From 86670bb0d066ebefc40a54171a80af572a789c6a Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 19 Feb 2024 04:17:17 +0000 Subject: [PATCH 1/2] Updating workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b from 0.1 to 0.2 --- .../CHANGELOG.md | 10 ++ .../Purging-duplicates-one-haplotype-VGP6b.ga | 122 ++++++++++-------- 2 files changed, 77 insertions(+), 55 deletions(-) diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md index 59cbaa2a5..f1a1a54ec 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [0.2] 2024-02-19 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0` +- `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/merqury/merqury/1.3+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1` +- `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] - 2024-02-07 ### Added diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga index 2668b62f9..a8c52c4ae 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1", + "release": "0.2", "name": "Purging-duplicates-one-haplotype-VGP6b ", "steps": { "0": { @@ -286,7 +286,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0", "errors": null, "id": 9, "input_connections": { @@ -335,15 +335,15 @@ "output_name": "alignment_output" } }, - 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"tool_version": "2.24+galaxy0", + "tool_version": "2.26+galaxy0", "type": "tool", "uuid": "b6259cc9-6c33-48ff-bc0f-c7fcd0643809", "when": null, @@ -590,7 +590,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0", "errors": null, "id": 15, "input_connections": { @@ -634,15 +634,15 @@ "output_name": "alignment_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0", "tool_shed_repository": { - "changeset_revision": "11a0d50a54e6", + "changeset_revision": "be1d967337e4", "name": "minimap2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"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": "2.24+galaxy0", + "tool_version": "2.26+galaxy0", "type": "tool", "uuid": "6f009c42-6298-4db3-999e-b408c4ebedd6", "when": null, @@ -850,7 +850,7 @@ }, "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": { @@ -884,15 +884,15 @@ "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}", - 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