changeset 1:813aec57e9fd draft default tip

planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
author tduigou
date Thu, 31 Jul 2025 08:58:02 +0000
parents 4e2ae28020f7
children
files output.html output.json test-data/test-JSON_workflow1.json
diffstat 3 files changed, 64 insertions(+), 57 deletions(-) [+]
line wrap: on
line diff
--- a/output.html	Thu Jul 17 14:01:15 2025 +0000
+++ b/output.html	Thu Jul 31 08:58:02 2025 +0000
@@ -285,7 +285,7 @@
         var md = window.markdownit({
           html: true,
         });
-        target.innerHTML = md.render(atob('## Test Summary

<div class="progress">
  <div class="progress-bar progress-bar-success" style="width: 100.0%" aria-valuenow="2" aria-valuemin="0" aria-valuemax="2" data-toggle="tooltip" title="2 Passed">
  </div>
  <div class="progress-bar progress-bar-warning" style="width: 0.0%" aria-valuenow="0" aria-valuemin="0" aria-valuemax="2" data-toggle="tooltip" title="0 Skipped">
  </div>
  <div class="progress-bar progress-bar-danger" style="width: 0.0%" aria-valuenow="0" aria-valuemin="0" aria-valuemax="2" title="0 Failed or Errored">
  </div>
</div>

| Test State | Count |
| ---------- | ----- |
| Total      | 2 |
| Passed     | 2 |
| Error      | 0 |
| Failure    | 0 |
| Skipped    | 0 |


<details ><summary>Passed Tests</summary>

* <details class="rcorners light-green"><summary class="light-green">&#9989; parameters_maystro_workflow_2 (Test # 1)</summary><div class="padded">

    **Command Line:**

    * ```console
      python3 -c "import json; params = { 'DnaOptimizationProblemClass': 'DnaOptimizationProblem', 'methylation_protection': 'true', 'allow_edits': 'true', 'avoid_patterns': 'BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer', 'hairpin_constraints': 'stem_size=20, hairpin_window=200', 'gc_constraints': 'mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100', 'kmer_size': '15', 'assembly_plan_name': 'Type2sRestrictionAssembly', 'topology': 'circular', 'enzyme': 'auto', 'execution': 'true', 'db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'table': 'sample', 'fragment_column': 'fragment', 'sequence_column': 'sequence', 'annotation_column': 'annotation' }; f = open('/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Output:**

    * ```console
      DEBG
      {
          "DnaOptimizationProblemClass": "DnaOptimizationProblem",
          "methylation_protection": "true",
          "allow_edits": "true",
          "avoid_patterns": "BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer",
          "hairpin_constraints": "stem_size=20, hairpin_window=200",
          "gc_constraints": "mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100",
          "kmer_size": "15",
          "assembly_plan_name": "Type2sRestrictionAssembly",
          "topology": "circular",
          "enzyme": "auto",
          "execution": "true",
          "db_uri": "postgresql://postgres:RK17__at__localhost:5432/test_fragments_db",
          "table": "sample",
          "fragment_column": "fragment",
          "sequence_column": "sequence",
          "annotation_column": "annotation"
      }DEBG
      {
          "DnaOptimizationProblemClass": "DnaOptimizationProblem",
          "methylation_protection": "true",
          "allow_edits": "true",
          "avoid_patterns": "BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer",
          "hairpin_constraints": "stem_size=20, hairpin_window=200",
          "gc_constraints": "mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100",
          "kmer_size": "15",
          "assembly_plan_name": "Type2sRestrictionAssembly",
          "topology": "circular",
          "enzyme": "auto",
          "execution": "true",
          "db_uri": "postgresql://postgres:RK17__at__localhost:5432/test_fragments_db",
          "table": "sample",
          "fragment_column": "fragment",
          "sequence_column": "sequence",
          "annotation_column": "annotation"
      }
      ```
    **Traceback:**

    * ```console
      
      ```
   **Job Parameters:**

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | DnaOptimizationProblemClass | ` "DnaOptimizationProblem" ` |
       | avoid\_patterns | ` "BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer" ` |
       | hairpin\_constraints | ` "stem_size=20, hairpin_window=200" ` |
       | gc\_constraints | ` "mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100" ` |
       | kmer\_size | ` "15" ` |
       | methylation\_protection | ` true ` |
       | allow\_edits | ` true ` |
       | assembly\_plan\_name | ` "Type2sRestrictionAssembly" ` |
       | topology | ` "circular" ` |
       | enzyme | ` "auto" ` |
       | DB | ` {"annotation_column": "annotation", "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", "execution": true, "fragment_column": "fragment", "sequence_column": "sequence", "table_name": "sample", "user_json": null} ` |
       | chromInfo | ` "/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
       | dbkey | ` "?" ` |
       | \_\_input\_ext | ` "input" ` |



    </div></details>


* <details class="rcorners light-green"><summary class="light-green">&#9989; parameters_maystro_workflow_2 (Test # 2)</summary><div class="padded">

    **Command Line:**

    * ```console
      cp '/tmp/tmpnxavcgf5/files/b/b/d/dataset_bbd9a440-a787-439e-9b36-2c1c45dae0a3.dat' '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Output:**

    * ```console
      DEBG
      {
          "DnaOptimizationProblemClass":"DnaOptimizationProblem",
          "avoid_patterns": "BsaI_site\nNotI_site\nXbaI_site\nClaI_site\n8x1mer",
          "hairpin_constraints": "stem_size=20, hairpin_window=200\nstem_size=10, hairpin_window=100",
          "gc_constraints": "mini=0.1, maxi=0.9\nmini-0.3, maxi=0.7, window=50",
          "kmer_size": "15",
          "methylation_protection":"methylation_protection",
          "allow_edits":"True",
          "assembly_plan_name": "Type2sRestrictionAssembly",
          "topology": "circular",
          "enzyme": "auto",
          "execution": "true",
          "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
          "table": "sample",
          "fragment_column": "fragment",
          "sequence_column": "sequence",
          "annotation_column": "annotation"
      }

      ```
    **Traceback:**

    * ```console
      
      ```
   **Job Parameters:**

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | DnaOptimizationProblemClass | ` "DnaOptimizationProblem" ` |
       | avoid\_patterns | ` None ` |
       | hairpin\_constraints | ` None ` |
       | gc\_constraints | ` None ` |
       | kmer\_size | ` "" ` |
       | methylation\_protection | ` false ` |
       | allow\_edits | ` true ` |
       | assembly\_plan\_name | ` "Type2sRestrictionAssembly" ` |
       | topology | ` "circular" ` |
       | enzyme | ` "auto" ` |
       | DB | ` {"annotation_column": null, "db_uri": null, "execution": false, "fragment_column": null, "sequence_column": null, "table_name": null, "user_json": {"values": [{"id": 2, "src": "hda"}]}} ` |
       | chromInfo | ` "/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
       | dbkey | ` "?" ` |
       | \_\_input\_ext | ` "input" ` |



    </div></details>


</details>
'));
+        target.innerHTML = md.render(atob('## Test Summary

<div class="progress">
  <div class="progress-bar progress-bar-success" style="width: 100.0%" aria-valuenow="2" aria-valuemin="0" aria-valuemax="2" data-toggle="tooltip" title="2 Passed">
  </div>
  <div class="progress-bar progress-bar-warning" style="width: 0.0%" aria-valuenow="0" aria-valuemin="0" aria-valuemax="2" data-toggle="tooltip" title="0 Skipped">
  </div>
  <div class="progress-bar progress-bar-danger" style="width: 0.0%" aria-valuenow="0" aria-valuemin="0" aria-valuemax="2" title="0 Failed or Errored">
  </div>
</div>

| Test State | Count |
| ---------- | ----- |
| Total      | 2 |
| Passed     | 2 |
| Error      | 0 |
| Failure    | 0 |
| Skipped    | 0 |


<details ><summary>Passed Tests</summary>

* <details class="rcorners light-green"><summary class="light-green">&#9989; parameters_maystro_workflow_1 (Test # 1)</summary><div class="padded">

    **Command Line:**

    * ```console
      python3 -c "import json; params = { 'avoid_patterns': 'BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer', 'hairpin_constraints': 'stem_size=20, hairpin_window=200', 'gc_constraints': 'mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100', 'kmer_size': '15', 'assembly_plan_name': 'Type2sRestrictionAssembly', 'topology': 'circular', 'enzyme': 'auto', 'execution': 'true', 'db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'table': 'sample', 'fragment_column': 'fragment', 'sequence_column': 'sequence', 'annotation_column': 'annotation' }; f = open('/tmp/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat' && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Output:**

    * ```console
      DEBG
      {
          "avoid_patterns": "BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer",
          "hairpin_constraints": "stem_size=20, hairpin_window=200",
          "gc_constraints": "mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100",
          "kmer_size": "15",
          "assembly_plan_name": "Type2sRestrictionAssembly",
          "topology": "circular",
          "enzyme": "auto",
          "execution": "true",
          "db_uri": "postgresql://postgres:RK17__at__localhost:5432/test_fragments_db",
          "table": "sample",
          "fragment_column": "fragment",
          "sequence_column": "sequence",
          "annotation_column": "annotation"
      }DEBG
      {
          "avoid_patterns": "BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer",
          "hairpin_constraints": "stem_size=20, hairpin_window=200",
          "gc_constraints": "mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100",
          "kmer_size": "15",
          "assembly_plan_name": "Type2sRestrictionAssembly",
          "topology": "circular",
          "enzyme": "auto",
          "execution": "true",
          "db_uri": "postgresql://postgres:RK17__at__localhost:5432/test_fragments_db",
          "table": "sample",
          "fragment_column": "fragment",
          "sequence_column": "sequence",
          "annotation_column": "annotation"
      }
      ```
    **Traceback:**

    * ```console
      
      ```
   **Job Parameters:**

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | avoid\_patterns | ` "BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer" ` |
       | hairpin\_constraints | ` "stem_size=20, hairpin_window=200" ` |
       | gc\_constraints | ` "mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100" ` |
       | kmer\_size | ` "15" ` |
       | assembly\_plan\_name | ` "Type2sRestrictionAssembly" ` |
       | topology | ` "circular" ` |
       | enzyme | ` "auto" ` |
       | execution | ` true ` |
       | db\_uri | ` "postgresql://postgres:RK17@localhost:5432/test_fragments_db" ` |
       | table\_name | ` "sample" ` |
       | fragment\_column | ` "fragment" ` |
       | sequence\_column | ` "sequence" ` |
       | annotation\_column | ` "annotation" ` |
       | user\_json | ` None ` |
       | chromInfo | ` "/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
       | dbkey | ` "?" ` |
       | \_\_input\_ext | ` "input" ` |



    </div></details>


* <details class="rcorners light-green"><summary class="light-green">&#9989; parameters_maystro_workflow_1 (Test # 2)</summary><div class="padded">

    **Command Line:**

    * ```console
      cp '/tmp/tmpt0l5fyog/files/d/7/9/dataset_d79830ca-f30e-4f82-8b67-150bf816c265.dat' '/tmp/tmpt0l5fyog/job_working_directory/000/3/outputs/dataset_cd60237f-3d8d-4a7e-ac4c-b10728db646e.dat' && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/3/outputs/dataset_cd60237f-3d8d-4a7e-ac4c-b10728db646e.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Output:**

    * ```console
      DEBG
      {
        "avoid_patterns": "BsaI_site\nBsmBI_site\nBbsI_site\nSapI_site\n8x1mer\n5x3mer\n9x2mer",
        "hairpin_constraints": "stem_size=20, hairpin_window=200",
        "gc_constraints": "mini=0.1, maxi=0.9,, window=100\nmini=0.3, maxi=0.7, window=100",
        "kmer_size": "15",
        "execution": "true",
        "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
        "table": "sample",
        "fragment_column": "fragment",
        "sequence_column": "sequence",
        "annotation_column": "annotation",
        "assembly_plan_name": "Type2sRestrictionAssembly",
        "topology": "circular",
        "enzyme": "auto"
      }

      ```
    **Traceback:**

    * ```console
      
      ```
   **Job Parameters:**

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | avoid\_patterns | ` None ` |
       | hairpin\_constraints | ` None ` |
       | gc\_constraints | ` None ` |
       | kmer\_size | ` "" ` |
       | assembly\_plan\_name | ` "Type2sRestrictionAssembly" ` |
       | topology | ` "circular" ` |
       | enzyme | ` "auto" ` |
       | execution | ` false ` |
       | db\_uri | ` None ` |
       | table\_name | ` None ` |
       | fragment\_column | ` None ` |
       | sequence\_column | ` None ` |
       | annotation\_column | ` None ` |
       | chromInfo | ` "/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
       | dbkey | ` "?" ` |
       | \_\_input\_ext | ` "input" ` |



    </div></details>


</details>
'));
     </script>
   </body>
 </html>
\ No newline at end of file
--- a/output.json	Thu Jul 17 14:01:15 2025 +0000
+++ b/output.json	Thu Jul 31 08:58:02 2025 +0000
@@ -9,34 +9,32 @@
         {
             "data": {
                 "inputs": {
-                    "DB|annotation_column": "annotation",
-                    "DB|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
-                    "DB|execution": true,
-                    "DB|fragment_column": "fragment",
-                    "DB|sequence_column": "sequence",
-                    "DB|table_name": "sample",
-                    "DnaOptimizationProblemClass": "DnaOptimizationProblem",
+                    "annotation_column": "annotation",
                     "assembly_plan_name": "Type2sRestrictionAssembly",
-                    "avoid_patterns": "BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer",
+                    "avoid_patterns": "BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer",
+                    "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
                     "enzyme": "auto",
+                    "execution": true,
+                    "fragment_column": "fragment",
                     "gc_constraints": "mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100",
                     "hairpin_constraints": "stem_size=20, hairpin_window=200",
                     "kmer_size": "15",
-                    "methylation_protection": true,
+                    "sequence_column": "sequence",
+                    "table_name": "sample",
                     "topology": "circular"
                 },
                 "job": {
-                    "command_line": "python3 -c \"import json; params = { 'DnaOptimizationProblemClass': 'DnaOptimizationProblem', 'methylation_protection': 'true', 'allow_edits': 'true', 'avoid_patterns': 'BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer', 'hairpin_constraints': 'stem_size=20, hairpin_window=200', 'gc_constraints': 'mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100', 'kmer_size': '15', 'assembly_plan_name': 'Type2sRestrictionAssembly', 'topology': 'circular', 'enzyme': 'auto', 'execution': 'true', 'db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'table': 'sample', 'fragment_column': 'fragment', 'sequence_column': 'sequence', 'annotation_column': 'annotation' }; f = open('/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat'",
+                    "command_line": "python3 -c \"import json; params = { 'avoid_patterns': 'BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer', 'hairpin_constraints': 'stem_size=20, hairpin_window=200', 'gc_constraints': 'mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100', 'kmer_size': '15', 'assembly_plan_name': 'Type2sRestrictionAssembly', 'topology': 'circular', 'enzyme': 'auto', 'execution': 'true', 'db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'table': 'sample', 'fragment_column': 'fragment', 'sequence_column': 'sequence', 'annotation_column': 'annotation' }; f = open('/tmp/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat' && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-07-17T12:08:28.832103",
+                    "create_time": "2025-07-31T08:57:00.548068",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "135810",
+                    "external_id": "205407",
                     "galaxy_version": "25.0",
                     "handler": null,
-                    "history_id": "d952758136b0c83c",
-                    "id": "d952758136b0c83c",
+                    "history_id": "57c9e3825b6e5989",
+                    "id": "57c9e3825b6e5989",
                     "inputs": {},
                     "job_messages": [],
                     "job_metrics": [],
@@ -47,71 +45,74 @@
                     "output_collections": {},
                     "outputs": {
                         "output_json": {
-                            "id": "d952758136b0c83c",
+                            "id": "57c9e3825b6e5989",
                             "src": "hda",
-                            "uuid": "53ffa695-5fab-48b3-b5f5-ff93f77bfc10"
+                            "uuid": "1bfb5292-6b8f-4b66-9d74-cedaf9200451"
                         }
                     },
                     "params": {
-                        "DB": "{\"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"execution\": true, \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table_name\": \"sample\", \"user_json\": null}",
-                        "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
                         "__input_ext": "\"input\"",
-                        "allow_edits": "true",
+                        "annotation_column": "\"annotation\"",
                         "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-                        "avoid_patterns": "\"BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer\"",
-                        "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "avoid_patterns": "\"BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer\"",
+                        "chromInfo": "\"/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
                         "dbkey": "\"?\"",
                         "enzyme": "\"auto\"",
+                        "execution": "true",
+                        "fragment_column": "\"fragment\"",
                         "gc_constraints": "\"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\"",
                         "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"",
                         "kmer_size": "\"15\"",
-                        "methylation_protection": "true",
-                        "topology": "\"circular\""
+                        "sequence_column": "\"sequence\"",
+                        "table_name": "\"sample\"",
+                        "topology": "\"circular\"",
+                        "user_json": null
                     },
                     "state": "ok",
                     "stderr": "",
-                    "stdout": "DEBG\n{\n    \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n    \"methylation_protection\": \"true\",\n    \"allow_edits\": \"true\",\n    \"avoid_patterns\": \"BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n    \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\",\n    \"kmer_size\": \"15\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}DEBG\n{\n    \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n    \"methylation_protection\": \"true\",\n    \"allow_edits\": \"true\",\n    \"avoid_patterns\": \"BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n    \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\",\n    \"kmer_size\": \"15\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}",
-                    "tool_id": "parameters_maystro_workflow_2",
+                    "stdout": "DEBG\n{\n    \"avoid_patterns\": \"BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n    \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\",\n    \"kmer_size\": \"15\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}DEBG\n{\n    \"avoid_patterns\": \"BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n    \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\",\n    \"kmer_size\": \"15\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}",
+                    "tool_id": "parameters_maystro_workflow_1",
                     "tool_stderr": "",
-                    "tool_stdout": "DEBG\n{\n    \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n    \"methylation_protection\": \"true\",\n    \"allow_edits\": \"true\",\n    \"avoid_patterns\": \"BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n    \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\",\n    \"kmer_size\": \"15\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}DEBG\n{\n    \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n    \"methylation_protection\": \"true\",\n    \"allow_edits\": \"true\",\n    \"avoid_patterns\": \"BsaI_site             nNotI_site             nXbaI_site             nClaI_site             n8x1mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n    \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\",\n    \"kmer_size\": \"15\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}",
-                    "update_time": "2025-07-17T12:08:33.771569",
+                    "tool_stdout": "DEBG\n{\n    \"avoid_patterns\": \"BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n    \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\",\n    \"kmer_size\": \"15\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}DEBG\n{\n    \"avoid_patterns\": \"BsaI_site             BsmBI_site             BbsI_site             SapI_site             8x1mer             5x3mer             9x2mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n    \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100             mini=0.1, maxi=0.9, window=100\",\n    \"kmer_size\": \"15\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}",
+                    "update_time": "2025-07-31T08:57:06.352395",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "d952758136b0c83c"
+                    "user_id": "57c9e3825b6e5989"
                 },
                 "status": "success",
                 "test_index": 0,
-                "time_seconds": 5.093859434127808,
-                "tool_id": "parameters_maystro_workflow_2",
+                "time_seconds": 6.245003700256348,
+                "tool_id": "parameters_maystro_workflow_1",
                 "tool_version": "0.1.0"
             },
             "has_data": true,
-            "id": "parameters_maystro_workflow_2-0"
+            "id": "parameters_maystro_workflow_1-0"
         },
         {
             "data": {
                 "inputs": {
-                    "DB|user_json": {
-                        "id": "b08444d846605ee4",
+                    "user_json": {
+                        "id": "b8cd89e8131d3fe7",
                         "src": "hda"
                     }
                 },
                 "job": {
-                    "command_line": "cp '/tmp/tmpnxavcgf5/files/b/b/d/dataset_bbd9a440-a787-439e-9b36-2c1c45dae0a3.dat' '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat'",
+                    "command_line": "cp '/tmp/tmpt0l5fyog/files/d/7/9/dataset_d79830ca-f30e-4f82-8b67-150bf816c265.dat' '/tmp/tmpt0l5fyog/job_working_directory/000/3/outputs/dataset_cd60237f-3d8d-4a7e-ac4c-b10728db646e.dat' && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/3/outputs/dataset_cd60237f-3d8d-4a7e-ac4c-b10728db646e.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-07-17T12:08:43.857384",
+                    "create_time": "2025-07-31T08:57:16.707828",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "135995",
+                    "external_id": "205636",
                     "galaxy_version": "25.0",
                     "handler": null,
-                    "history_id": "b08444d846605ee4",
-                    "id": "e67c2cbedbcb0da1",
+                    "history_id": "b8cd89e8131d3fe7",
+                    "id": "abe44dd8383948e0",
                     "inputs": {
-                        "DB|user_json": {
-                            "id": "b08444d846605ee4",
+                        "user_json": {
+                            "id": "b8cd89e8131d3fe7",
                             "src": "hda",
-                            "uuid": "bbd9a440-a787-439e-9b36-2c1c45dae0a3"
+                            "uuid": "d79830ca-f30e-4f82-8b67-150bf816c265"
                         }
                     },
                     "job_messages": [],
@@ -123,45 +124,47 @@
                     "output_collections": {},
                     "outputs": {
                         "output_json": {
-                            "id": "e67c2cbedbcb0da1",
+                            "id": "abe44dd8383948e0",
                             "src": "hda",
-                            "uuid": "6eed7c7c-77ce-4d77-b2ef-0a367df7e250"
+                            "uuid": "cd60237f-3d8d-4a7e-ac4c-b10728db646e"
                         }
                     },
                     "params": {
-                        "DB": "{\"annotation_column\": null, \"db_uri\": null, \"execution\": false, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null, \"user_json\": {\"values\": [{\"id\": 2, \"src\": \"hda\"}]}}",
-                        "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
                         "__input_ext": "\"input\"",
-                        "allow_edits": "true",
+                        "annotation_column": null,
                         "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
                         "avoid_patterns": null,
-                        "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "chromInfo": "\"/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "db_uri": null,
                         "dbkey": "\"?\"",
                         "enzyme": "\"auto\"",
+                        "execution": "false",
+                        "fragment_column": null,
                         "gc_constraints": null,
                         "hairpin_constraints": null,
                         "kmer_size": "\"\"",
-                        "methylation_protection": "false",
+                        "sequence_column": null,
+                        "table_name": null,
                         "topology": "\"circular\""
                     },
                     "state": "ok",
                     "stderr": "",
-                    "stdout": "DEBG\n{\n    \"DnaOptimizationProblemClass\":\"DnaOptimizationProblem\",\n    \"avoid_patterns\": \"BsaI_site\\nNotI_site\\nXbaI_site\\nClaI_site\\n8x1mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\\nstem_size=10, hairpin_window=100\",\n    \"gc_constraints\": \"mini=0.1, maxi=0.9\\nmini-0.3, maxi=0.7, window=50\",\n    \"kmer_size\": \"15\",\n    \"methylation_protection\":\"methylation_protection\",\n    \"allow_edits\":\"True\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}\n",
-                    "tool_id": "parameters_maystro_workflow_2",
+                    "stdout": "DEBG\n{\n  \"avoid_patterns\": \"BsaI_site\\nBsmBI_site\\nBbsI_site\\nSapI_site\\n8x1mer\\n5x3mer\\n9x2mer\",\n  \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n  \"gc_constraints\": \"mini=0.1, maxi=0.9,, window=100\\nmini=0.3, maxi=0.7, window=100\",\n  \"kmer_size\": \"15\",\n  \"execution\": \"true\",\n  \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n  \"table\": \"sample\",\n  \"fragment_column\": \"fragment\",\n  \"sequence_column\": \"sequence\",\n  \"annotation_column\": \"annotation\",\n  \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n  \"topology\": \"circular\",\n  \"enzyme\": \"auto\"\n}\n",
+                    "tool_id": "parameters_maystro_workflow_1",
                     "tool_stderr": "",
-                    "tool_stdout": "DEBG\n{\n    \"DnaOptimizationProblemClass\":\"DnaOptimizationProblem\",\n    \"avoid_patterns\": \"BsaI_site\\nNotI_site\\nXbaI_site\\nClaI_site\\n8x1mer\",\n    \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\\nstem_size=10, hairpin_window=100\",\n    \"gc_constraints\": \"mini=0.1, maxi=0.9\\nmini-0.3, maxi=0.7, window=50\",\n    \"kmer_size\": \"15\",\n    \"methylation_protection\":\"methylation_protection\",\n    \"allow_edits\":\"True\",\n    \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n    \"topology\": \"circular\",\n    \"enzyme\": \"auto\",\n    \"execution\": \"true\",\n    \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n    \"table\": \"sample\",\n    \"fragment_column\": \"fragment\",\n    \"sequence_column\": \"sequence\",\n    \"annotation_column\": \"annotation\"\n}\n",
-                    "update_time": "2025-07-17T12:08:49.096516",
+                    "tool_stdout": "DEBG\n{\n  \"avoid_patterns\": \"BsaI_site\\nBsmBI_site\\nBbsI_site\\nSapI_site\\n8x1mer\\n5x3mer\\n9x2mer\",\n  \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n  \"gc_constraints\": \"mini=0.1, maxi=0.9,, window=100\\nmini=0.3, maxi=0.7, window=100\",\n  \"kmer_size\": \"15\",\n  \"execution\": \"true\",\n  \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n  \"table\": \"sample\",\n  \"fragment_column\": \"fragment\",\n  \"sequence_column\": \"sequence\",\n  \"annotation_column\": \"annotation\",\n  \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n  \"topology\": \"circular\",\n  \"enzyme\": \"auto\"\n}\n",
+                    "update_time": "2025-07-31T08:57:22.628561",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "d952758136b0c83c"
+                    "user_id": "57c9e3825b6e5989"
                 },
                 "status": "success",
                 "test_index": 1,
-                "time_seconds": 15.298557996749878,
-                "tool_id": "parameters_maystro_workflow_2",
+                "time_seconds": 15.919075965881348,
+                "tool_id": "parameters_maystro_workflow_1",
                 "tool_version": "0.1.0"
             },
             "has_data": true,
-            "id": "parameters_maystro_workflow_2-1"
+            "id": "parameters_maystro_workflow_1-1"
         }
     ],
     "version": "0.1"
--- a/test-data/test-JSON_workflow1.json	Thu Jul 17 14:01:15 2025 +0000
+++ b/test-data/test-JSON_workflow1.json	Thu Jul 31 08:58:02 2025 +0000
@@ -1,4 +1,8 @@
 {
+  "avoid_patterns": "BsaI_site\nBsmBI_site\nBbsI_site\nSapI_site\n8x1mer\n5x3mer\n9x2mer",
+  "hairpin_constraints": "stem_size=20, hairpin_window=200",
+  "gc_constraints": "mini=0.1, maxi=0.9,, window=100\nmini=0.3, maxi=0.7, window=100",
+  "kmer_size": "15",
   "execution": "true",
   "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
   "table": "sample",