Mercurial > repos > tduigou > domestication
changeset 10:c52967fb95da draft default tip
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Tue, 27 May 2025 08:08:21 +0000 |
| parents | 450ed9dca5d5 |
| children | |
| files | domestication.xml output.html output.json |
| diffstat | 3 files changed, 97 insertions(+), 97 deletions(-) [+] |
line wrap: on
line diff
--- a/domestication.xml Fri May 23 09:07:37 2025 +0000 +++ b/domestication.xml Tue May 27 08:08:21 2025 +0000 @@ -30,7 +30,7 @@ --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection '$methylation_protection' && - cp 'output_zip.zip' '$output_zip' + cp 'output_zip.zip' '$domesticated_zip' ]]></command> <inputs> <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/> @@ -45,7 +45,7 @@ </section> </inputs> <outputs> - <data format="zip" name="output_zip" label="domestication results"/> + <data format="zip" name="domesticated_zip" label="domestication results"/> <collection name="domesticated_gb" type="list" label="Domesticated GenBank Files"> <filter>methylation_protection == False</filter> <discover_datasets pattern="(?P<name>.*).gb" format="genbank" directory="outdir_gb" /> @@ -73,7 +73,7 @@ <param name='methylation_protection' value='false' /> <param name="adv|use_file_names_as_ids" value="True" /> <param name="adv|allow_edits" value="True" /> - <output name="output_zip" ftype='zip'> + <output name="domesticated_zip" ftype='zip'> <assert_contents> <has_archive_member path=".*" n="24"/> <has_archive_member path="order_ids.csv"> @@ -136,7 +136,7 @@ <param name="methylation_protection" value="true" /> <param name="adv|use_file_names_as_ids" value="True" /> <param name="adv|allow_edits" value="True" /> - <output name="output_zip" ftype='zip'> + <output name="domesticated_zip" ftype='zip'> <assert_contents> <has_archive_member path=".*" n="24"/> <has_archive_member path="order_ids.csv">
--- a/output.html Fri May 23 09:07:37 2025 +0000 +++ b/output.html Tue May 27 08:08:21 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; domestication (Test # 1)</summary><div class="padded">

    **Command Line:**

    * ```console
      mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpa__rr6q2/files/1/8/d/dataset_18d1bdeb-a69c-4f9a-8d59-4d4d12fbff4c.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpa__rr6q2/files/f/3/b/dataset_f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb.dat,/tmp/tmpa__rr6q2/files/f/f/6/dataset_ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8.dat,/tmp/tmpa__rr6q2/files/8/c/d/dataset_8cd82e26-da60-4c91-bb80-d65d9ac0864d.dat,/tmp/tmpa__rr6q2/files/a/f/6/dataset_af6f5158-3c00-4e30-a07f-b9cee1381d6c.dat,/tmp/tmpa__rr6q2/files/b/9/7/dataset_b97d206b-3b81-41ad-96a6-462a3ebcbbf2.dat,/tmp/tmpa__rr6q2/files/a/8/9/dataset_a8913c13-0cca-4e1e-9496-2c7f0bbcc485.dat,/tmp/tmpa__rr6q2/files/6/c/c/dataset_6cc8ecc8-2001-4b71-8cd5-3d42f368a626.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpa__rr6q2/files/f/3/b/dataset_f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb.dat:p3_2_CAG.gb,/tmp/tmpa__rr6q2/files/f/f/6/dataset_ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8.dat:p7_gfp_sequence.gb,/tmp/tmpa__rr6q2/files/8/c/d/dataset_8cd82e26-da60-4c91-bb80-d65d9ac0864d.dat:p14_CMVp.gb,/tmp/tmpa__rr6q2/files/a/f/6/dataset_af6f5158-3c00-4e30-a07f-b9cee1381d6c.dat:p16_bGHpolyA.gb,/tmp/tmpa__rr6q2/files/b/9/7/dataset_b97d206b-3b81-41ad-96a6-462a3ebcbbf2.dat:p18_CMVp.gb,/tmp/tmpa__rr6q2/files/a/8/9/dataset_a8913c13-0cca-4e1e-9496-2c7f0bbcc485.dat:p19_mNeoGreen.gb,/tmp/tmpa__rr6q2/files/6/c/c/dataset_6cc8ecc8-2001-4b71-8cd5-3d42f368a626.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpa__rr6q2/job_working_directory/000/9/outputs/dataset_3847af4a-c6f8-4bc2-92e6-a5111f36e863.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Error:**

    * ```console
      
      record:   0%|          | 0/7 [00:00<?, ?it/s, now=None]
      record:  43%|████▎     | 3/7 [00:01<00:02,  1.75it/s, now=None]
                                                                     
      ```
    **Standard Output:**

    * ```console
      Part names were not truncated

      ```
    **Traceback:**

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

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | genbank\_files | ` {"values": [{"id": 1, "src": "hdca"}]} ` |
       | methylation\_protection | ` false ` |
       | adv | ` {"allow_edits": true, "use_file_names_as_ids": true} ` |
       | chromInfo | ` "/tmp/tmpa__rr6q2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
       | dbkey | ` "?" ` |
       | \_\_input\_ext | ` "input" ` |



    </div></details>


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

    **Command Line:**

    * ```console
      mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpa__rr6q2/files/8/9/c/dataset_89c41e63-3985-4c33-9154-735d98f3f2bb.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpa__rr6q2/files/3/7/a/dataset_37a61c0f-4043-404f-97c9-1b2e4b277a0b.dat,/tmp/tmpa__rr6q2/files/a/c/d/dataset_acd5b8cd-260a-4eed-bbaa-083097afd437.dat,/tmp/tmpa__rr6q2/files/b/4/2/dataset_b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd.dat,/tmp/tmpa__rr6q2/files/6/4/3/dataset_643037ae-a752-4ce5-80e9-921fa8b24d3b.dat,/tmp/tmpa__rr6q2/files/d/c/e/dataset_dce00e9a-8b99-4bce-a1c2-b17377db99cf.dat,/tmp/tmpa__rr6q2/files/0/2/0/dataset_020c2948-6eb0-4860-b17b-a3f35d138965.dat,/tmp/tmpa__rr6q2/files/2/c/6/dataset_2c6f9cf6-bf93-4c97-9ea8-17ad34702969.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpa__rr6q2/files/3/7/a/dataset_37a61c0f-4043-404f-97c9-1b2e4b277a0b.dat:p3_2_CAG.gb,/tmp/tmpa__rr6q2/files/a/c/d/dataset_acd5b8cd-260a-4eed-bbaa-083097afd437.dat:p7_gfp_sequence.gb,/tmp/tmpa__rr6q2/files/b/4/2/dataset_b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd.dat:p14_CMVp.gb,/tmp/tmpa__rr6q2/files/6/4/3/dataset_643037ae-a752-4ce5-80e9-921fa8b24d3b.dat:p16_bGHpolyA.gb,/tmp/tmpa__rr6q2/files/d/c/e/dataset_dce00e9a-8b99-4bce-a1c2-b17377db99cf.dat:p18_CMVp.gb,/tmp/tmpa__rr6q2/files/0/2/0/dataset_020c2948-6eb0-4860-b17b-a3f35d138965.dat:p19_mNeoGreen.gb,/tmp/tmpa__rr6q2/files/2/c/6/dataset_2c6f9cf6-bf93-4c97-9ea8-17ad34702969.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpa__rr6q2/job_working_directory/000/18/outputs/dataset_257e63c3-87b5-459a-b118-921e6217abe8.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Error:**

    * ```console
      
      record:   0%|          | 0/7 [00:00<?, ?it/s, now=None]
      record:  43%|████▎     | 3/7 [00:01<00:02,  1.73it/s, now=None]
                                                                     
      ```
    **Standard Output:**

    * ```console
      Part names were not truncated

      ```
    **Traceback:**

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

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | genbank\_files | ` {"values": [{"id": 3, "src": "hdca"}]} ` |
       | methylation\_protection | ` true ` |
       | adv | ` {"allow_edits": true, "use_file_names_as_ids": true} ` |
       | chromInfo | ` "/tmp/tmpa__rr6q2/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; domestication (Test # 1)</summary><div class="padded">

    **Command Line:**

    * ```console
      mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpmo0pk3jj/files/6/1/a/dataset_61aea63f-fa8f-4855-b597-d298379d415c.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmo0pk3jj/files/2/f/f/dataset_2ff46bb9-5b06-4cad-b98f-afa1443697b5.dat,/tmp/tmpmo0pk3jj/files/9/9/c/dataset_99c508b5-234a-4eba-b9d2-05204eaa2ec8.dat,/tmp/tmpmo0pk3jj/files/0/a/0/dataset_0a0b7db9-a3ac-4999-b1c9-498618831d59.dat,/tmp/tmpmo0pk3jj/files/a/2/9/dataset_a2994595-0a40-48ba-a369-db577710e99a.dat,/tmp/tmpmo0pk3jj/files/c/8/b/dataset_c8b3e40f-a0a8-414e-a56c-bd71775b2218.dat,/tmp/tmpmo0pk3jj/files/c/8/1/dataset_c813a93e-97c6-4f6a-bcd0-dcdbd93728e2.dat,/tmp/tmpmo0pk3jj/files/3/6/8/dataset_368b2cf8-f34e-427d-888e-b431a4b28c87.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpmo0pk3jj/files/2/f/f/dataset_2ff46bb9-5b06-4cad-b98f-afa1443697b5.dat:p3_2_CAG.gb,/tmp/tmpmo0pk3jj/files/9/9/c/dataset_99c508b5-234a-4eba-b9d2-05204eaa2ec8.dat:p7_gfp_sequence.gb,/tmp/tmpmo0pk3jj/files/0/a/0/dataset_0a0b7db9-a3ac-4999-b1c9-498618831d59.dat:p14_CMVp.gb,/tmp/tmpmo0pk3jj/files/a/2/9/dataset_a2994595-0a40-48ba-a369-db577710e99a.dat:p16_bGHpolyA.gb,/tmp/tmpmo0pk3jj/files/c/8/b/dataset_c8b3e40f-a0a8-414e-a56c-bd71775b2218.dat:p18_CMVp.gb,/tmp/tmpmo0pk3jj/files/c/8/1/dataset_c813a93e-97c6-4f6a-bcd0-dcdbd93728e2.dat:p19_mNeoGreen.gb,/tmp/tmpmo0pk3jj/files/3/6/8/dataset_368b2cf8-f34e-427d-888e-b431a4b28c87.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpmo0pk3jj/job_working_directory/000/9/outputs/dataset_598cd11f-0878-422d-b265-3e7d109f52d4.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Error:**

    * ```console
      
      record:   0%|          | 0/7 [00:00<?, ?it/s, now=None]
      record:  43%|████▎     | 3/7 [00:01<00:02,  1.68it/s, now=None]
                                                                     
      ```
    **Standard Output:**

    * ```console
      Part names were not truncated

      ```
    **Traceback:**

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

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | genbank\_files | ` {"values": [{"id": 1, "src": "hdca"}]} ` |
       | methylation\_protection | ` false ` |
       | adv | ` {"allow_edits": true, "use_file_names_as_ids": true} ` |
       | chromInfo | ` "/tmp/tmpmo0pk3jj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
       | dbkey | ` "?" ` |
       | \_\_input\_ext | ` "input" ` |



    </div></details>


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

    **Command Line:**

    * ```console
      mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpmo0pk3jj/files/8/8/c/dataset_88ce7dbb-b512-47e2-b4c4-a33e25f510f5.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmo0pk3jj/files/3/e/0/dataset_3e0edcaf-c663-4aaa-833b-4d28d353ff86.dat,/tmp/tmpmo0pk3jj/files/c/b/e/dataset_cbeb8071-98da-4bcd-829a-3eebaaec359e.dat,/tmp/tmpmo0pk3jj/files/1/9/9/dataset_199870d8-d8a6-4437-8843-802fe43f55a3.dat,/tmp/tmpmo0pk3jj/files/5/8/2/dataset_582e346f-d990-4e67-aa16-75c5854a9c4e.dat,/tmp/tmpmo0pk3jj/files/5/a/9/dataset_5a962295-b81c-4eac-95f9-cb9b715227ec.dat,/tmp/tmpmo0pk3jj/files/a/d/6/dataset_ad62bd0c-a6a8-40dc-b75e-5caff07b002f.dat,/tmp/tmpmo0pk3jj/files/2/4/6/dataset_2462927e-bb24-4865-b0d7-233193737d9b.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpmo0pk3jj/files/3/e/0/dataset_3e0edcaf-c663-4aaa-833b-4d28d353ff86.dat:p3_2_CAG.gb,/tmp/tmpmo0pk3jj/files/c/b/e/dataset_cbeb8071-98da-4bcd-829a-3eebaaec359e.dat:p7_gfp_sequence.gb,/tmp/tmpmo0pk3jj/files/1/9/9/dataset_199870d8-d8a6-4437-8843-802fe43f55a3.dat:p14_CMVp.gb,/tmp/tmpmo0pk3jj/files/5/8/2/dataset_582e346f-d990-4e67-aa16-75c5854a9c4e.dat:p16_bGHpolyA.gb,/tmp/tmpmo0pk3jj/files/5/a/9/dataset_5a962295-b81c-4eac-95f9-cb9b715227ec.dat:p18_CMVp.gb,/tmp/tmpmo0pk3jj/files/a/d/6/dataset_ad62bd0c-a6a8-40dc-b75e-5caff07b002f.dat:p19_mNeoGreen.gb,/tmp/tmpmo0pk3jj/files/2/4/6/dataset_2462927e-bb24-4865-b0d7-233193737d9b.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpmo0pk3jj/job_working_directory/000/18/outputs/dataset_b8f77694-af17-44c7-8ca7-94039b4f9f10.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Error:**

    * ```console
      
      record:   0%|          | 0/7 [00:00<?, ?it/s, now=None]
      record:  43%|████▎     | 3/7 [00:01<00:02,  1.73it/s, now=None]
                                                                     
      ```
    **Standard Output:**

    * ```console
      Part names were not truncated

      ```
    **Traceback:**

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

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | genbank\_files | ` {"values": [{"id": 3, "src": "hdca"}]} ` |
       | methylation\_protection | ` true ` |
       | adv | ` {"allow_edits": true, "use_file_names_as_ids": true} ` |
       | chromInfo | ` "/tmp/tmpmo0pk3jj/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 May 23 09:07:37 2025 +0000 +++ b/output.json Tue May 27 08:08:21 2025 +0000 @@ -12,67 +12,67 @@ "adv|allow_edits": true, "adv|use_file_names_as_ids": true, "domestication_csv": { - "id": "3f0c528bcd0d2af0", + "id": "df3910bf12e3ecf9", "src": "hda" }, "genbank_files": { - "id": "2d588720727ac897", + "id": "40971d80b8a8a53c", "src": "hdca" }, "methylation_protection": false }, "job": { - "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpa__rr6q2/files/1/8/d/dataset_18d1bdeb-a69c-4f9a-8d59-4d4d12fbff4c.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpa__rr6q2/files/f/3/b/dataset_f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb.dat,/tmp/tmpa__rr6q2/files/f/f/6/dataset_ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8.dat,/tmp/tmpa__rr6q2/files/8/c/d/dataset_8cd82e26-da60-4c91-bb80-d65d9ac0864d.dat,/tmp/tmpa__rr6q2/files/a/f/6/dataset_af6f5158-3c00-4e30-a07f-b9cee1381d6c.dat,/tmp/tmpa__rr6q2/files/b/9/7/dataset_b97d206b-3b81-41ad-96a6-462a3ebcbbf2.dat,/tmp/tmpa__rr6q2/files/a/8/9/dataset_a8913c13-0cca-4e1e-9496-2c7f0bbcc485.dat,/tmp/tmpa__rr6q2/files/6/c/c/dataset_6cc8ecc8-2001-4b71-8cd5-3d42f368a626.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpa__rr6q2/files/f/3/b/dataset_f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb.dat:p3_2_CAG.gb,/tmp/tmpa__rr6q2/files/f/f/6/dataset_ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8.dat:p7_gfp_sequence.gb,/tmp/tmpa__rr6q2/files/8/c/d/dataset_8cd82e26-da60-4c91-bb80-d65d9ac0864d.dat:p14_CMVp.gb,/tmp/tmpa__rr6q2/files/a/f/6/dataset_af6f5158-3c00-4e30-a07f-b9cee1381d6c.dat:p16_bGHpolyA.gb,/tmp/tmpa__rr6q2/files/b/9/7/dataset_b97d206b-3b81-41ad-96a6-462a3ebcbbf2.dat:p18_CMVp.gb,/tmp/tmpa__rr6q2/files/a/8/9/dataset_a8913c13-0cca-4e1e-9496-2c7f0bbcc485.dat:p19_mNeoGreen.gb,/tmp/tmpa__rr6q2/files/6/c/c/dataset_6cc8ecc8-2001-4b71-8cd5-3d42f368a626.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpa__rr6q2/job_working_directory/000/9/outputs/dataset_3847af4a-c6f8-4bc2-92e6-a5111f36e863.dat'", + "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpmo0pk3jj/files/6/1/a/dataset_61aea63f-fa8f-4855-b597-d298379d415c.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmo0pk3jj/files/2/f/f/dataset_2ff46bb9-5b06-4cad-b98f-afa1443697b5.dat,/tmp/tmpmo0pk3jj/files/9/9/c/dataset_99c508b5-234a-4eba-b9d2-05204eaa2ec8.dat,/tmp/tmpmo0pk3jj/files/0/a/0/dataset_0a0b7db9-a3ac-4999-b1c9-498618831d59.dat,/tmp/tmpmo0pk3jj/files/a/2/9/dataset_a2994595-0a40-48ba-a369-db577710e99a.dat,/tmp/tmpmo0pk3jj/files/c/8/b/dataset_c8b3e40f-a0a8-414e-a56c-bd71775b2218.dat,/tmp/tmpmo0pk3jj/files/c/8/1/dataset_c813a93e-97c6-4f6a-bcd0-dcdbd93728e2.dat,/tmp/tmpmo0pk3jj/files/3/6/8/dataset_368b2cf8-f34e-427d-888e-b431a4b28c87.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpmo0pk3jj/files/2/f/f/dataset_2ff46bb9-5b06-4cad-b98f-afa1443697b5.dat:p3_2_CAG.gb,/tmp/tmpmo0pk3jj/files/9/9/c/dataset_99c508b5-234a-4eba-b9d2-05204eaa2ec8.dat:p7_gfp_sequence.gb,/tmp/tmpmo0pk3jj/files/0/a/0/dataset_0a0b7db9-a3ac-4999-b1c9-498618831d59.dat:p14_CMVp.gb,/tmp/tmpmo0pk3jj/files/a/2/9/dataset_a2994595-0a40-48ba-a369-db577710e99a.dat:p16_bGHpolyA.gb,/tmp/tmpmo0pk3jj/files/c/8/b/dataset_c8b3e40f-a0a8-414e-a56c-bd71775b2218.dat:p18_CMVp.gb,/tmp/tmpmo0pk3jj/files/c/8/1/dataset_c813a93e-97c6-4f6a-bcd0-dcdbd93728e2.dat:p19_mNeoGreen.gb,/tmp/tmpmo0pk3jj/files/3/6/8/dataset_368b2cf8-f34e-427d-888e-b431a4b28c87.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpmo0pk3jj/job_working_directory/000/9/outputs/dataset_598cd11f-0878-422d-b265-3e7d109f52d4.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T09:02:47.568318", + "create_time": "2025-05-27T08:07:08.549227", "dependencies": [], "exit_code": 0, - "external_id": "59522", + "external_id": "15664", "galaxy_version": "24.2", "handler": null, - "history_id": "2d588720727ac897", - "id": "05d1fab5f2f95c6e", + "history_id": "40971d80b8a8a53c", + "id": "beecbc66855f4047", "inputs": { "domestication_csv": { - "id": "3f0c528bcd0d2af0", + "id": "df3910bf12e3ecf9", "src": "hda", - "uuid": "18d1bdeb-a69c-4f9a-8d59-4d4d12fbff4c" + "uuid": "61aea63f-fa8f-4855-b597-d298379d415c" }, "genbank_files1": { - "id": "2d588720727ac897", + "id": "40971d80b8a8a53c", "src": "hda", - "uuid": "f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb" + "uuid": "2ff46bb9-5b06-4cad-b98f-afa1443697b5" }, "genbank_files2": { - "id": "62972d51292f48e6", + "id": "722a3e09b8314bb2", "src": "hda", - "uuid": "ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8" + "uuid": "99c508b5-234a-4eba-b9d2-05204eaa2ec8" }, "genbank_files3": { - "id": "e362c0fcc265e8f8", + "id": "1cc8aca787b2436a", "src": "hda", - "uuid": "8cd82e26-da60-4c91-bb80-d65d9ac0864d" + "uuid": "0a0b7db9-a3ac-4999-b1c9-498618831d59" }, "genbank_files4": { - "id": "9106613ee8ff8561", + "id": "8026227525c5f951", "src": "hda", - "uuid": "af6f5158-3c00-4e30-a07f-b9cee1381d6c" + "uuid": "a2994595-0a40-48ba-a369-db577710e99a" }, "genbank_files5": { - "id": "0973ce805f0b9fc9", + "id": "38afb044c6b21b09", "src": "hda", - "uuid": "b97d206b-3b81-41ad-96a6-462a3ebcbbf2" + "uuid": "c8b3e40f-a0a8-414e-a56c-bd71775b2218" }, "genbank_files6": { - "id": "3f7b9edb7f21ca84", + "id": "58f07e41a8a4674f", "src": "hda", - "uuid": "a8913c13-0cca-4e1e-9496-2c7f0bbcc485" + "uuid": "c813a93e-97c6-4f6a-bcd0-dcdbd93728e2" }, "genbank_files7": { - "id": "898926e359e5028c", + "id": "3e34fe414480d6bc", "src": "hda", - "uuid": "6cc8ecc8-2001-4b71-8cd5-3d42f368a626" + "uuid": "368b2cf8-f34e-427d-888e-b431a4b28c87" } }, "job_messages": [], @@ -83,73 +83,73 @@ "model_class": "Job", "output_collections": { "domesticated_gb": { - "id": "62972d51292f48e6", + "id": "722a3e09b8314bb2", "src": "hdca" } }, "outputs": { "__new_primary_file_domesticated_gb|p14_CMVp__": { - "id": "0481fa54d30635c9", + "id": "8b52218386489a1b", "src": "hda", - "uuid": "a0555d82-443f-4b4b-8431-2a9d4e049017" + "uuid": "9ec489c3-d7d2-4c8e-85ed-7c608bfffc49" }, "__new_primary_file_domesticated_gb|p16_bGHpolyA__": { - "id": "813bd8a24377d169", + "id": "7df4279c30fbf11a", "src": "hda", - "uuid": "e506a4e3-7524-4360-abe1-b49ed99833d7" + "uuid": "e56aa342-fc45-4a28-befa-290f5722a67c" }, "__new_primary_file_domesticated_gb|p18_CMVp__": { - "id": "d79d6af225946b08", + "id": "5a11a7ea1c4a0b78", "src": "hda", - "uuid": "851cdd02-8f5a-400a-9b51-483c43d67028" + "uuid": "8beec3f0-36c6-4994-b890-35fbba7d1c32" }, "__new_primary_file_domesticated_gb|p19_mNeoGreen__": { - "id": "3ab85ee8e71bbdd5", + "id": "f727b077209f6bea", "src": "hda", - "uuid": "118d7f40-4850-466b-9f40-e360f1748011" + "uuid": "7309490c-224e-46b1-82d1-94102829a851" }, "__new_primary_file_domesticated_gb|p22_PGKpolyA__": { - "id": "5480ebfe4604885a", + "id": "77c3effc68e335c0", "src": "hda", - "uuid": "b82fcc71-a34f-44f8-9dcf-546a10a5f2d6" + "uuid": "4d4c783f-d229-44b3-af52-0e6616cd140b" }, "__new_primary_file_domesticated_gb|p3_2_CAG__": { - "id": "f174fd93dd20b3fc", + "id": "a5683b91f8081320", "src": "hda", - "uuid": "fa38ea29-3950-4e40-aed2-427b47597fc7" + "uuid": "08b3572e-4f1c-4fe3-ac3c-8dcf2ec05ce2" }, "__new_primary_file_domesticated_gb|p7_gfp_sequence__": { - "id": "58f99e5516a773cd", + "id": "3e3b60188e62bb8d", "src": "hda", - "uuid": "538b66c4-b4d0-41b8-9355-afadc944621c" + "uuid": "6fe9d54a-584a-470a-82a5-b16b0ed0b7e1" }, - "output_zip": { - "id": "05d1fab5f2f95c6e", + "domesticated_zip": { + "id": "beecbc66855f4047", "src": "hda", - "uuid": "3847af4a-c6f8-4bc2-92e6-a5111f36e863" + "uuid": "598cd11f-0878-422d-b265-3e7d109f52d4" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}", - "chromInfo": "\"/tmp/tmpa__rr6q2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpmo0pk3jj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", "methylation_protection": "false" }, "state": "ok", - "stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.75it/s, now=None]\r \r", + "stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.68it/s, now=None]\r \r", "stdout": "Part names were not truncated\n", "tool_id": "domestication", - "tool_stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.75it/s, now=None]\r \r", + "tool_stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.68it/s, now=None]\r \r", "tool_stdout": "Part names were not truncated\n", - "update_time": "2025-05-23T09:02:58.973787", + "update_time": "2025-05-27T08:07:20.210958", "user_email": "planemo@galaxyproject.org", - "user_id": "2d588720727ac897" + "user_id": "40971d80b8a8a53c" }, "status": "success", "test_index": 0, - "time_seconds": 34.70007658004761, + "time_seconds": 34.19329214096069, "tool_id": "domestication", "tool_version": "0.1.0+galaxy1" }, @@ -162,20 +162,20 @@ "adv|allow_edits": true, "adv|use_file_names_as_ids": true, "domestication_csv": { - "id": "0ac23d4d0b88827c", + "id": "2d30278c16dd9bf8", "src": "hda" }, "genbank_files": { - "id": "e362c0fcc265e8f8", + "id": "1cc8aca787b2436a", "src": "hdca" }, "methylation_protection": true }, "job": { - "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpa__rr6q2/files/8/9/c/dataset_89c41e63-3985-4c33-9154-735d98f3f2bb.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpa__rr6q2/files/3/7/a/dataset_37a61c0f-4043-404f-97c9-1b2e4b277a0b.dat,/tmp/tmpa__rr6q2/files/a/c/d/dataset_acd5b8cd-260a-4eed-bbaa-083097afd437.dat,/tmp/tmpa__rr6q2/files/b/4/2/dataset_b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd.dat,/tmp/tmpa__rr6q2/files/6/4/3/dataset_643037ae-a752-4ce5-80e9-921fa8b24d3b.dat,/tmp/tmpa__rr6q2/files/d/c/e/dataset_dce00e9a-8b99-4bce-a1c2-b17377db99cf.dat,/tmp/tmpa__rr6q2/files/0/2/0/dataset_020c2948-6eb0-4860-b17b-a3f35d138965.dat,/tmp/tmpa__rr6q2/files/2/c/6/dataset_2c6f9cf6-bf93-4c97-9ea8-17ad34702969.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpa__rr6q2/files/3/7/a/dataset_37a61c0f-4043-404f-97c9-1b2e4b277a0b.dat:p3_2_CAG.gb,/tmp/tmpa__rr6q2/files/a/c/d/dataset_acd5b8cd-260a-4eed-bbaa-083097afd437.dat:p7_gfp_sequence.gb,/tmp/tmpa__rr6q2/files/b/4/2/dataset_b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd.dat:p14_CMVp.gb,/tmp/tmpa__rr6q2/files/6/4/3/dataset_643037ae-a752-4ce5-80e9-921fa8b24d3b.dat:p16_bGHpolyA.gb,/tmp/tmpa__rr6q2/files/d/c/e/dataset_dce00e9a-8b99-4bce-a1c2-b17377db99cf.dat:p18_CMVp.gb,/tmp/tmpa__rr6q2/files/0/2/0/dataset_020c2948-6eb0-4860-b17b-a3f35d138965.dat:p19_mNeoGreen.gb,/tmp/tmpa__rr6q2/files/2/c/6/dataset_2c6f9cf6-bf93-4c97-9ea8-17ad34702969.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpa__rr6q2/job_working_directory/000/18/outputs/dataset_257e63c3-87b5-459a-b118-921e6217abe8.dat'", + "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpmo0pk3jj/files/8/8/c/dataset_88ce7dbb-b512-47e2-b4c4-a33e25f510f5.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmo0pk3jj/files/3/e/0/dataset_3e0edcaf-c663-4aaa-833b-4d28d353ff86.dat,/tmp/tmpmo0pk3jj/files/c/b/e/dataset_cbeb8071-98da-4bcd-829a-3eebaaec359e.dat,/tmp/tmpmo0pk3jj/files/1/9/9/dataset_199870d8-d8a6-4437-8843-802fe43f55a3.dat,/tmp/tmpmo0pk3jj/files/5/8/2/dataset_582e346f-d990-4e67-aa16-75c5854a9c4e.dat,/tmp/tmpmo0pk3jj/files/5/a/9/dataset_5a962295-b81c-4eac-95f9-cb9b715227ec.dat,/tmp/tmpmo0pk3jj/files/a/d/6/dataset_ad62bd0c-a6a8-40dc-b75e-5caff07b002f.dat,/tmp/tmpmo0pk3jj/files/2/4/6/dataset_2462927e-bb24-4865-b0d7-233193737d9b.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpmo0pk3jj/files/3/e/0/dataset_3e0edcaf-c663-4aaa-833b-4d28d353ff86.dat:p3_2_CAG.gb,/tmp/tmpmo0pk3jj/files/c/b/e/dataset_cbeb8071-98da-4bcd-829a-3eebaaec359e.dat:p7_gfp_sequence.gb,/tmp/tmpmo0pk3jj/files/1/9/9/dataset_199870d8-d8a6-4437-8843-802fe43f55a3.dat:p14_CMVp.gb,/tmp/tmpmo0pk3jj/files/5/8/2/dataset_582e346f-d990-4e67-aa16-75c5854a9c4e.dat:p16_bGHpolyA.gb,/tmp/tmpmo0pk3jj/files/5/a/9/dataset_5a962295-b81c-4eac-95f9-cb9b715227ec.dat:p18_CMVp.gb,/tmp/tmpmo0pk3jj/files/a/d/6/dataset_ad62bd0c-a6a8-40dc-b75e-5caff07b002f.dat:p19_mNeoGreen.gb,/tmp/tmpmo0pk3jj/files/2/4/6/dataset_2462927e-bb24-4865-b0d7-233193737d9b.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpmo0pk3jj/job_working_directory/000/18/outputs/dataset_b8f77694-af17-44c7-8ca7-94039b4f9f10.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T09:03:22.156202", + "create_time": "2025-05-27T08:07:43.266253", "dependencies": [ { "cacheable": false, @@ -377,51 +377,51 @@ } ], "exit_code": 0, - "external_id": "60268", + "external_id": "16351", "galaxy_version": "24.2", "handler": null, - "history_id": "62972d51292f48e6", - "id": "e08d37863731003c", + "history_id": "722a3e09b8314bb2", + "id": "6c90a7736cfec646", "inputs": { "domestication_csv": { - "id": "0ac23d4d0b88827c", + "id": "2d30278c16dd9bf8", "src": "hda", - "uuid": "89c41e63-3985-4c33-9154-735d98f3f2bb" + "uuid": "88ce7dbb-b512-47e2-b4c4-a33e25f510f5" }, "genbank_files1": { - "id": "55d915b26d3a354e", + "id": "92861e8424eabf5a", "src": "hda", - "uuid": "37a61c0f-4043-404f-97c9-1b2e4b277a0b" + "uuid": "3e0edcaf-c663-4aaa-833b-4d28d353ff86" }, "genbank_files2": { - "id": "e08d37863731003c", + "id": "6c90a7736cfec646", "src": "hda", - "uuid": "acd5b8cd-260a-4eed-bbaa-083097afd437" + "uuid": "cbeb8071-98da-4bcd-829a-3eebaaec359e" }, "genbank_files3": { - "id": "72fd2001a1c00c74", + "id": "d833721564461fe0", "src": "hda", - "uuid": "b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd" + "uuid": "199870d8-d8a6-4437-8843-802fe43f55a3" }, "genbank_files4": { - "id": "535975adfebcbd66", + "id": "bc67cca121169b32", "src": "hda", - "uuid": "643037ae-a752-4ce5-80e9-921fa8b24d3b" + "uuid": "582e346f-d990-4e67-aa16-75c5854a9c4e" }, "genbank_files5": { - "id": "44c226435b38bb38", + "id": "2c119c7d607245b7", "src": "hda", - "uuid": "dce00e9a-8b99-4bce-a1c2-b17377db99cf" + "uuid": "5a962295-b81c-4eac-95f9-cb9b715227ec" }, "genbank_files6": { - "id": "bbe178e57c4f8c81", + "id": "654b689f382d7faf", "src": "hda", - "uuid": "020c2948-6eb0-4860-b17b-a3f35d138965" + "uuid": "ad62bd0c-a6a8-40dc-b75e-5caff07b002f" }, "genbank_files7": { - "id": "11bdfc4549627602", + "id": "848a7ec9db54f91c", "src": "hda", - "uuid": "2c6f9cf6-bf93-4c97-9ea8-17ad34702969" + "uuid": "2462927e-bb24-4865-b0d7-233193737d9b" } }, "job_messages": [], @@ -432,56 +432,56 @@ "model_class": "Job", "output_collections": { "methprot_gb": { - "id": "9106613ee8ff8561", + "id": "8026227525c5f951", "src": "hdca" } }, "outputs": { "__new_primary_file_methprot_gb|p14_CMVp__": { - "id": "63657e65b797e156", + "id": "552487cd77e5739b", "src": "hda", - "uuid": "ff3d4f80-e86b-4391-b395-1f11f74883e0" + "uuid": "47a78a3c-f714-4a3b-baf6-db74ec3e57ec" }, "__new_primary_file_methprot_gb|p16_bGHpolyA__": { - "id": "7000d26bf45ffb00", + "id": "c150df1632d3bf7a", "src": "hda", - "uuid": "0ea8ad54-9cee-4a88-9352-cbf201923fb8" + "uuid": "9ec7ff7e-c752-40ab-8e30-d00bce534323" }, "__new_primary_file_methprot_gb|p18_CMVp__": { - "id": "36313fb553e6e307", + "id": "3b8df2fa2b4da081", "src": "hda", - "uuid": "e6a1e8a2-1881-4ea9-9e2f-c2bc40a273a6" + "uuid": "ef3876f0-595c-4e36-b1d2-424ac4f3c495" }, "__new_primary_file_methprot_gb|p19_mNeoGreen__": { - "id": "12401c2b6811fee0", + "id": "ea8abe36fc9e84c6", "src": "hda", - "uuid": "a73b7443-df14-4dea-84f3-381db57cca18" + "uuid": "d9db4707-d9a0-4578-861a-4536b24e3d55" }, "__new_primary_file_methprot_gb|p22_PGKpolyA__": { - "id": "0eb41dc2e09a8361", + "id": "195917444a0d1fd3", "src": "hda", - "uuid": "67791634-ccbb-4984-82b6-5f6dabf17fd3" + "uuid": "ebcddc78-8aec-4aa7-a99f-1f6c98312abf" }, "__new_primary_file_methprot_gb|p3_2_CAG__": { - "id": "963b9ee6a9b85043", + "id": "07090fd15ab7700f", "src": "hda", - "uuid": "a79b48fa-4414-4de6-9747-be228b0650ff" + "uuid": "f565adba-00b9-4476-a1dc-f917d7695ed7" }, "__new_primary_file_methprot_gb|p7_gfp_sequence__": { - "id": "3716318b258c039e", + "id": "181ca79c6e3f2d04", "src": "hda", - "uuid": "3834e7e4-4365-4020-88d7-554281f0836f" + "uuid": "d36b2983-c229-453a-b3c5-d6e44ab877f5" }, - "output_zip": { - "id": "c2e357d169213b81", + "domesticated_zip": { + "id": "bbfdb6491da014b1", "src": "hda", - "uuid": "257e63c3-87b5-459a-b118-921e6217abe8" + "uuid": "b8f77694-af17-44c7-8ca7-94039b4f9f10" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}", - "chromInfo": "\"/tmp/tmpa__rr6q2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpmo0pk3jj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", "methylation_protection": "true" @@ -492,13 +492,13 @@ "tool_id": "domestication", "tool_stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.73it/s, now=None]\r \r", "tool_stdout": "Part names were not truncated\n", - "update_time": "2025-05-23T09:03:33.301866", + "update_time": "2025-05-27T08:07:54.372698", "user_email": "planemo@galaxyproject.org", - "user_id": "2d588720727ac897" + "user_id": "40971d80b8a8a53c" }, "status": "success", "test_index": 1, - "time_seconds": 34.21326494216919, + "time_seconds": 34.02547550201416, "tool_id": "domestication", "tool_version": "0.1.0+galaxy1" },