Mercurial > repos > tduigou > parameters_maystro
changeset 1:34135dac85b0 draft default tip
planemo upload for repository https://github.com/brsynth commit d8cc8b87fdb0374745b5420f2da7f08ae905c222-dirty
| author | tduigou |
|---|---|
| date | Wed, 16 Jul 2025 14:28:21 +0000 |
| parents | 1a766d8d3883 |
| children | |
| files | json_db_config_generating_boolean.xml output.html output.json test-data/test_json.json |
| diffstat | 4 files changed, 180 insertions(+), 185 deletions(-) [+] |
line wrap: on
line diff
--- a/json_db_config_generating_boolean.xml Fri Jul 11 10:10:16 2025 +0000 +++ b/json_db_config_generating_boolean.xml Wed Jul 16 14:28:21 2025 +0000 @@ -1,58 +1,76 @@ -<tool id="parameters_maystro" name="Parameters Maystro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> - <description>Store parameters of tools in a workflow to be used again</description> +<tool id="parameters_maystro" name="Workflow-0 Parameters Maystro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> + <description>Store parameters of workflow-0 to be used again</description> <macros> - <token name="@VERSION_SUFFIX@">1</token> - <token name="@TOOL_VERSION@">0.1.0</token> + <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">1.1.0</token> </macros> <command detect_errors="exit_code"><![CDATA[ - #set $json_files = ' '.join(['"%s"' % file for file in $json_from_workflow]) - #set $json_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $json_from_workflow]) - python '$__tool_directory__/maystro.py' - --distribute_json '$distribute_json' - --json_from_workflow $json_files - --json_from_user '$json_from_user' - --json_name_mapping $json_name_mapping - --output_workflow '$output_workflow' - --output_user '$output_user' && echo 'DEBUB' && cat '$output_user' + #if $user_json and str($user_json) != 'None': + cp '$user_json' '$output_json' + #else + python3 -c "import json; params = { + 'avoid_patterns': '$avoid_patterns', + 'hairpin_constraints': '$hairpin_constraints', + 'gc_constraints': '$gc_constraints', + 'kmer_size': '$kmer_size', + 'execution': '$execution', + 'db_uri': '$db_uri', + 'table': '$table_name', + 'fragment_column': '$fragment_column', + 'sequence_column': '$sequence_column', + 'annotation_column': '$annotation_column' + }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json' + #end if + && echo DEBG && cat '$output_json' ]]></command> <inputs> - <param name="distribute_json" type="boolean" label="Input Your Parameters As JSON" checked ='false' help="If True user should set workflow parameters as json file" /> - <param name="json_from_workflow" type="data" format="json" multiple="true" optional="true" help='Only if Input Your Parameters As JSON is FALSE' /> - <param name="json_from_user" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' /> + <param name="avoid_patterns" type="text" area="true" optional="true" label="Avoid Patterns (one per line)" /> + <param name="hairpin_constraints" type="text" area="true" label="Hairpins Constraints" optional="true" help="e.g. (you can add others Hairpins Constraints on a new line): stem_size=20, hairpin_window=200"/> + <param name="gc_constraints" type="text" area="true" label="Enforce GC Content Constraints" optional="true" help="e.g. (you can add others Enforce GC Content Constraints on a new line): mini=0.3, maxi=0.7, window=100"/> + <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/> + <param name="execution" type="boolean" label="Save To DB ?" checked ='false' optional="true" help="If True data will be saved in the DB" /> + <param name="db_uri" type="text" optional="true" help='Only if Input Your Parameters As JSON is FALSE' /> + <param name="table_name" type="text" optional="true" help='table name in DB' /> + <param name="fragment_column" type="text" optional="true" help='Fragmnet column in DB' /> + <param name="sequence_column" type="text" optional="true" help='Sequence column in DB' /> + <param name="annotation_column" type="text" optional="true" help='Annotation column in DB' /> + <param name="user_json" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' /> </inputs> <outputs> - <data name="output_workflow" format="json" label="workflow param"/> - <data name="output_user" format="json" label="user_workflow param"/> + <data name="output_json" format="json" label="Workflow-0 Parameters"/> </outputs> <tests> - <!--distribute_json is false--> + <!--manual parameters set--> <test> - <param name="distribute_json" value='false'/> - <param name="json_from_workflow" value="seq_from_db_param.json,seq_to_db_param.json"/> - <output name="output_user"> + <param name="avoid_patterns" value="BsaI_site + BsmBI_site + BbsI_site + SapI_site + 8x1mer + 5x3mer + 9x2mer" /> + <param name="hairpin_constraints" value='stem_size=20, hairpin_window=200'/> + <param name="gc_constraints" value="mini=0.3, maxi=0.7, window=100 + mini=0.1, maxi=0.9, window=100"/> + <param name="kmer_size" value="15" /> + <param name="execution" value="true" /> + <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> + <param name="table_name" value="sample" /> + <param name="fragment_column" value="fragment" /> + <param name="sequence_column" value="sequence" /> + <param name="annotation_column" value="annotation" /> + <output name="output_json"> <assert_contents> - <has_n_lines n="17" /> - </assert_contents> - </output> - <output name="output_workflow"> - <assert_contents> - <has_n_lines n="0" /> + <has_n_lines n="12" /> </assert_contents> </output> </test> - <!--distribute_json is true --> + <!--JSON parameters set--> <test> - <param name="distribute_json" value='true'/> - <param name="json_from_workflow" value="seq_from_db_param.json,seq_to_db_param.json"/> - <param name="json_from_user" value='merged_test.json'/> - <output name="output_workflow"> + <param name="user_json" value='test_json.json'/> + <output name="output_json"> <assert_contents> - <has_n_lines n="17" /> - </assert_contents> - </output> - <output name="output_user"> - <assert_contents> - <has_n_lines n="0" /> + <has_n_lines n="12" /> </assert_contents> </output> </test> @@ -61,8 +79,8 @@ Parameters Maystro =================== -Store and Generate a JSON file to be used as a workflow configuration. This JSON file can later be used to pass workflow parameters -This tool is recieve parameters from tools in workflow and return them as a JSON file that can be used later to pass thos parameters again. +Store and Generate a JSON file to be used as workflow-0 configuration. This JSON file can later be used as input to pass workflow-0 parameters + ]]></help> <citations> <citation type="bibtex">
--- a/output.html Fri Jul 11 10:10:16 2025 +0000 +++ b/output.html Wed Jul 16 14:28:21 2025 +0000 @@ -285,7 +285,7 @@ var md = window.markdownit({ html: true, }); - target.innerHTML = md.render(atob('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')); + 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 (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', '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/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat' && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.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",
          "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",
          "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" ` |
       | 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/tmpojrs64js/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 (Test # 2)</summary><div class="padded">

    **Command Line:**

    * ```console
      cp '/tmp/tmpojrs64js/files/a/6/4/dataset_a64b8b4b-290b-4b2e-bf77-d0d4ebc35137.dat' '/tmp/tmpojrs64js/job_working_directory/000/3/outputs/dataset_0dedeb7c-7969-452f-a162-25e70662b775.dat' && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/3/outputs/dataset_0dedeb7c-7969-452f-a162-25e70662b775.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=0.3, maxi=0.7, window=100\nmini=0.1, maxi=0.9, 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"
      }

      ```
    **Traceback:**

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

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | avoid\_patterns | ` None ` |
       | hairpin\_constraints | ` None ` |
       | gc\_constraints | ` None ` |
       | kmer\_size | ` "" ` |
       | execution | ` false ` |
       | db\_uri | ` None ` |
       | table\_name | ` None ` |
       | fragment\_column | ` None ` |
       | sequence\_column | ` None ` |
       | annotation\_column | ` None ` |
       | chromInfo | ` "/tmp/tmpojrs64js/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 Fri Jul 11 10:10:16 2025 +0000 +++ b/output.json Wed Jul 16 14:28:21 2025 +0000 @@ -9,45 +9,104 @@ { "data": { "inputs": { - "distribute_json": false, - "json_from_workflow": [ - { - "id": "051ed7ff50845d8c", - "src": "hda" - }, - { - "id": "25656ddfec77a3b3", - "src": "hda" - } - ] + "annotation_column": "annotation", + "avoid_patterns": "BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer", + "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "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", + "sequence_column": "sequence", + "table_name": "sample" }, "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/parameters_maystro/maystro.py' --distribute_json 'false' --json_from_workflow \"/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat\" \"/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat\" --json_from_user 'None' --json_name_mapping /tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat:seq_from_db_param.json,/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat:seq_to_db_param.json --output_workflow '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_d100f4ee-f845-4a68-be68-004c7af9679d.dat' --output_user '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat' && echo 'DEBUB' && cat '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.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', '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/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat' && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-07-11T09:42:39.854743", + "create_time": "2025-07-16T14:25:13.835798", "dependencies": [], "exit_code": 0, - "external_id": "79277", + "external_id": "153937", "galaxy_version": "25.0", "handler": null, - "history_id": "051ed7ff50845d8c", - "id": "d66447d427a79ce4", - "inputs": { - "json_from_workflow": { - "id": "051ed7ff50845d8c", + "history_id": "479ca6463d0132e0", + "id": "479ca6463d0132e0", + "inputs": {}, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_json": { + "id": "479ca6463d0132e0", "src": "hda", - "uuid": "2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6" - }, - "json_from_workflow1": { - "id": "051ed7ff50845d8c", + "uuid": "ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c" + } + }, + "params": { + "__input_ext": "\"input\"", + "annotation_column": "\"annotation\"", + "avoid_patterns": "\"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\"", + "chromInfo": "\"/tmp/tmpojrs64js/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", + "dbkey": "\"?\"", + "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\"", + "sequence_column": "\"sequence\"", + "table_name": "\"sample\"", + "user_json": null + }, + "state": "ok", + "stderr": "", + "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 \"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 \"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", + "tool_stderr": "", + "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 \"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 \"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": "2025-07-16T14:25:27.820187", + "user_email": "planemo@galaxyproject.org", + "user_id": "479ca6463d0132e0" + }, + "status": "success", + "test_index": 0, + "time_seconds": 14.118565320968628, + "tool_id": "parameters_maystro", + "tool_version": "1.1.0+galaxy3" + }, + "has_data": true, + "id": "parameters_maystro-0" + }, + { + "data": { + "inputs": { + "user_json": { + "id": "0311cb8bec9eec65", + "src": "hda" + } + }, + "job": { + "command_line": "cp '/tmp/tmpojrs64js/files/a/6/4/dataset_a64b8b4b-290b-4b2e-bf77-d0d4ebc35137.dat' '/tmp/tmpojrs64js/job_working_directory/000/3/outputs/dataset_0dedeb7c-7969-452f-a162-25e70662b775.dat' && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/3/outputs/dataset_0dedeb7c-7969-452f-a162-25e70662b775.dat'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-07-16T14:25:36.982208", + "dependencies": [], + "exit_code": 0, + "external_id": "154115", + "galaxy_version": "25.0", + "handler": null, + "history_id": "0311cb8bec9eec65", + "id": "da029efde06939a6", + "inputs": { + "user_json": { + "id": "0311cb8bec9eec65", "src": "hda", - "uuid": "2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6" - }, - "json_from_workflow2": { - "id": "25656ddfec77a3b3", - "src": "hda", - "uuid": "960eac8e-fb66-4982-8009-4896c9e57b38" + "uuid": "a64b8b4b-290b-4b2e-bf77-d0d4ebc35137" } }, "job_messages": [], @@ -58,136 +117,42 @@ "model_class": "Job", "output_collections": {}, "outputs": { - "output_user": { - "id": "39496c7f8d685f43", + "output_json": { + "id": "da029efde06939a6", "src": "hda", - "uuid": "1e2a9024-ad29-4d18-b95d-645817393383" - }, - "output_workflow": { - "id": "d66447d427a79ce4", - "src": "hda", - "uuid": "d100f4ee-f845-4a68-be68-004c7af9679d" + "uuid": "0dedeb7c-7969-452f-a162-25e70662b775" } }, "params": { "__input_ext": "\"input\"", - "chromInfo": "\"/tmp/tmpfpd6tei1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "annotation_column": null, + "avoid_patterns": null, + "chromInfo": "\"/tmp/tmpojrs64js/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": null, "dbkey": "\"?\"", - "distribute_json": "false", - "json_from_user": null + "execution": "false", + "fragment_column": null, + "gc_constraints": null, + "hairpin_constraints": null, + "kmer_size": "\"\"", + "sequence_column": null, + "table_name": null }, "state": "ok", "stderr": "", - "stdout": "[INFO] Watching temp dir for new JSONs: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\n[INFO] Initial JSONs from workflow: ['/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat', '/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat']\n[INFO] Added data under key: seq_from_db_param\n[INFO] Added data under key: seq_to_db_param\n[INFO] Merged JSON written to: /tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat\n[INFO] Cleaning up: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\nDEBUB\n{\n \"seq_from_db_param\": {\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 \"seq_to_db_param\": {\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}", + "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=0.3, maxi=0.7, window=100\\nmini=0.1, maxi=0.9, 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}\n", "tool_id": "parameters_maystro", "tool_stderr": "", - "tool_stdout": "[INFO] Watching temp dir for new JSONs: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\n[INFO] Initial JSONs from workflow: ['/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat', '/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat']\n[INFO] Added data under key: seq_from_db_param\n[INFO] Added data under key: seq_to_db_param\n[INFO] Merged JSON written to: /tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat\n[INFO] Cleaning up: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\nDEBUB\n{\n \"seq_from_db_param\": {\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 \"seq_to_db_param\": {\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": "2025-07-11T09:42:45.494563", + "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=0.3, maxi=0.7, window=100\\nmini=0.1, maxi=0.9, 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}\n", + "update_time": "2025-07-16T14:25:42.101497", "user_email": "planemo@galaxyproject.org", - "user_id": "051ed7ff50845d8c" - }, - "status": "success", - "test_index": 0, - "time_seconds": 16.301273107528687, - "tool_id": "parameters_maystro", - "tool_version": "0.1.0+galaxy1" - }, - "has_data": true, - "id": "parameters_maystro-0" - }, - { - "data": { - "inputs": { - "distribute_json": true, - "json_from_user": { - "id": "10ea9be91661a5fd", - "src": "hda" - }, - "json_from_workflow": [ - { - "id": "b7e19a053756efb9", - "src": "hda" - }, - { - "id": "45e8a4dfb17d83f9", - "src": "hda" - } - ] - }, - "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/parameters_maystro/maystro.py' --distribute_json 'true' --json_from_workflow \"/tmp/tmpfpd6tei1/files/c/1/e/dataset_c1e98b32-965c-4a0d-9c7f-26973a7e0fe6.dat\" \"/tmp/tmpfpd6tei1/files/3/a/5/dataset_3a560c20-0d3f-4aae-abd4-4a460698f28f.dat\" --json_from_user '/tmp/tmpfpd6tei1/files/0/a/b/dataset_0abf65a6-bd5b-47fc-94ba-a6a97fa6d88b.dat' --json_name_mapping /tmp/tmpfpd6tei1/files/c/1/e/dataset_c1e98b32-965c-4a0d-9c7f-26973a7e0fe6.dat:seq_from_db_param.json,/tmp/tmpfpd6tei1/files/3/a/5/dataset_3a560c20-0d3f-4aae-abd4-4a460698f28f.dat:seq_to_db_param.json --output_workflow '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_5254084b-4d71-4098-b933-f73a9e7d5a28.dat' --output_user '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_04c60445-2ff4-4b59-bcbc-75f08b68625a.dat' && echo 'DEBUB' && cat '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_04c60445-2ff4-4b59-bcbc-75f08b68625a.dat'", - "command_version": "", - "copied_from_job_id": null, - "create_time": "2025-07-11T09:42:56.883885", - "dependencies": [], - "exit_code": 0, - "external_id": "79598", - "galaxy_version": "25.0", - "handler": null, - "history_id": "25656ddfec77a3b3", - "id": "10ea9be91661a5fd", - "inputs": { - "json_from_user": { - "id": "10ea9be91661a5fd", - "src": "hda", - "uuid": "0abf65a6-bd5b-47fc-94ba-a6a97fa6d88b" - }, - "json_from_workflow": { - "id": "b7e19a053756efb9", - "src": "hda", - "uuid": "c1e98b32-965c-4a0d-9c7f-26973a7e0fe6" - }, - "json_from_workflow1": { - "id": "b7e19a053756efb9", - "src": "hda", - "uuid": "c1e98b32-965c-4a0d-9c7f-26973a7e0fe6" - }, - "json_from_workflow2": { - "id": "45e8a4dfb17d83f9", - "src": "hda", - "uuid": "3a560c20-0d3f-4aae-abd4-4a460698f28f" - } - }, - "job_messages": [], - "job_metrics": [], - "job_runner_name": null, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_collections": {}, - "outputs": { - "output_user": { - "id": "295d652904818249", - "src": "hda", - "uuid": "04c60445-2ff4-4b59-bcbc-75f08b68625a" - }, - "output_workflow": { - "id": "8c61ed432685cfe0", - "src": "hda", - "uuid": "5254084b-4d71-4098-b933-f73a9e7d5a28" - } - }, - "params": { - "__input_ext": "\"input\"", - "chromInfo": "\"/tmp/tmpfpd6tei1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "dbkey": "\"?\"", - "distribute_json": "true" - }, - "state": "ok", - "stderr": "", - "stdout": "DEBUB\n", - "tool_id": "parameters_maystro", - "tool_stderr": "", - "tool_stdout": "DEBUB\n", - "update_time": "2025-07-11T09:43:02.149865", - "user_email": "planemo@galaxyproject.org", - "user_id": "051ed7ff50845d8c" + "user_id": "479ca6463d0132e0" }, "status": "success", "test_index": 1, - "time_seconds": 16.54760479927063, + "time_seconds": 14.252628803253174, "tool_id": "parameters_maystro", - "tool_version": "0.1.0+galaxy1" + "tool_version": "1.1.0+galaxy3" }, "has_data": true, "id": "parameters_maystro-1"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_json.json Wed Jul 16 14:28:21 2025 +0000 @@ -0,0 +1,12 @@ +{ + "avoid_patterns": "BsaI_site\nBsmBI_site\nBbsI_site\nSapI_site\n8x1mer\n5x3mer\n9x2mer", + "hairpin_constraints": "stem_size=20, hairpin_window=200", + "gc_constraints": "mini=0.3, maxi=0.7, window=100\nmini=0.1, maxi=0.9, 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" +} \ No newline at end of file