Merge pull request #498 from planemo-autoupdate/workflows/amplicon/qi…

…ime2/qiime2-III-VI-downsteam Updating workflows/amplicon/qiime2/qiime2-III-VI-downsteam from 0.1 to 0.2
galaxyproject · Nov 25, 2024 · f140bc4 · f140bc4
2 parents 386bda6 + f387426
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diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md
@@ -1,4 +1,17 @@
 # Changelog
 
+## [0.2] 2024-11-04
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.10.0+q2galaxy.2024.10.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.10.0+q2galaxy.2024.10.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.10.0+q2galaxy.2024.10.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2023.5.1+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.10.0+dist.h3d8a7e27`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2023.5.1+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2024.10.0+q2galaxy.2024.10.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2023.5.1+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2024.10.0+q2galaxy.2024.10.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2023.5.1+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2024.10.0+q2galaxy.2024.10.0`
+
 ## [0.1] 2024-06-22
 First release.
diff --git a/...2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml b/...2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml
@@ -16,7 +16,7 @@
     Maximum depth: 2019
     Taxonomic classifier:
       class: File
-      location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza
+      location: https://docs.qiime2.org/2024.10/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza
       filetype: qza
     SEPP fragment insertion reference:
       class: File
@@ -66,7 +66,7 @@
       ftype: qza
       asserts:
         - has_size:
-            min: 70k
+            min: 40k
             max: 80k
         - has_archive_member:
             path: "^[^/]*/metadata.yaml"
@@ -105,4 +105,4 @@
             n: 1
             asserts:
               - has_n_lines:
-                  n: 289
+                  n: 289
diff --git a/...n/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga b/...n/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga
@@ -17,7 +17,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis",
-    "release": "0.1",
+    "release": "0.2",
     "steps": {
         "0": {
             "annotation": "Representative sequences, e.g. from DADA2",
@@ -223,7 +223,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "Phylogenetic tree for diversity analysis",
+                    "name": "Phylogenetic tree for diversity analysis"
+                }
+            ],
             "label": "Phylogenetic tree for diversity analysis",
             "name": "QIIME2 III: Phylogenetic tree for diversity analysis",
             "outputs": [],
@@ -307,7 +312,7 @@
                     },
                     "2": {
                         "annotation": "qiime2 fragment-insertion sepp\nInsert fragment sequences using SEPP into reference phylogenies.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2023.5.0+q2galaxy.2023.5.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.10.0+q2galaxy.2024.10.0",
                         "errors": null,
                         "id": 2,
                         "input_connections": {
@@ -358,15 +363,15 @@
                                 "output_name": "tree"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2023.5.0+q2galaxy.2023.5.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__fragment_insertion__sepp/qiime2__fragment_insertion__sepp/2024.10.0+q2galaxy.2024.10.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2fa85eae206e",
+                            "changeset_revision": "a74f06287b8c",
                             "name": "qiime2__fragment_insertion__sepp",
                             "owner": "q2d2",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"alignment_subset_size\": \"1000\", \"placement_subset_size\": \"5000\", \"threads\": \"1\", \"debug\": false}, \"reference_database\": {\"__class__\": \"ConnectedValue\"}, \"representative_sequences\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2023.5.0+q2galaxy.2023.5.0.2",
+                        "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"alignment_subset_size\": \"1000\", \"placement_subset_size\": \"5000\", \"debug\": false}, \"reference_database\": {\"__class__\": \"ConnectedValue\"}, \"representative_sequences\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2024.10.0+q2galaxy.2024.10.0",
                         "type": "tool",
                         "uuid": "f6aa969f-1bdf-4d74-8b0a-af93a0640040",
                         "when": null,
@@ -379,8 +384,8 @@
                         ]
                     }
                 },
-                "tags": "",
-                "uuid": "4a96a5b2-f8cc-41a3-9f16-a84e47e05afe"
+                "tags": [],
+                "uuid": "ea7b99e7-ee7b-4fd5-bda8-cd00ddfe6ade"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -419,7 +424,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "Taxonomic analysis",
+                    "name": "Taxonomic analysis"
+                }
+            ],
             "label": "Taxonomic analysis",
             "name": "QIIME2 V: Taxonomic analysis",
             "outputs": [],
@@ -557,7 +567,7 @@
                     },
                     "4": {
                         "annotation": "qiime2 feature-classifier classify-sklearn\nPre-fitted sklearn-based taxonomy classifier",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2023.5.0+q2galaxy.2023.5.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.10.0+q2galaxy.2024.10.0",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
@@ -592,15 +602,15 @@
                                 "output_name": "classification"
                             }
                         },
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+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.10.0+q2galaxy.2024.10.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8aa82af30760",
+                            "changeset_revision": "771d8be25d7a",
                             "name": "qiime2__feature_classifier__classify_sklearn",
                             "owner": "q2d2",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"__q2galaxy__GUI__conditional__reads_per_batch__\": {\"__q2galaxy__GUI__select__\": \"auto\", \"__current_case__\": 0, \"reads_per_batch\": \"auto\"}, \"n_jobs\": \"1\", \"pre_dispatch\": \"2*n_jobs\", \"__q2galaxy__GUI__conditional__confidence__\": {\"__q2galaxy__GUI__select__\": \"__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)\", \"__current_case__\": 1, \"confidence\": \"0.7\"}, \"read_orientation\": \"auto\"}, \"classifier\": {\"__class__\": \"ConnectedValue\"}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2023.5.0+q2galaxy.2023.5.0.2",
+                        "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"__q2galaxy__GUI__conditional__reads_per_batch__\": {\"__q2galaxy__GUI__select__\": \"auto\", \"__current_case__\": 0, \"reads_per_batch\": \"auto\"}, \"pre_dispatch\": \"2*n_jobs\", \"__q2galaxy__GUI__conditional__confidence__\": {\"__q2galaxy__GUI__select__\": \"__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)\", \"__current_case__\": 1, \"confidence\": \"0.7\"}, \"read_orientation\": \"auto\"}, \"classifier\": {\"__class__\": \"ConnectedValue\"}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2024.10.0+q2galaxy.2024.10.0",
                         "type": "tool",
                         "uuid": "cf9e003e-bcd4-4819-88cf-98d3bc8bf531",
                         "when": null,
@@ -614,7 +624,7 @@
                     },
                     "5": {
                         "annotation": "qiime2 taxa barplot\nVisualize taxonomy with an interactive bar plot",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2023.5.0+q2galaxy.2023.5.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.10.0+q2galaxy.2024.10.0",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
@@ -658,15 +668,15 @@
                                 "output_name": "visualization"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2023.5.0+q2galaxy.2023.5.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/2024.10.0+q2galaxy.2024.10.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "124673b2e9e7",
+                            "changeset_revision": "3da2f87501ee",
                             "name": "qiime2__taxa__barplot",
                             "owner": "q2d2",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
                         "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"taxonomy\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__q2galaxy__GUI__conditional__level_delimiter__\": {\"__q2galaxy__GUI__select__\": \"__q2galaxy__::control::default\", \"__current_case__\": 0, \"level_delimiter\": \"__q2galaxy__::literal::None\"}}, \"table\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2023.5.0+q2galaxy.2023.5.0.2",
+                        "tool_version": "2024.10.0+q2galaxy.2024.10.0",
                         "type": "tool",
                         "uuid": "a2146130-d5a3-4f0d-814f-61677f57709b",
                         "when": null,
@@ -680,7 +690,7 @@
                     },
                     "6": {
                         "annotation": "qiime2 metadata tabulate\nInteractively explore Metadata in an HTML table",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
@@ -711,15 +721,15 @@
                                 "output_name": "visualization"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "d6e1b976c373",
+                            "changeset_revision": "9857be21dcaf",
                             "name": "qiime2__metadata__tabulate",
                             "owner": "q2d2",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
                         "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"page_size\": \"100\"}, \"input\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__input__\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2023.5.0+q2galaxy.2023.5.0.2",
+                        "tool_version": "2024.10.0+q2galaxy.2024.10.0",
                         "type": "tool",
                         "uuid": "380548c3-b9b6-4ebd-ae68-e3fbb891f7e5",
                         "when": null,
@@ -732,8 +742,8 @@
                         ]
                     }
                 },
-                "tags": "",
-                "uuid": "41bae731-2f27-4e57-b94d-683e0ab94b43"
+                "tags": [],
+                "uuid": "d0309a9d-66d8-46e2-b103-674377fa0de8"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -787,7 +797,12 @@
                     "output_name": "Rooted tree"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "Rarefaction",
+                    "name": "Rarefaction"
+                }
+            ],
             "label": "Rarefaction",
             "name": "QIIME2 IV: Rarefaction",
             "outputs": [],
@@ -964,7 +979,7 @@
                     },
                     "5": {
                         "annotation": "qiime2 diversity alpha-rarefaction\nAlpha rarefaction curves\n(Galaxy Version 2023.5.1+q2galaxy.2023.5.0.2)",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2023.5.1+q2galaxy.2023.5.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
@@ -1020,15 +1035,15 @@
                                 "output_name": "visualization"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2023.5.1+q2galaxy.2023.5.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_rarefaction/qiime2__diversity__alpha_rarefaction/2024.10.0+q2galaxy.2024.10.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "97cb20f77d50",
+                            "changeset_revision": "22bfda174157",
                             "name": "qiime2__diversity__alpha_rarefaction",
                             "owner": "q2d2",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
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                         "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"phylogeny\": {\"__class__\": \"ConnectedValue\"}, \"metrics\": [], \"metadata\": [{\"__index__\": 0, \"__q2galaxy__GUI__conditional__metadata__\": {\"type\": \"tsv\", \"__current_case__\": 0, \"source\": {\"__class__\": \"ConnectedValue\"}}}], \"min_depth\": {\"__class__\": \"ConnectedValue\"}, \"steps\": \"10\", \"iterations\": \"10\"}, \"max_depth\": {\"__class__\": \"ConnectedValue\"}, \"table\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2023.5.1+q2galaxy.2023.5.0.2",
+                        "tool_version": "2024.10.0+q2galaxy.2024.10.0",
                         "type": "tool",
                         "uuid": "489f6ea1-d13a-48ae-b71d-40c413f3b45e",
                         "when": null,
@@ -1041,8 +1056,8 @@
                         ]
                     }
                 },
-                "tags": "",
-                "uuid": "3c96b4fd-c67a-4c79-9e78-6f77e72b4bdf"
+                "tags": [],
+                "uuid": "28382e50-9000-48f1-ae97-d468934f4962"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -1060,4 +1075,4 @@
     "tags": [],
     "uuid": "3163175d-7673-42d9-8aae-505afbd74946",
     "version": 30
-}
+}