Merge pull request #548 from clsiguret/amr_gene_detection-update

Updating workflows/bacterial_genomics/amr_gene_detection from 1.1.2 to 1.1.3
galaxyproject · Oct 2, 2024 · b8b0e84 · b8b0e84
2 parents 838d46d + 4cf41e9
commit b8b0e84
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diff --git a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [1.1.3] 2024-09-30
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0`
+
 ## [1.1.2] 2024-09-19
 
 ### Manual update

diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml
@@ -54,9 +54,9 @@
           n: 15
     tooldistillator_summarize:
       asserts:
-        has_text:
+        - that: "has_text"
           text: "% Identity to reference sequence"
-        has_text:
+        - that: "has_text"
           text: "Enterococcus faecalis V583"
-        has_text:
-          text: "CGE Predicted Phenotype"
+        - that: "has_text"
+          text: "Fibrinogen binding protein"
diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga
@@ -27,7 +27,7 @@
     ],
     "format-version": "0.1",
     "license": "GPL-3.0-or-later",
-    "release": "1.1.2",
+    "release": "1.1.3",
     "name": "amr_gene_detection",
     "steps": {
         "0": {
@@ -528,7 +528,7 @@
         },
         "7": {
             "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0",
             "errors": null,
             "id": 7,
             "input_connections": {
@@ -598,15 +598,15 @@
                     "output_name": "output_json"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "a7387ce2a8ca",
+                "changeset_revision": "8d6686664021",
                 "name": "tooldistillator",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"abricate\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.0.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"staramr\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mlst_file_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmidfinder_file_path\": {\"__class__\": \"RuntimeValue\"}, \"pointfinder_file_path\": {\"__class__\": \"RuntimeValue\"}, \"setting_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.10.0\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"amrfinderplus\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"point_mutation_report_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_sequence_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"3.12.8\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.9+galaxy0",
+            "tool_version": "0.9.1+galaxy0",
             "type": "tool",
             "uuid": "1589f8a1-65b6-43f0-9e75-cad9b1752e5c",
             "when": null,
@@ -620,7 +620,7 @@
         },
         "8": {
             "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0",
             "errors": null,
             "id": 8,
             "input_connections": {
@@ -658,15 +658,15 @@
                     "output_name": "summary_json"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "def7a82d23e1",
+                "changeset_revision": "f3233d395549",
                 "name": "tooldistillator_summarize",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.9+galaxy0",
+            "tool_version": "0.9.1+galaxy0",
             "type": "tool",
             "uuid": "a88f6b82-502c-46cf-a174-2c8361e8e8dd",
             "when": null,