Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 5 additions & 0 deletions workflows/comparative_genomics/hyphy/CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -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
Expand Down
20 changes: 10 additions & 10 deletions workflows/comparative_genomics/hyphy/capheine-core-and-compare.ga
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down Expand Up @@ -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\": false}, \"partition_model\": {\"model_selection\": {\"model\": \"none\", \"__current_case__\": 0}}, \"site_specific_frequency\": {\"tree_freq\": {\"__class__\": \"RuntimeValue\"}, \"site_freq\": null, \"freq_max\": false}}, \"time_tree\": {\"date_source\": {\"select_source\": \"none\", \"__current_case__\": 0}, \"date_tip\": null, \"date_root\": null, \"date_ci\": null, \"clock_sd\": null, \"date_no_outgroup\": false, \"date_outlier\": null, \"date_options\": null}, \"tree_parameters\": {\"tree_search\": {\"n\": null, \"ninit\": \"100\", \"ntop\": \"20\", \"nbest\": \"5\", \"nstop\": \"100\", \"radius\": \"6\", \"perturb\": \"0.5\", \"allnni\": false, \"tree_fix\": false, \"g\": {\"__class__\": \"RuntimeValue\"}, \"fast\": false, \"polytomy\": false, \"treels\": false, \"show_lh\": false, \"terrace\": false}, \"single_branch\": {\"alrt\": null, \"abayes\": false, \"lbp\": null}, \"tree_topology\": {\"trees\": {\"__class__\": \"RuntimeValue\"}, \"test\": null, \"test_weight\": false, \"test_au\": false}, \"constructing_consensus\": {\"contree\": false, \"connet\": false, \"sup_min\": \"0.0\", \"burnin\": null, \"support\": {\"__class__\": \"RuntimeValue\"}, \"suptag\": null}, \"computing_robinson_foulds\": {\"tree_dist_all\": false, \"tree_dist\": {\"__class__\": \"RuntimeValue\"}, \"tree_dist2\": {\"__class__\": \"RuntimeValue\"}}, \"generating_random\": {\"r\": null, \"rand\": null, \"branch_min\": null, \"branch_mean\": null, \"branch_max\": null}, \"ancestral_state\": {\"ancestral\": false, \"asr_min\": null}, \"symmetry_test\": {\"symtest\": 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_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\": false}, \"partition_model\": {\"model_selection\": {\"model\": \"none\", \"__current_case__\": 0}}, \"site_specific_frequency\": {\"tree_freq\": {\"__class__\": \"RuntimeValue\"}, \"site_freq\": null, \"freq_max\": false}}, \"time_tree\": {\"date_source\": {\"select_source\": \"none\", \"__current_case__\": 0}, \"date_tip\": null, \"date_root\": null, \"date_ci\": null, \"clock_sd\": null, \"date_no_outgroup\": false, \"date_outlier\": null, \"date_options\": null}, \"tree_parameters\": {\"tree_search\": {\"n\": null, \"ninit\": \"100\", \"ntop\": \"20\", \"nbest\": \"5\", \"nstop\": \"100\", \"radius\": \"6\", \"perturb\": \"0.5\", \"allnni\": false, \"tree_fix\": false, \"g\": {\"__class__\": \"RuntimeValue\"}, \"fast\": false, \"polytomy\": false, \"treels\": false, \"show_lh\": false, \"terrace\": false}, \"single_branch\": {\"alrt\": null, \"abayes\": false, \"lbp\": null}, \"tree_topology\": {\"trees\": {\"__class__\": \"RuntimeValue\"}, \"test\": null, \"test_weight\": false, \"test_au\": false}, \"constructing_consensus\": {\"con_tree\": false, \"con_net\": false, \"sup_min\": \"0.0\", \"burnin\": null, \"support\": {\"__class__\": \"RuntimeValue\"}, \"suptag\": null}, \"computing_robinson_foulds\": {\"tree_dist_all\": false, \"tree_dist\": {\"__class__\": \"RuntimeValue\"}, \"tree_dist2\": {\"__class__\": \"RuntimeValue\"}}, \"generating_random\": {\"r\": null, \"rand\": null, \"branch_min\": null, \"branch_mean\": null, \"branch_max\": null}, \"ancestral_state\": {\"ancestral\": false, \"asr_min\": null}, \"symmetry_test\": {\"symtest\": 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,
Expand All @@ -693,7 +693,7 @@
}
},
"tags": [],
"uuid": "17e07d94-656d-4f77-8a87-a4386ce80cf8"
"uuid": "44ef2325-6854-417b-8ef4-bc8e61a3216b"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -930,7 +930,7 @@
}
},
"tags": [],
"uuid": "d9ff8d46-05c5-4ba5-ab44-fbace76bc5b2"
"uuid": "b80031ae-c6ea-4430-a8a8-345da78b406b"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -1889,7 +1889,7 @@
}
},
"tags": [],
"uuid": "81799349-b595-46e0-8e32-cbfc7607e93b"
"uuid": "758359d4-4a81-4d0d-ae15-2e444f1a2e73"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -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"
}
16 changes: 8 additions & 8 deletions workflows/comparative_genomics/hyphy/hyphy-core.ga
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down Expand Up @@ -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\"}, \"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\": false}, \"partition_model\": {\"model_selection\": {\"model\": \"none\", \"__current_case__\": 0}}, \"site_specific_frequency\": {\"tree_freq\": {\"__class__\": \"RuntimeValue\"}, \"site_freq\": null, \"freq_max\": false}}, \"time_tree\": {\"date_source\": {\"select_source\": \"none\", \"__current_case__\": 0}, \"date_tip\": null, \"date_root\": null, \"date_ci\": null, \"clock_sd\": null, \"date_no_outgroup\": false, \"date_outlier\": null, \"date_options\": null}, \"tree_parameters\": {\"tree_search\": {\"n\": null, \"ninit\": \"100\", \"ntop\": \"20\", \"nbest\": \"5\", \"nstop\": \"100\", \"radius\": \"6\", \"perturb\": \"0.5\", \"allnni\": false, \"tree_fix\": false, \"g\": {\"__class__\": \"RuntimeValue\"}, \"fast\": false, \"polytomy\": false, \"treels\": false, \"show_lh\": false, \"terrace\": false}, \"single_branch\": {\"alrt\": null, \"abayes\": false, \"lbp\": null}, \"tree_topology\": {\"trees\": {\"__class__\": \"RuntimeValue\"}, \"test\": null, \"test_weight\": false, \"test_au\": false}, \"constructing_consensus\": {\"contree\": false, \"connet\": false, \"sup_min\": \"0.0\", \"burnin\": null, \"support\": {\"__class__\": \"RuntimeValue\"}, \"suptag\": null}, \"computing_robinson_foulds\": {\"tree_dist_all\": false, \"tree_dist\": {\"__class__\": \"RuntimeValue\"}, \"tree_dist2\": {\"__class__\": \"RuntimeValue\"}}, \"generating_random\": {\"r\": null, \"rand\": null, \"branch_min\": null, \"branch_mean\": null, \"branch_max\": null}, \"ancestral_state\": {\"ancestral\": false, \"asr_min\": null}, \"symmetry_test\": {\"symtest\": 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_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\": false}, \"partition_model\": {\"model_selection\": {\"model\": \"none\", \"__current_case__\": 0}}, \"site_specific_frequency\": {\"tree_freq\": {\"__class__\": \"RuntimeValue\"}, \"site_freq\": null, \"freq_max\": false}}, \"time_tree\": {\"date_source\": {\"select_source\": \"none\", \"__current_case__\": 0}, \"date_tip\": null, \"date_root\": null, \"date_ci\": null, \"clock_sd\": null, \"date_no_outgroup\": false, \"date_outlier\": null, \"date_options\": null}, \"tree_parameters\": {\"tree_search\": {\"n\": null, \"ninit\": \"100\", \"ntop\": \"20\", \"nbest\": \"5\", \"nstop\": \"100\", \"radius\": \"6\", \"perturb\": \"0.5\", \"allnni\": false, \"tree_fix\": false, \"g\": {\"__class__\": \"RuntimeValue\"}, \"fast\": false, \"polytomy\": false, \"treels\": false, \"show_lh\": false, \"terrace\": false}, \"single_branch\": {\"alrt\": null, \"abayes\": false, \"lbp\": null}, \"tree_topology\": {\"trees\": {\"__class__\": \"RuntimeValue\"}, \"test\": null, \"test_weight\": false, \"test_au\": false}, \"constructing_consensus\": {\"con_tree\": false, \"con_net\": false, \"sup_min\": \"0.0\", \"burnin\": null, \"support\": {\"__class__\": \"RuntimeValue\"}, \"suptag\": null}, \"computing_robinson_foulds\": {\"tree_dist_all\": false, \"tree_dist\": {\"__class__\": \"RuntimeValue\"}, \"tree_dist2\": {\"__class__\": \"RuntimeValue\"}}, \"generating_random\": {\"r\": null, \"rand\": null, \"branch_min\": null, \"branch_mean\": null, \"branch_max\": null}, \"ancestral_state\": {\"ancestral\": false, \"asr_min\": null}, \"symmetry_test\": {\"symtest\": 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,
Expand All @@ -527,7 +527,7 @@
}
},
"tags": [],
"uuid": "788d1d72-5704-45dd-ba65-fd3f5e0947af"
"uuid": "3e4f3170-7d18-4cd8-bd00-16750975554a"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -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"
}
Loading
Loading