Merge pull request #6727 from Delphine-L/mitochondrion

Update mitcochondrion assembly tutorial

Author: shiltemann

topics/assembly/tutorials/mitochondrion-assembly/tutorial.md

@@ -94,7 +94,7 @@ To assemble the mitogenome from our PacBio Data,  MitoHiFi needs a reference mit
 
 > <hands-on-title>  Find a related mitogenome reference  </hands-on-title>
 >
-> 1. {% tool [MitoHiFi](toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0) %} with the following parameters:
+> 1. {% tool [MitoHiFi](toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0) %} with the following parameters:
 >    - *"Operation type selector"*: `Find a close-related mitochondrial reference genome`
 >        - *"Species name"*: `Taeniopygia guttata` Enter the latin name of the species you are assembling
 >        - *"Email"*: `your.email@service.com` Enter your email 
@@ -112,7 +112,7 @@ To assemble the mitogenome from our PacBio Data,  MitoHiFi needs a reference mit
 >
 >    {% snippet faqs/galaxy/collections_build_list.md name="PacBio Reads" datasets_description="the fastq.gz containing the HiFi reads" n="1" %}
 > 
-> 2. {% tool [MitoHiFi](toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0) %} with the following parameters:
+> 2. {% tool [MitoHiFi](toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0) %} with the following parameters:
 >    - *"Operation type selector"*: `Run MitoHiFi`
 >        - *"Input mode"*: `Pacbio Hifi Reads`
 >            - {% icon param-collection %} *"Pacbio Hifi reads"*: `PacBio Reads` (Input dataset collection)

topics/assembly/tutorials/mitochondrion-assembly/workflows/main_workflow.ga

@@ -118,7 +118,7 @@
         },
         "3": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0",
             "errors": null,
             "id": 3,
             "input_connections": {
@@ -158,23 +158,23 @@
                 "top": 242.234375
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "99ddbf037d98",
+                "changeset_revision": "bfab6f5b449d",
                 "name": "mitohifi",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"operation_mode\": {\"command\": \"find_reference\", \"__current_case__\": 0, \"species\": {\"__class__\": \"ConnectedValue\"}, \"email\": {\"__class__\": \"ConnectedValue\"}, \"min_length\": \"15000\", \"exact_species\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "3+galaxy0",
+            "tool_version": "3.2.3+galaxy0",
             "type": "tool",
             "uuid": "e59aea2d-9bc3-4e2e-9af2-711f0cdea373",
             "when": null,
             "workflow_outputs": []
         },
         "4": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0",
             "errors": null,
             "id": 4,
             "input_connections": {
@@ -258,15 +258,15 @@
                     "output_name": "hifiasm_filtered"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "99ddbf037d98",
+                "changeset_revision": "bfab6f5b449d",
                 "name": "mitohifi",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"operation_mode\": {\"command\": \"mitohifi\", \"__current_case__\": 1, \"input_option\": {\"input\": \"pacbio\", \"__current_case__\": 0, \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"bloom_filter\": \"0\"}, \"reference_fasta\": {\"__class__\": \"ConnectedValue\"}, \"reference_genbank\": {\"__class__\": \"ConnectedValue\"}, \"genetic_code\": \"2\", \"advanced_options\": {\"query_blast\": \"70\", \"circular_size\": null, \"circular_offset\": null, \"outputs\": null}, \"output_zip\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "3+galaxy0",
+            "tool_state": "{\"operation_mode\": {\"command\": \"mitohifi\", \"__current_case__\": 1, \"input_option\": {\"input\": \"pacbio\", \"__current_case__\": 0, \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"bloom_filter\": \"0\"}, \"reference_fasta\": {\"__class__\": \"ConnectedValue\"}, \"reference_genbank\": {\"__class__\": \"ConnectedValue\"}, \"organism_selection\": \"animal\", \"genetic_code\": \"2\", \"advanced_options\": {\"query_blast\": \"70\", \"circular_size\": null, \"circular_offset\": null, \"outputs\": null}, \"output_zip\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "3.2.3+galaxy0",
             "type": "tool",
             "uuid": "ccd83410-608a-4b9d-a43a-11cecd6c2d42",
             "when": null,