diff --git a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md index 41c6c42ee..3ce415e35 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.1.1] 2023-11-14 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1` + ## [0.1] - 2023-11-01 Addition of the workflow to the iwc repository. diff --git a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga index 3677a73e5..dfad81092 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga @@ -14,7 +14,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release":"0.1", + "release": "0.1.1", "name": "Scaffolding-BioNano-VGP7", "steps": { "0": { @@ -216,7 +216,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3", "errors": null, "id": 6, "input_connections": { @@ -317,15 +317,15 @@ "output_name": "results" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3", "tool_shed_repository": { - "changeset_revision": "5258e18bbe23", + "changeset_revision": "3371c5bdc17a", "name": "bionano_scaffold", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"bionano_cmap\": {\"__class__\": \"ConnectedValue\"}, \"configuration_options\": {\"configuration\": \"vgp\", \"__current_case__\": 0, \"enzyme\": \"CTTAAG\"}, \"conflict_filter_genome\": \"3\", \"conflict_filter_sequence\": \"3\", \"conflict_resolution\": {\"__class__\": \"ConnectedValue\"}, \"ngs_fasta\": {\"__class__\": \"ConnectedValue\"}, \"trim_cut_sites\": true, \"zip_file\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.7.0+galaxy0", + "tool_state": "{\"all_files\": false, \"bionano_cmap\": {\"__class__\": \"ConnectedValue\"}, \"configuration_options\": {\"configuration\": \"vgp\", \"__current_case__\": 0, \"enzyme\": \"CTTAAG\"}, \"conflict_filter_genome\": \"3\", \"conflict_filter_sequence\": \"3\", \"conflict_resolution\": {\"__class__\": \"ConnectedValue\"}, \"ngs_fasta\": {\"__class__\": \"ConnectedValue\"}, \"trim_cut_sites\": true, \"zip_file\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.7.0+galaxy3", "type": "tool", "uuid": "acbf9c02-c273-42a9-a809-d515f724b180", "when": null, @@ -678,7 +678,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -692,7 +692,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", "errors": null, "id": 3, "input_connections": { @@ -721,15 +721,15 @@ "output_name": "out_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "746e8e4bf929", + "changeset_revision": "4c07ddedc198", "name": "datamash_ops", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"grouping\": \"\", \"header_in\": false, \"header_out\": false, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"absmax\", \"op_column\": \"3\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0+galaxy2", + "tool_version": "1.8+galaxy0", "type": "tool", "uuid": "1cdafa6b-ccdb-4b90-8dc6-ea1f92425715", "when": null, @@ -873,12 +873,7 @@ "output_name": "out1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Compute", "outputs": [ @@ -907,7 +902,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0", "type": "tool", "uuid": "c93568ca-103f-4d8e-af88-d6de721e30cd", @@ -922,7 +917,7 @@ } }, "tags": "", - "uuid": "4672e57f-fc1f-49e4-90f6-61720a85ffa2" + "uuid": "ee2567e9-9666-43d3-9bf9-939b48e56573" }, "tool_id": null, "type": "subworkflow", @@ -1010,7 +1005,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, "id": 14, "input_connections": { @@ -1041,15 +1036,15 @@ "output_name": "output1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "5fe1dc76176e", + "changeset_revision": "3b12bf9b4b87", "name": "ggplot2_point", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Default\", \"__current_case__\": 0}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"x\", \"xplot\": \"1\", \"ylab\": \"Nx (Mb)\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.4.0+galaxy0", + "tool_version": "3.4.0+galaxy1", "type": "tool", "uuid": "1be952f7-cfe8-4d39-b0e8-97eef0d0ee08", "when": null, @@ -1063,7 +1058,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, "id": 15, "input_connections": { @@ -1094,15 +1089,15 @@ "output_name": "output1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "5fe1dc76176e", + "changeset_revision": "3b12bf9b4b87", "name": "ggplot2_point", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Default\", \"__current_case__\": 0}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"Scaffold number\", \"xplot\": \"1\", \"ylab\": \"Cumulative Size (Mb)\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.4.0+galaxy0", + "tool_version": "3.4.0+galaxy1", "type": "tool", "uuid": "56f214f7-0d63-4c5c-8464-ff54843ddb4e", "when": null,