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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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Test pangolin 3.1.17+galaxy1 #7

Closed natefoo closed 2 years ago

natefoo commented 2 years ago

Installed in galaxyproject/usegalaxy-tools#451

natefoo commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/3.1.17+galaxy1

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 2
Error 2
Failure 0
Skipped 0
Errored s *
❌ toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin (Test #1)
**Execution Problem:** * ``` Input staging problem: Expecting value: line 1 column 1 (char 0) ```
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin (Test #2)
    **Execution Problem:** * ``` Input staging problem: Expecting value: line 1 column 1 (char 0) ```

Passed s *
✅ toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin (Test #3)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console pangolearn already latest release (2021-12-06) constellations updated to v0.1.1 pango-designation already latest release (v1.2.112) Job stats: job count min threads max threads -------------------- ------- ------------- ------------- add_failed_seqs 1 1 1 align_to_reference 1 1 1 all 1 1 1 generate_report 1 1 1 get_constellations 1 1 1 hash_sequence_assign 1 1 1 pangolearn 1 1 1 scorpio 1 1 1 total 8 1 1 ``` **Standard Output:** * ```console loading model 12/16/2021, 21:05:23 processing block of 1 sequences 12/16/2021, 21:05:25 complete 12/16/2021, 21:05:25 Output file written to: /corral4/main/jobs/039/705/39705554/working/report.csv Output alignment written to: /corral4/main/jobs/039/705/39705554/working/sequences.aln.fasta All dependencies satisfied. The query file is:/corral4/main/objects/5/8/3/dataset_5830703f-01a1-498a-94be-9eb2a4309059.dat ** Running sequence QC ** Number of sequences detected: 1 Total passing QC: 1  Data files found: Trained model: /usr/local/lib/python3.8/site-packages/pangoLEARN/data/decisionTree_v1.joblib Header file: /usr/local/lib/python3.8/site-packages/pangoLEARN/data/decisionTreeHeaders_v1.joblib Designated hash: /usr/local/lib/python3.8/site-packages/pangoLEARN/data/lineages.hash.csv ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | usher | ` "false" ` | | alignment | ` "true" ` | | max\_ambig | ` "0.5" ` | | min\_length | ` "10000" ` | | include\_header | ` "false" ` | | db | ` {"__current_case__": 0, "source": "download"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin (Test #4)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console pangolearn already latest release (2021-12-06) constellations updated to v0.1.1 pango-designation already latest release (v1.2.112) Job stats: job count min threads max threads -------------------- ------- ------------- ------------- add_failed_seqs 1 1 1 align_to_reference 1 1 1 all 1 1 1 generate_report 1 1 1 get_constellations 1 1 1 hash_sequence_assign 1 1 1 pangolearn 1 1 1 scorpio 1 1 1 total 8 1 1 ``` **Standard Output:** * ```console loading model 12/16/2021, 21:04:27 processing block of 6 sequences 12/16/2021, 21:04:28 complete 12/16/2021, 21:04:28 Output file written to: /corral4/main/jobs/039/705/39705556/working/report.csv All dependencies satisfied. The query file is:/corral4/main/objects/4/d/f/dataset_4df88074-3eb4-49f9-91ee-ca8bdf5cdd5c.dat ** Running sequence QC ** Number of sequences detected: 34 Total passing QC: 34  Data files found: Trained model: /usr/local/lib/python3.8/site-packages/pangoLEARN/data/decisionTree_v1.joblib Header file: /usr/local/lib/python3.8/site-packages/pangoLEARN/data/decisionTreeHeaders_v1.joblib Designated hash: /usr/local/lib/python3.8/site-packages/pangoLEARN/data/lineages.hash.csv ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | usher | ` "false" ` | | alignment | ` "false" ` | | max\_ambig | ` "0.5" ` | | min\_length | ` "10000" ` | | include\_header | ` "true" ` | | db | ` {"__current_case__": 0, "source": "download"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

natefoo commented 2 years ago

Again all 4 passed when run from the command line. =/