Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Updating workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 from 0.1 to 0.2 #269

Merged
merged 1 commit into from
Nov 15, 2023
Merged

Updating workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 from 0.1 to 0.2 #269

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
7 changes: 7 additions & 0 deletions workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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.
49 changes: 22 additions & 27 deletions workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down Expand Up @@ -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": {
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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"
Expand All @@ -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": {
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -873,12 +873,7 @@
"output_name": "out1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Compute",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "Compute",
"outputs": [
Expand Down Expand Up @@ -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",
Expand All @@ -922,7 +917,7 @@
}
},
"tags": "",
"uuid": "4672e57f-fc1f-49e4-90f6-61720a85ffa2"
"uuid": "ee2567e9-9666-43d3-9bf9-939b48e56573"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -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": {
Expand Down Expand Up @@ -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,
Expand All @@ -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": {
Expand Down Expand Up @@ -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,
Expand Down