Skip to content
Merged
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
Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# Changelog

## [0.10.3] - 2025-08-11

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2`
- `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0`

## [0.10.2] - 2025-06-09

### Automatic update
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@
"top": 475.92988427809064
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
"tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "0df002ab-91cf-4767-a348-9ce31f439a01",
Expand Down Expand Up @@ -448,7 +448,7 @@
},
"14": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
"errors": null,
"id": 14,
"input_connections": {
Expand Down Expand Up @@ -488,15 +488,15 @@
"output_name": "alignment_output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
"tool_shed_repository": {
"changeset_revision": "66367287b4e6",
"changeset_revision": "6945cd53bd2d",
"name": "minimap2",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"asm5\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.28+galaxy1",
"tool_version": "2.28+galaxy2",
"type": "tool",
"uuid": "37c8f9b6-ec2e-43f7-9055-5f4f92436903",
"when": null,
Expand Down Expand Up @@ -770,7 +770,7 @@
},
"21": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
"errors": null,
"id": 21,
"input_connections": {
Expand Down Expand Up @@ -805,15 +805,15 @@
"output_name": "alignment_output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
"tool_shed_repository": {
"changeset_revision": "66367287b4e6",
"changeset_revision": "6945cd53bd2d",
"name": "minimap2",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": \"1\", \"B\": \"19\", \"O\": \"39\", \"O2\": \"81\", \"E\": \"3\", \"E2\": \"1\", \"z\": \"200\", \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"self-homology\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": \"100\", \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": \"40\", \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.28+galaxy1",
"tool_version": "2.28+galaxy2",
"type": "tool",
"uuid": "9bceadad-bf25-46f7-8d3f-d9ab18dde578",
"when": null,
Expand Down Expand Up @@ -1696,7 +1696,7 @@
},
"35": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
"errors": null,
"id": 35,
"input_connections": {
Expand Down Expand Up @@ -1738,15 +1738,15 @@
"output_name": "alignment_output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
"tool_shed_repository": {
"changeset_revision": "66367287b4e6",
"changeset_revision": "6945cd53bd2d",
"name": "minimap2",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"asm5\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.28+galaxy1",
"tool_version": "2.28+galaxy2",
"type": "tool",
"uuid": "895ca00e-3eaf-4c8a-9147-be1d62459cf9",
"when": null,
Expand Down Expand Up @@ -1984,7 +1984,7 @@
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0",
"errors": null,
"id": 3,
"input_connections": {
Expand Down Expand Up @@ -2013,15 +2013,15 @@
"output_name": "out_file"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0",
"tool_shed_repository": {
"changeset_revision": "4c07ddedc198",
"changeset_revision": "61e2aa6bb55d",
"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": "1.8+galaxy0",
"tool_version": "1.9+galaxy0",
"type": "tool",
"uuid": "4beb22a7-74f7-4dff-abf9-3d1bfd263ecd",
"when": null,
Expand Down Expand Up @@ -2215,7 +2215,7 @@
}
},
"tags": [],
"uuid": "c9bcc5a9-c77d-4d9a-b3de-acf6ab4a2328"
"uuid": "f533c37d-221b-4318-bdb9-467703567fd9"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -2353,7 +2353,7 @@
},
"40": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
"errors": null,
"id": 40,
"input_connections": {
Expand Down Expand Up @@ -2395,15 +2395,15 @@
"output_name": "alignment_output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
"tool_shed_repository": {
"changeset_revision": "66367287b4e6",
"changeset_revision": "6945cd53bd2d",
"name": "minimap2",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": \"1\", \"B\": \"19\", \"O\": \"39\", \"O2\": \"81\", \"E\": \"3\", \"E2\": \"1\", \"z\": \"200\", \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"self-homology\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": \"100\", \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": \"40\", \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.28+galaxy1",
"tool_version": "2.28+galaxy2",
"type": "tool",
"uuid": "735ef0da-2e48-404e-b57d-837dc2f161fd",
"when": null,
Expand Down Expand Up @@ -3271,7 +3271,7 @@
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0",
"errors": null,
"id": 3,
"input_connections": {
Expand Down Expand Up @@ -3300,15 +3300,15 @@
"output_name": "out_file"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0",
"tool_shed_repository": {
"changeset_revision": "4c07ddedc198",
"changeset_revision": "61e2aa6bb55d",
"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": "1.8+galaxy0",
"tool_version": "1.9+galaxy0",
"type": "tool",
"uuid": "053d0561-98e5-46b2-b554-685802fdb0ed",
"when": null,
Expand Down Expand Up @@ -3502,7 +3502,7 @@
}
},
"tags": [],
"uuid": "af78022c-82a5-4aff-88f1-fe9120c77148"
"uuid": "7617a0b1-f562-43a6-b696-2cc29ead2a38"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -3543,7 +3543,7 @@
},
"tool_id": "__EXTRACT_DATASET__",
"tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.1",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "7d4f1ffc-5e09-4db5-aebd-1d1c9383e6b8",
"when": null,
Expand Down Expand Up @@ -3588,7 +3588,7 @@
},
"tool_id": "__EXTRACT_DATASET__",
"tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.spectra-cn.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.1",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "706cf485-92c5-43c3-8a04-23af75cf56c8",
"when": null,
Expand Down Expand Up @@ -3633,7 +3633,7 @@
},
"tool_id": "__EXTRACT_DATASET__",
"tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.spectra-asm.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.1",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "4edba3bb-2444-4d91-87cc-50acc24923e9",
"when": null,
Expand Down Expand Up @@ -3678,7 +3678,7 @@
},
"tool_id": "__EXTRACT_DATASET__",
"tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.assembly_01.spectra-cn.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.1",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "41fd4355-7ef4-43be-b71c-0c4a897ddc5e",
"when": null,
Expand Down Expand Up @@ -3723,7 +3723,7 @@
},
"tool_id": "__EXTRACT_DATASET__",
"tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"first\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.1",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "5a62f7c5-2e97-44d8-8002-ab66dd0cd17c",
"when": null,
Expand Down Expand Up @@ -3768,7 +3768,7 @@
},
"tool_id": "__EXTRACT_DATASET__",
"tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_identifier\", \"__current_case__\": 1, \"identifier\": \"output_merqury.assembly_02.spectra-cn.fl\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.1",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "035085e5-6b04-4a50-bb0a-6b3477528921",
"when": null,
Expand Down Expand Up @@ -4333,7 +4333,7 @@
}
},
"tags": [],
"uuid": "e92d5f8c-182c-4978-9887-fe66934bd86a"
"uuid": "f245a525-195f-46f0-a0df-b8ba33e90413"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -4467,7 +4467,7 @@
"tags": [
"VGP_curated"
],
"uuid": "2831484a-76e6-4373-acd1-0e3c33c2becc",
"uuid": "6829c780-6a52-4629-bf36-1e4755978725",
"version": 1,
"release": "0.10.2"
"release": "0.10.3"
}