"2.0\", \"trunc_q\": \"2\", \"min_overlap\": \"12\", \"pooling_method\": \"independent\", \"chimera_method\": \"consensus\", \"min_fold_parent_over_abundance\": \"1.0\", \"allow_one_off\": false, \"n_threads\": \"1\", \"n_reads_learn\": \"1000000\", \"hashed_feature_ids\": true}, \"demultiplexed_seqs\": {\"__class__\": \"ConnectedValue\"}, \"trunc_len_f\": {\"__class__\": \"ConnectedValue\"}, \"trunc_len_r\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"trim_left_f\": {\"__class__\": \"ConnectedValue\"}, \"trim_left_r\": {\"__class__\": \"ConnectedValue\"}, \"max_ee_f\": \"2.0\", \"max_ee_r\": \"2.0\", \"trunc_q\": \"2\", \"min_overlap\": \"12\", \"pooling_method\": \"independent\", \"chimera_method\": \"consensus\", \"min_fold_parent_over_abundance\": \"1.0\", \"allow_one_off\": false, \"n_reads_learn\": \"1000000\", \"hashed_feature_ids\": true, \"retain_all_samples\": true}, \"demultiplexed_seqs\": {\"__class__\": \"ConnectedValue\"}, \"trunc_len_f\": {\"__class__\": \"ConnectedValue\"}, \"trunc_len_r\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "93e5c884-d782-4b97-96ba-d9abdf4ce4ed", "when": null, @@ -271,7 +271,7 @@ }, "7": { "annotation": "qiime2 feature-table tabulate-seqs\nView sequence associated with each feature", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 7, "input_connections": { @@ -280,7 +280,12 @@ "output_name": "representative_sequences" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool qiime2 feature-table tabulate-seqs", + "name": "__q2galaxy__GUI__section__extra_opts__" + } + ], "label": "Tabulate DADA2 denoised representative sequences", "name": "qiime2 feature-table tabulate-seqs", "outputs": [ @@ -302,15 +307,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "6d5cd7bcc0d0", + "changeset_revision": "c4570ced1d88", "name": "qiime2__feature_table__tabulate_seqs", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"taxonomy\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [], \"merge_method\": \"strict\"}, \"data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "221fe314-49e9-48bd-979e-1b6d0c2f4192", "when": null, @@ -324,7 +329,7 @@ }, "8": { "annotation": "qiime2 metadata tabulate\nInteractively explore Metadata in an HTML table", - "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0", "errors": null, "id": 8, "input_connections": { @@ -355,15 +360,15 @@ "output_name": "visualization" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0", "tool_shed_repository": { - "changeset_revision": "d6e1b976c373", + "changeset_revision": "9857be21dcaf", "name": "qiime2__metadata__tabulate", "owner": "q2d2", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"page_size\": \"100\"}, \"input\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__input__\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "082c2df8-422c-4661-b39d-181ef7ff3072", "when": null, @@ -377,7 +382,7 @@ }, "9": { "annotation": "qiime2 feature-table summarize\nSummarize table\n", - 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"tool_version": "2023.5.0+q2galaxy.2023.5.0.2", + "tool_version": "2024.10.0+q2galaxy.2024.10.0", "type": "tool", "uuid": "f6376403-1be3-4bc0-af85-d5e2e04984b2", "when": null,