diff --git a/workflows/comparative_genomics/hyphy/CHANGELOG.md b/workflows/comparative_genomics/hyphy/CHANGELOG.md index c02ae034e6..997dc7a8fe 100644 --- a/workflows/comparative_genomics/hyphy/CHANGELOG.md +++ b/workflows/comparative_genomics/hyphy/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2] - 2026-04-27 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy2` + ## [0.1] - 2026-02-26 ### Added diff --git a/workflows/comparative_genomics/hyphy/capheine-core-and-compare.ga b/workflows/comparative_genomics/hyphy/capheine-core-and-compare.ga index 7b11815e21..451a541b36 100644 --- a/workflows/comparative_genomics/hyphy/capheine-core-and-compare.ga +++ b/workflows/comparative_genomics/hyphy/capheine-core-and-compare.ga @@ -618,7 +618,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy2", "errors": null, "id": 8, "input_connections": { @@ -670,16 +670,16 @@ "top": 170 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy2", "tool_shed_repository": { - "changeset_revision": "18a61a9c1601", + "changeset_revision": "e727e82945af", "name": "iqtree", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"bootstrap_parameters\": {\"ultrafast_bootstrap\": {\"ufboot\": null, \"ufjack\": null, \"jack_prop\": null, \"boot_trees\": false, \"wbtl\": false, \"nmax\": \"1000\", \"bcor\": \"0.99\", \"nstep\": \"100\", \"beps\": \"0.5\", \"sampling\": null, \"bnni\": false}, \"nonparametric_bootstrap\": {\"boot\": null, \"jack\": null, \"jack_prop\": null, \"bcon\": null, \"bonly\": null, \"tbe\": false}}, \"general_options\": {\"s\": {\"__class__\": \"ConnectedValue\"}, \"o\": null, \"short_alignments\": false, \"seqtype\": \"DNA\", \"t\": {\"__class__\": \"RuntimeValue\"}, \"seed\": null, \"keep_ident\": false, \"epsilon\": null, \"safe\": false}, \"likelihood_mapping\": {\"lmap\": null, \"lmclust\": {\"__class__\": \"RuntimeValue\"}, \"quartetlh\": false}, \"miscellaneous_options\": {\"fconst\": null, \"blmin\": null, \"blmax\": null}, \"modelling_parameters\": {\"automatic_model\": {\"cond_model\": {\"opt_custommodel\": \"true\", \"__current_case__\": 0, \"m\": null}, \"merge_strategy\": {\"merge\": \"none\", \"__current_case__\": 0}, \"mset\": null, \"msub\": \"nuclear\", \"mfreq\": null, \"mrate\": null, \"cmin\": \"2\", \"cmax\": \"10\", \"merit\": \"AIC\", \"mtree\": false, \"madd\": null, \"mdef\": {\"__class__\": \"RuntimeValue\"}, \"modelomatic\": false}, \"specifying_substitution\": {\"mix_opt\": false}, \"rate_heterogeneity\": {\"alpha_min\": null, \"gamma_median\": false, \"i\": null, \"opt_gamma_inv\": false, \"rate\": false, \"mlrate\": 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false, \"symtest_remove_bad\": false, \"symtest_remove_good\": false, \"symtest_type\": null, \"symtest_pval\": null, \"symtest_keep_zero\": false}, \"concordance_factor\": {\"gcf\": {\"__class__\": \"RuntimeValue\"}, \"df_tree\": false, \"scf\": null, \"cf_verbose\": false, \"cf_quartet\": false}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "2.4.0+galaxy1", + "tool_version": "2.4.0+galaxy2", "type": "tool", "uuid": "ac7542a5-1352-4699-a54c-bef15be8ede0", "when": null, @@ -693,7 +693,7 @@ } }, "tags": [], - "uuid": "17e07d94-656d-4f77-8a87-a4386ce80cf8" + "uuid": "44ef2325-6854-417b-8ef4-bc8e61a3216b" }, "tool_id": null, "type": "subworkflow", @@ -930,7 +930,7 @@ } }, "tags": [], - "uuid": "d9ff8d46-05c5-4ba5-ab44-fbace76bc5b2" + "uuid": "b80031ae-c6ea-4430-a8a8-345da78b406b" }, "tool_id": null, "type": "subworkflow", @@ -1889,7 +1889,7 @@ } }, "tags": [], - "uuid": "81799349-b595-46e0-8e32-cbfc7607e93b" + "uuid": "758359d4-4a81-4d0d-ae15-2e444f1a2e73" }, "tool_id": null, "type": "subworkflow", @@ -1992,7 +1992,7 @@ } }, "tags": [], - "uuid": "e1fbea6f-563e-40d1-b580-f97883fca29f", + "uuid": "6657ea20-cbee-4039-8032-2014e27f2fc7", "version": 1, - "release": "0.1" + "release": "0.2" } \ No newline at end of file diff --git a/workflows/comparative_genomics/hyphy/hyphy-core.ga b/workflows/comparative_genomics/hyphy/hyphy-core.ga index bd13ed24a2..cfd32151a2 100644 --- a/workflows/comparative_genomics/hyphy/hyphy-core.ga +++ b/workflows/comparative_genomics/hyphy/hyphy-core.ga @@ -452,7 +452,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy2", "errors": null, "id": 8, "input_connections": { @@ -504,16 +504,16 @@ "top": 170 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy2", "tool_shed_repository": { - "changeset_revision": "18a61a9c1601", + "changeset_revision": "e727e82945af", "name": "iqtree", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"bootstrap_parameters\": {\"ultrafast_bootstrap\": {\"ufboot\": null, \"ufjack\": null, \"jack_prop\": null, \"boot_trees\": false, \"wbtl\": false, \"nmax\": \"1000\", \"bcor\": \"0.99\", \"nstep\": \"100\", \"beps\": \"0.5\", \"sampling\": null, \"bnni\": false}, \"nonparametric_bootstrap\": {\"boot\": null, \"jack\": null, \"jack_prop\": null, \"bcon\": null, \"bonly\": null, \"tbe\": false}}, \"general_options\": {\"s\": {\"__class__\": \"ConnectedValue\"}, \"o\": null, \"short_alignments\": false, \"seqtype\": \"DNA\", \"t\": {\"__class__\": \"RuntimeValue\"}, \"seed\": null, \"keep_ident\": false, \"epsilon\": null, \"safe\": false}, \"likelihood_mapping\": {\"lmap\": null, \"lmclust\": {\"__class__\": \"RuntimeValue\"}, 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\"cf_verbose\": false, \"cf_quartet\": false}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "2.4.0+galaxy1", + "tool_version": "2.4.0+galaxy2", "type": "tool", "uuid": "ac7542a5-1352-4699-a54c-bef15be8ede0", "when": null, @@ -527,7 +527,7 @@ } }, "tags": [], - "uuid": "788d1d72-5704-45dd-ba65-fd3f5e0947af" + "uuid": "3e4f3170-7d18-4cd8-bd00-16750975554a" }, "tool_id": null, "type": "subworkflow", @@ -764,7 +764,7 @@ } }, "tags": [], - "uuid": "d193df0d-c6b9-44b1-9517-7d6b3874d067", + "uuid": "8a490d79-4611-4bd9-bd25-c099dc77c8b8", "version": 1, - "release": "0.1" + "release": "0.2" } \ No newline at end of file diff --git a/workflows/comparative_genomics/hyphy/hyphy-preprocessing.ga b/workflows/comparative_genomics/hyphy/hyphy-preprocessing.ga index 0f3367b7b2..0a3da60300 100644 --- a/workflows/comparative_genomics/hyphy/hyphy-preprocessing.ga +++ b/workflows/comparative_genomics/hyphy/hyphy-preprocessing.ga @@ -346,7 +346,7 @@ }, "8": { 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