From 7851874250f43f7a51444723274ff3d73d669cbc Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 24 Jun 2024 04:19:57 +0000
Subject: [PATCH] Updating workflows/bacterial_genomics/amr_gene_detection from
 1.0 to 1.1

---
 .../amr_gene_detection/CHANGELOG.md           |  5 ++++
 .../amr_gene_detection/amr_gene_detection.ga  | 30 ++++++++++++-------
 2 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md
index cfbdf5f33..e84d497cc 100644
--- a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md
+++ b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [1.1] 2024-06-24
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1`
+
 ## [1.0] - 05-06-2024
 
 - First release
\ No newline at end of file
diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga
index 17915347d..6727f9835 100644
--- a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga
+++ b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga
@@ -16,20 +16,18 @@
             "alternateName": "pimarin",
             "class": "Person",
             "identifier": "https://orcid.org/0000-0002-8304-138X",
-            "name": "Pierre Marin",
-            "alternateName": "pimarin"
+            "name": "Pierre Marin"
         },
         {
             "alternateName": "clsiguret",
             "class": "Person",
             "identifier": "https://orcid.org/0000-0002-8304-138X",
-            "name": "Clea Siguret",
-            "alternateName": "clsiguret"
+            "name": "Clea Siguret"
         }
     ],
     "format-version": "0.1",
     "license": "GPL-3.0-or-later",
-    "release": "1.0",
+    "release": "1.1",
     "name": "amr_gene_detection",
     "steps": {
         "0": {
@@ -142,7 +140,7 @@
         },
         "4": {
             "annotation": "staramr_amr_genes",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1",
             "errors": null,
             "id": 4,
             "input_connections": {
@@ -306,15 +304,15 @@
                     "output_name": "summary"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "141afacabcfa",
+                "changeset_revision": "3b22de20bd4b",
                 "name": "staramr",
                 "owner": "nml",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advanced\": {\"pid_threshold\": \"98.0\", \"plength_resfinder\": \"60.0\", \"plength_pointfinder\": \"95.0\", \"plength_plasmidfinder\": \"60.0\", \"genome_size_lower_bound\": \"4000000\", \"genome_size_upper_bound\": \"6000000\", \"minimum_N50_value\": \"10000\", \"minimum_contig_length\": \"300\", \"unacceptable_number_contigs\": \"1000\", \"report_all_blast\": false, \"exclude_negatives\": false, \"exclude_resistance_phenotypes\": false, \"mlst_scheme\": \"auto\", \"exclude_genes\": {\"exclude_genes_condition\": \"default\", \"__current_case__\": 0}, \"complex_mutations\": {\"complex_mutations_condition\": \"default\", \"__current_case__\": 0}, \"plasmidfinder_type\": \"include_all\"}, \"genomes\": {\"__class__\": \"ConnectedValue\"}, \"pointfinder_db\": {\"use_pointfinder\": \"disabled\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.10.0+galaxy0",
+            "tool_version": "0.10.0+galaxy1",
             "type": "tool",
             "uuid": "10eed503-9e5b-4acf-8cd8-29e81d7668a5",
             "when": null,
@@ -380,7 +378,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool AMRFinderPlus",
+                    "name": "input_option"
+                }
+            ],
             "label": "amrfinderplus_point_mutation",
             "name": "AMRFinderPlus",
             "outputs": [
@@ -469,7 +472,12 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool ABRicate",
+                    "name": "adv"
+                }
+            ],
             "label": "abricate_virulence",
             "name": "ABRicate",
             "outputs": [