46668bb54c3c8a7a57bda515be6881edb2382563
hiram
  Wed Apr 22 14:55:23 2026 -0700
correctly connecting scoringMatrix input to kegAlign scores refs #31811

diff --git src/hg/utils/automation/kegAlign.json.ga src/hg/utils/automation/kegAlign.json.ga
index 484b059de68..fcd892feb26 100644
--- src/hg/utils/automation/kegAlign.json.ga
+++ src/hg/utils/automation/kegAlign.json.ga
@@ -1,57 +1,57 @@
 {
     "a_galaxy_workflow": "true",
     "annotation": "Should now have axtChainScoreScheme and axtChainLinearGap input options",
     "comments": [
+        {
+            "color": "none",
+            "data": {
+                "text": "Assemblies in fasta format, masked. "
+            },
+            "id": 1,
+            "position": [
+                42.09072708051447,
+                778.882939520563
+            ],
+            "size": [
+                310,
+                55
+            ],
+            "type": "markdown"
+        },
         {
             "child_comments": [
                 1
             ],
             "child_steps": [
-                9,
-                8
+                11,
+                9
             ],
             "color": "blue",
             "data": {
                 "title": ""
             },
             "id": 0,
             "position": [
                 17.29072708051447,
-                695.0356491033881
+                738.882939520563
             ],
             "size": [
                 414,
                 276
             ],
             "type": "frame"
-        },
-        {
-            "color": "none",
-            "data": {
-                "text": "Assemblies in fasta format, masked. "
-            },
-            "id": 1,
-            "position": [
-                42.09072708051447,
-                735.0356491033881
-            ],
-            "size": [
-                310,
-                55
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-            "type": "markdown"
         }
     ],
     "creator": [
         {
             "class": "Organization",
             "name": "Penn State University",
             "url": "https://www.ccbb.psu.edu/"
         },
         {
             "class": "Person",
             "identifier": "https://orcid.org/0000-0002-9318-1781",
             "name": "Martin \u010cech"
         }
     ],
     "format-version": "0.1",
@@ -65,489 +65,520 @@
             "annotation": "default: both - can be: minus or plus BLASTZ_B=2",
             "content_id": null,
             "errors": null,
             "id": 0,
             "input_connections": {},
             "inputs": [
                 {
                     "description": "default: both - can be: minus or plus BLASTZ_B=2",
                     "name": "strand_selectorB"
                 }
             ],
             "label": "strand_selectorB",
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 6.969707608149614,
-                "top": 22.086266148506436
+                "left": 16.792180016306407,
+                "top": 0.0
             },
             "tool_id": null,
             "tool_state": "{\"default\": \"both\", \"multiple\": false, \"validators\": [], \"restrictions\": [\"both\", \"minus\", \"plus\"], \"parameter_type\": \"text\", \"optional\": false}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "4bd8509b-bd3c-458e-bec7-8eb33693918a",
             "when": null,
             "workflow_outputs": []
         },
         "1": {
-            "annotation": "--step or Z=1 default",
+            "annotation": "to supply a score matrix to the lastz operation",
             "content_id": null,
             "errors": null,
             "id": 1,
             "input_connections": {},
+            "inputs": [
+                {
+                    "description": "to supply a score matrix to the lastz operation",
+                    "name": "scoringMatrix"
+                }
+            ],
+            "label": "scoringMatrix",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 11.0183670147745,
+                "top": 95.33299906946252
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": true, \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "98c64d32-3f93-46c0-8d65-ac602eb2b6cf",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "--step or Z=1 default",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
             "inputs": [
                 {
                     "description": "--step or Z=1 default",
                     "name": "stepZ"
                 }
             ],
             "label": "stepZ",
             "name": "Input parameter",
             "outputs": [],
             "position": {
                 "left": 3.529330207209202,
-                "top": 130.1734203457517
+                "top": 174.02071076292663
             },
             "tool_id": null,
             "tool_state": "{\"default\": 1, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "a9327d57-01f6-4e5d-908c-3d88a99fd0b2",
             "when": null,
             "workflow_outputs": []
         },
-        "2": {
+        "3": {
             "annotation": "true == --notransition false == -transition this is BLASTZ_T default 1 or 3",
             "content_id": null,
             "errors": null,
-            "id": 2,
+            "id": 3,
             "input_connections": {},
             "inputs": [
                 {
                     "description": "true == --notransition false == -transition this is BLASTZ_T default 1 or 3",
                     "name": "noTransitionT"
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             "label": "noTransitionT",
             "name": "Input parameter",
             "outputs": [],
             "position": {
                 "left": 4.413474126983308,
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+                "top": 253.69032438141477
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             "tool_id": null,
             "tool_state": "{\"default\": true, \"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "c871c94d-d1e8-4cc0-ab18-0d1b6413dcb8",
             "when": null,
             "workflow_outputs": []
         },
-        "3": {
+        "4": {
             "annotation": "xdrop option to lastz, default 910",
             "content_id": null,
             "errors": null,
-            "id": 3,
+            "id": 4,
             "input_connections": {},
             "inputs": [
                 {
                     "description": "xdrop option to lastz, default 910",
                     "name": "xdropX"
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             ],
             "label": "xdropX",
             "name": "Input parameter",
             "outputs": [],
             "position": {
                 "left": 0.17426400315015156,
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         },
-        "4": {
+        "5": {
             "annotation": "BLASTZ_K == --hspthresh default 3000",
             "content_id": null,
             "errors": null,
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+            "id": 5,
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                     "description": "BLASTZ_K == --hspthresh default 3000",
                     "name": "hspthreshK"
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             "name": "Input parameter",
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             "tool_state": "{\"default\": 3000, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}",
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             "uuid": "b9c13a54-08e7-4007-bfde-52e20fcc6a9a",
             "when": null,
             "workflow_outputs": []
         },
-        "5": {
+        "6": {
             "annotation": "default 9400",
             "content_id": null,
             "errors": null,
-            "id": 5,
+            "id": 6,
             "input_connections": {},
             "inputs": [
                 {
                     "description": "default 9400",
                     "name": "ydropY"
                 }
             ],
             "label": "ydropY",
             "name": "Input parameter",
             "outputs": [],
             "position": {
                 "left": 2.9781360951763647,
-                "top": 455.0827362160491
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             "tool_id": null,
             "tool_state": "{\"default\": 9400, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}",
             "tool_version": null,
             "type": "parameter_input",
             "uuid": "93652cc4-7c1a-4ec3-8928-d30e6f8a59dc",
             "when": null,
             "workflow_outputs": []
         },
-        "6": {
+        "7": {
             "annotation": "integer for the --gappedthresh BLASTZ_L argument",
             "content_id": null,
             "errors": null,
-            "id": 6,
+            "id": 7,
             "input_connections": {},
             "inputs": [
                 {
                     "description": "integer for the --gappedthresh BLASTZ_L argument",
                     "name": "gappedthreshL"
                 }
             ],
             "label": "gappedthreshL",
             "name": "Input parameter",
             "outputs": [],
             "position": {
                 "left": 4.3597736220213745,
-                "top": 528.4530394194131
+                "top": 572.300329836588
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             "tool_id": null,
             "tool_state": "{\"default\": 3000, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}",
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             "uuid": "e97d87e0-2df4-494d-af78-c7b49664f027",
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+        "8": {
             "annotation": "",
             "content_id": null,
             "errors": null,
-            "id": 7,
+            "id": 8,
             "input_connections": {},
             "inputs": [
                 {
                     "description": "",
                     "name": "innerH"
                 }
             ],
             "label": "innerH",
             "name": "Input parameter",
             "outputs": [],
             "position": {
                 "left": 0,
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+                "top": 646.4754574473421
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             "tool_id": null,
             "tool_state": "{\"default\": 3000, \"validators\": [{\"min\": null, \"max\": null, \"negate\": false, \"type\": \"in_range\"}], \"parameter_type\": \"integer\", \"optional\": false}",
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             "type": "parameter_input",
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             "when": null,
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-        "8": {
+        "9": {
             "annotation": "Assemblies in fasta format, masked. ",
             "content_id": null,
             "errors": null,
-            "id": 8,
+            "id": 9,
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                 {
                     "description": "Assemblies in fasta format, masked. ",
                     "name": "TARGET_Sequence"
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             ],
             "label": "TARGET_Sequence",
             "name": "Input dataset",
             "outputs": [],
             "position": {
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             "tool_id": null,
             "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}",
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             "uuid": "85fb7a10-67cf-42df-b1d8-ba4a90c07e2e",
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-        "9": {
-            "annotation": "Assemblies in fasta format, masked. ",
+        "10": {
+            "annotation": "the -minScore argument to axtChain",
             "content_id": null,
             "errors": null,
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+            "id": 10,
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             "inputs": [
                 {
-                    "description": "Assemblies in fasta format, masked. ",
-                    "name": "QUERY_Sequence"
+                    "description": "the -minScore argument to axtChain",
+                    "name": "axtChainMinScore"
                 }
             ],
-            "label": "QUERY_Sequence",
-            "name": "Input dataset",
+            "label": "axtChainMinScore",
+            "name": "Input parameter",
             "outputs": [],
             "position": {
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+                "left": 847.1784982523703,
+                "top": 371.71494365212374
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             "tool_version": null,
-            "type": "data_input",
-            "uuid": "6e8cdde2-a9f4-4ee5-936d-5eee44c1e257",
+            "type": "parameter_input",
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-        "10": {
-            "annotation": "the -minScore argument to axtChain",
+        "11": {
+            "annotation": "Assemblies in fasta format, masked. ",
             "content_id": null,
             "errors": null,
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+            "id": 11,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "the -minScore argument to axtChain",
-                    "name": "axtChainMinScore"
+                    "description": "Assemblies in fasta format, masked. ",
+                    "name": "QUERY_Sequence"
                 }
             ],
-            "label": "axtChainMinScore",
-            "name": "Input parameter",
+            "label": "QUERY_Sequence",
+            "name": "Input dataset",
             "outputs": [],
             "position": {
-                "left": 847.1784982523703,
-                "top": 327.8676532349488
+                "left": 65.41210375986545,
+                "top": 927.379254393056
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+            "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
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+        "12": {
             "annotation": "To supply the -linearGap option",
             "content_id": null,
             "errors": null,
-            "id": 11,
+            "id": 12,
             "input_connections": {},
             "inputs": [
                 {
                     "description": "To supply the -linearGap option",
                     "name": "axtChainLinearGap"
                 }
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             "label": "axtChainLinearGap",
             "name": "Input dataset",
             "outputs": [],
             "position": {
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-        "12": {
+        "13": {
             "annotation": "input a scoring matrix to axtChain.  Going to be the 4 by 4 matrix of A C G T and with O=400 and E = 30",
             "content_id": null,
             "errors": null,
-            "id": 12,
+            "id": 13,
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             "inputs": [
                 {
                     "description": "input a scoring matrix to axtChain.  Going to be the 4 by 4 matrix of A C G T and with O=400 and E = 30",
                     "name": "axtChainScoreScheme"
                 }
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             "label": "axtChainScoreScheme",
             "name": "Input dataset",
             "outputs": [],
             "position": {
                 "left": 837.4832247419432,
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             "uuid": "f86d7c3c-b66c-42eb-863d-f027cc717dde",
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+        "14": {
             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3",
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+                    "id": 9,
                     "output_name": "output"
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             "inputs": [],
             "label": "TARGET trim sequence names",
             "name": "Text reformatting",
             "outputs": [
                 {
                     "name": "outfile",
                     "type": "input"
                 }
             ],
             "position": {
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             "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3",
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+                    "id": 11,
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             "inputs": [],
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                     "type": "input"
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-        "15": {
+        "16": {
             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/kegalign/kegalign/0.1.2.9+galaxy1",
             "errors": null,
-            "id": 15,
+            "id": 16,
             "input_connections": {
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-                    "id": 6,
+                    "id": 7,
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+                    "id": 6,
                     "output_name": "output"
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                 "interpolation_options|inner": {
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+                    "id": 8,
                     "output_name": "output"
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                 "query": {
-                    "id": 14,
+                    "id": 15,
                     "output_name": "outfile"
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+                "scoring_options|scoring": {
+                    "id": 1,
+                    "output_name": "output"
+                },
                 "seeding_options|notransition": {
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+                    "id": 3,
                     "output_name": "output"
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                 "seeding_options|step": {
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+                    "id": 2,
                     "output_name": "output"
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                 "sequence_options|strand_selector": {
                     "id": 0,
                     "output_name": "output"
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                 "target": {
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+                    "id": 14,
                     "output_name": "outfile"
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                 "ungapped_extension_options|hspthresh": {
-                    "id": 4,
+                    "id": 5,
                     "output_name": "output"
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                 "ungapped_extension_options|xdrop": {
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+                    "id": 4,
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             "inputs": [
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                     "description": "runtime parameter for tool KegAlign",
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                     "description": "runtime parameter for tool KegAlign",
                     "name": "gapped_extension_options"
                 },
                 {
                     "description": "runtime parameter for tool KegAlign",
                     "name": "interpolation_options"
@@ -575,77 +606,77 @@
                 {
                     "description": "runtime parameter for tool KegAlign",
                     "name": "ungapped_extension_options"
                 }
             ],
             "label": "kegalign_step",
             "name": "KegAlign",
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                 {
                     "name": "kegalign_output",
                     "type": "tgz"
                 }
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             "position": {
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+                "top": 43.847290417174904
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             "tool_shed_repository": {
                 "changeset_revision": "f885abcfe3a0",
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@@ -653,78 +684,78 @@
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                     "type": "chain"
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@@ -732,53 +763,53 @@
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\ No newline at end of file