From eaccbf7a7dd5f7cd00f017371fca49233192c05b Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Tue, 5 Sep 2023 13:02:56 +0000 Subject: [PATCH 1/7] Updating workflows/epigenetics/hic-hicup-cooler from 0.2.1 to 0.2.2 --- .../epigenetics/hic-hicup-cooler/CHANGELOG.md | 5 +++++ .../chic_fastq_to_cool_hicup_cooler.ga | 16 ++++++++-------- 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md b/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md index 93ba3a378..372705b35 100644 --- a/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md +++ b/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2.2] 2023-09-05 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2` + ## [0.2.1] 2023-09-01 Bug fix Fix dockstore (workflows are the same) diff --git a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga index c0d3968fa..d5d5d8933 100644 --- a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.2.2", "name": "cHi-C_fastqToCool_hicup_cooler", "steps": { "0": { @@ -741,7 +741,7 @@ } }, "tags": "", - "uuid": "4a815412-cadd-4df9-9559-15b365715f05" + "uuid": "9df7c037-6fe4-47e9-8311-e40bc5101b58" }, "tool_id": null, "type": "subworkflow", @@ -1342,7 +1342,7 @@ } }, "tags": "", - "uuid": "bb361160-3ee3-4f03-99a3-7870baee168e" + "uuid": "0f629683-f7b4-45be-8436-9f67ddd92697" }, "tool_id": null, "type": "subworkflow", @@ -1363,7 +1363,7 @@ }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2", "errors": null, "id": 16, "input_connections": { @@ -1398,15 +1398,15 @@ "output_name": "outFileName" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2", "tool_shed_repository": { - "changeset_revision": "7dd841a32245", + "changeset_revision": "59fd173ac850", "name": "pygenometracks", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"global_args\": {\"title\": \"\", \"fontsize\": \"12\", \"dpi\": \"72\", \"width\": \"40.0\", \"plotWidth\": null, \"height\": null, \"trackLabelFraction\": \"0.05\", \"trackLabelHAlign\": \"left\", \"decreasingXAxis\": false}, \"image_file_format\": \"png\", \"region\": {\"__class__\": \"ConnectedValue\"}, \"tracks\": [{\"__index__\": 0, \"track_file_style_conditional\": {\"track_file_style_selector\": \"hic_matrix_option\", \"__current_case__\": 0, \"title\": \"\", \"matrix_h5_cooler_multiple\": {\"__class__\": \"ConnectedValue\"}, \"colormap\": \"RdYlBu_r\", \"min_value\": null, \"max_value\": null, \"depth\": \"8000000\", \"transform\": \"no\", \"height_matrix\": null, \"show_masked_bins\": false, \"boundaries_file\": {\"__class__\": \"RuntimeValue\"}, \"scale_factor\": \"1.0\", \"rasterize\": true, \"invert_orientation\": false, \"spacer_height\": null}}, {\"__index__\": 1, \"track_file_style_conditional\": {\"track_file_style_selector\": \"xaxis_option\", \"__current_case__\": 13, \"title\": \"\", \"fontsize\": null, \"xaxis_where\": \"bottom\", \"spacer_height\": null}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.7+galaxy0", + "tool_version": "3.8+galaxy2", "type": "tool", "uuid": "dfbe45de-b2a7-479e-b717-29ec5b31379e", "when": null, @@ -1424,4 +1424,4 @@ ], "uuid": "f310abac-4a50-41fa-a59a-84c51816a462", "version": 1 -} +} \ No newline at end of file From ef59f7bb97b9a156333f90a1f4ecd6450817cb6c Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Fri, 8 Sep 2023 11:51:06 +0200 Subject: [PATCH 2/7] update cooler and pgt --- .../epigenetics/hic-hicup-cooler/CHANGELOG.md | 6 ++ .../chic_fastq_to_cool_hicup_cooler.ga | 80 +++++++++---------- .../hic_fastq_to_cool_hicup_cooler.ga | 51 +++++------- .../hic_fastq_to_pairs_hicup.ga | 2 +- .../hic_juicermediumtabix_to_cool_cooler.ga | 30 +++---- 5 files changed, 83 insertions(+), 86 deletions(-) diff --git a/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md b/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md index 93ba3a378..113c0665d 100644 --- a/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md +++ b/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.3] 2023-09-08 + +### Update tools +- all cooler tools were updated from 0.8.11 to 0.9.2 +- pyGenomeTracks was updated from 3.7 to 3.8 + ## [0.2.1] 2023-09-01 Bug fix Fix dockstore (workflows are the same) diff --git a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga index c0d3968fa..d76c394e6 100644 --- a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.3", "name": "cHi-C_fastqToCool_hicup_cooler", "steps": { "0": { @@ -319,7 +319,7 @@ "outputs": [], "position": { "left": 520, - "top": 0.0 + "top": 0 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -748,16 +748,6 @@ "uuid": "3584d879-0b7a-4a89-a5f6-8439db6f003e", "when": null, "workflow_outputs": [ - { - "label": "HiCUP report (txt)", - "output_name": "HiCUP report (tabular)", - "uuid": "b479e588-6d59-4b60-9dd7-036e58358eae" - }, - { - "label": "HiCUP report (html)", - "output_name": "HiCUP report (HTML)", - "uuid": "902f20ef-d51d-4fad-86a0-206cda2ef361" - }, { "label": "valid pairs in juicebox format", "output_name": "valid pairs in juicebox format", @@ -767,6 +757,16 @@ "label": "valid pairs in juicebox format MAPQ filtered", "output_name": "valid pairs in juicebox format MAPQ filtered", "uuid": "ec040a8e-883a-4cdb-b5bf-ea5a611a16a7" + }, + { + "label": "HiCUP report (html)", + "output_name": "HiCUP report (HTML)", + "uuid": "902f20ef-d51d-4fad-86a0-206cda2ef361" + }, + { + "label": "HiCUP report (txt)", + "output_name": "HiCUP report (tabular)", + "uuid": "b479e588-6d59-4b60-9dd7-036e58358eae" } ] }, @@ -933,7 +933,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.2+galaxy1", "errors": null, "id": 14, "input_connections": { @@ -975,15 +975,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "d56db0e1555d", + "changeset_revision": "5cb855a2dc9e", "name": "cooler_csort_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.2+galaxy1", "type": "tool", "uuid": "bbb479cd-c67c-4347-9c1d-ac8095d90aa9", "when": null, @@ -1170,7 +1170,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -1203,15 +1203,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", "tool_shed_repository": { - "changeset_revision": "c3dc51297bf8", + "changeset_revision": "f67664a4e1d6", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.2+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -1219,7 +1219,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -1258,15 +1258,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "3ff6eeca667e", + "changeset_revision": "c639f60ae76a", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.2+galaxy1", "type": "tool", "uuid": "d411eea7-7996-44f2-af2a-feecb854a067", "when": null, @@ -1280,7 +1280,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -1320,15 +1320,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", "tool_shed_repository": { - "changeset_revision": "8f71aaf6e59d", + "changeset_revision": "9655af207032", "name": "cooler_balance", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"cistrans\": {\"__class__\": \"ConnectedValue\"}, \"convergencepolicy\": \"error\", \"ignorediags\": \"2\", \"ignoredist\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"madmax\": \"5\", \"maxiters\": \"200\", \"mincount\": \"0\", \"minnnz\": \"10\", \"name\": \"weight\", \"tol\": \"1e-05\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.2+galaxy0", "type": "tool", "uuid": "44270887-1c96-4ede-8bb9-3db2a07eeb6e", "when": null, @@ -1342,28 +1342,28 @@ } }, "tags": "", - "uuid": "bb361160-3ee3-4f03-99a3-7870baee168e" + "uuid": "1a6f4422-8f82-4444-a30c-bde38d181e41" }, "tool_id": null, "type": "subworkflow", "uuid": "63c60960-bd33-436a-ac47-fdaf69c4bdfa", "when": null, "workflow_outputs": [ - { - "label": "matrix with raw values", - "output_name": "matrix with raw values", - "uuid": "606c3260-41a2-400e-a580-0db59b3bc11f" - }, { "label": "matrix with iced values", "output_name": "matrix with iced values", "uuid": "178c2801-e3b3-4398-8448-795d67ae5aa3" + }, + { + "label": "matrix with raw values", + "output_name": "matrix with raw values", + "uuid": "606c3260-41a2-400e-a580-0db59b3bc11f" } ] }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2", "errors": null, "id": 16, "input_connections": { @@ -1398,15 +1398,15 @@ "output_name": "outFileName" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2", "tool_shed_repository": { - "changeset_revision": "7dd841a32245", + "changeset_revision": "59fd173ac850", "name": "pygenometracks", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"global_args\": {\"title\": \"\", \"fontsize\": \"12\", \"dpi\": \"72\", \"width\": \"40.0\", \"plotWidth\": null, \"height\": null, \"trackLabelFraction\": \"0.05\", \"trackLabelHAlign\": \"left\", \"decreasingXAxis\": false}, \"image_file_format\": \"png\", \"region\": {\"__class__\": \"ConnectedValue\"}, \"tracks\": [{\"__index__\": 0, \"track_file_style_conditional\": {\"track_file_style_selector\": \"hic_matrix_option\", \"__current_case__\": 0, \"title\": \"\", \"matrix_h5_cooler_multiple\": {\"__class__\": \"ConnectedValue\"}, \"colormap\": \"RdYlBu_r\", \"min_value\": null, \"max_value\": null, \"depth\": \"8000000\", \"transform\": \"no\", \"height_matrix\": null, \"show_masked_bins\": false, \"boundaries_file\": {\"__class__\": \"RuntimeValue\"}, \"scale_factor\": \"1.0\", \"rasterize\": true, \"invert_orientation\": false, \"spacer_height\": null}}, {\"__index__\": 1, \"track_file_style_conditional\": {\"track_file_style_selector\": \"xaxis_option\", \"__current_case__\": 13, \"title\": \"\", \"fontsize\": null, \"xaxis_where\": \"bottom\", \"spacer_height\": null}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.7+galaxy0", + "tool_version": "3.8+galaxy2", "type": "tool", "uuid": "dfbe45de-b2a7-479e-b717-29ec5b31379e", "when": null, @@ -1422,6 +1422,6 @@ "tags": [ "Hi-C" ], - "uuid": "f310abac-4a50-41fa-a59a-84c51816a462", - "version": 1 + "uuid": "2a89cbe4-a69f-4bff-9465-2e04b0217e35", + "version": 4 } diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga index 2f34eb68d..5d493126c 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.3", "name": "Hi-C_fastqToCool_hicup_cooler", "steps": { "0": { @@ -592,16 +592,7 @@ "output_name": "dataset_hicup" } }, - "inputs": [ - { - "description": "runtime parameter for tool Hicup to juicer converter", - "name": "digester" - }, - { - "description": "runtime parameter for tool Hicup to juicer converter", - "name": "input_file" - } - ], + "inputs": [], "label": "valid pairs in juicebox format", "name": "Hicup to juicer converter", "outputs": [ @@ -630,7 +621,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"digester\": {\"provide_digester\": \"yes\", \"__current_case__\": 0, \"digester_file\": {\"__class__\": \"RuntimeValue\"}, \"usemid\": true}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"digester\": {\"provide_digester\": \"yes\", \"__current_case__\": 0, \"digester_file\": {\"__class__\": \"ConnectedValue\"}, \"usemid\": true}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.9.2+galaxy0", "type": "tool", "uuid": "659811cd-a212-4949-9693-074f6161ed11", @@ -696,7 +687,7 @@ } }, "tags": "", - "uuid": "48f579ea-eaac-49ee-b38f-93c82f8b7d76" + "uuid": "66a6daaa-028b-43e0-99ab-772dc13feab9" }, "tool_id": null, "type": "subworkflow", @@ -727,7 +718,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.2+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -769,15 +760,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "d56db0e1555d", + "changeset_revision": "5cb855a2dc9e", "name": "cooler_csort_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.2+galaxy1", "type": "tool", "uuid": "bbb479cd-c67c-4347-9c1d-ac8095d90aa9", "when": null, @@ -964,7 +955,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -997,15 +988,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", "tool_shed_repository": { - "changeset_revision": "c3dc51297bf8", + "changeset_revision": "f67664a4e1d6", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.2+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -1013,7 +1004,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -1052,15 +1043,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "3ff6eeca667e", + "changeset_revision": "c639f60ae76a", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.2+galaxy1", "type": "tool", "uuid": "d411eea7-7996-44f2-af2a-feecb854a067", "when": null, @@ -1074,7 +1065,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -1114,15 +1105,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", "tool_shed_repository": { - "changeset_revision": "8f71aaf6e59d", + "changeset_revision": "9655af207032", "name": "cooler_balance", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"cistrans\": {\"__class__\": \"ConnectedValue\"}, \"convergencepolicy\": \"error\", \"ignorediags\": \"2\", \"ignoredist\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"madmax\": \"5\", \"maxiters\": \"200\", \"mincount\": \"0\", \"minnnz\": \"10\", \"name\": \"weight\", \"tol\": \"1e-05\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.2+galaxy0", "type": "tool", "uuid": "44270887-1c96-4ede-8bb9-3db2a07eeb6e", "when": null, @@ -1136,7 +1127,7 @@ } }, "tags": "", - "uuid": "3b4cd11c-7937-4679-bb3c-9b067ad8f567" + "uuid": "a6b80258-0411-4f80-8f4f-2646647c3cea" }, "tool_id": null, "type": "subworkflow", diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga b/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga index 9f5c219b3..28c9666b7 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga +++ b/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.3", "name": "Hi-C_fastqToPairs_hicup", "steps": { "0": { diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga index 65ef368d5..31a012080 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.3", "name": "Hi-C_juicermediumtabixToCool_cooler", "steps": { "0": { @@ -123,7 +123,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -156,15 +156,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", "tool_shed_repository": { - "changeset_revision": "c3dc51297bf8", + "changeset_revision": "f67664a4e1d6", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.2+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -172,7 +172,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -211,15 +211,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "3ff6eeca667e", + "changeset_revision": "c639f60ae76a", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.2+galaxy1", "type": "tool", "uuid": "d411eea7-7996-44f2-af2a-feecb854a067", "when": null, @@ -233,7 +233,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -273,15 +273,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", "tool_shed_repository": { - "changeset_revision": "8f71aaf6e59d", + "changeset_revision": "9655af207032", "name": "cooler_balance", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"cistrans\": {\"__class__\": \"ConnectedValue\"}, \"convergencepolicy\": \"error\", \"ignorediags\": \"2\", \"ignoredist\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"madmax\": \"5\", \"maxiters\": \"200\", \"mincount\": \"0\", \"minnnz\": \"10\", \"name\": \"weight\", \"tol\": \"1e-05\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.2+galaxy0", "type": "tool", "uuid": "44270887-1c96-4ede-8bb9-3db2a07eeb6e", "when": null, @@ -297,6 +297,6 @@ "tags": [ "Hi-C" ], - "uuid": "e6220100-1dde-4701-ac54-db0d1e0dec0f", - "version": 2 + "uuid": "48733b55-4cde-45d4-a69e-78faff0db3f5", + "version": 1 } From a958302e789a9f69954f0eb09ac66fdbb18dd537 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Fri, 8 Sep 2023 11:54:11 +0200 Subject: [PATCH 3/7] use - instead of _ in file names --- .../hic-hicup-cooler/.dockstore.yml | 18 +++++++++--------- ... chic-fastq-to-cool-hicup-cooler-tests.yml} | 0 ...r.ga => chic-fastq-to-cool-hicup-cooler.ga} | 0 ...> hic-fastq-to-cool-hicup-cooler-tests.yml} | 0 ...er.ga => hic-fastq-to-cool-hicup-cooler.ga} | 0 ....yml => hic-fastq-to-pairs-hicup-tests.yml} | 0 ...rs_hicup.ga => hic-fastq-to-pairs-hicup.ga} | 0 ...juicermediumtabix-to-cool-cooler-tests.yml} | 0 ...=> hic-juicermediumtabix-to-cool-cooler.ga} | 0 9 files changed, 9 insertions(+), 9 deletions(-) rename workflows/epigenetics/hic-hicup-cooler/{chic_fastq_to_cool_hicup_cooler-tests.yml => chic-fastq-to-cool-hicup-cooler-tests.yml} (100%) rename workflows/epigenetics/hic-hicup-cooler/{chic_fastq_to_cool_hicup_cooler.ga => chic-fastq-to-cool-hicup-cooler.ga} (100%) rename workflows/epigenetics/hic-hicup-cooler/{hic_fastq_to_cool_hicup_cooler-tests.yml => hic-fastq-to-cool-hicup-cooler-tests.yml} (100%) rename workflows/epigenetics/hic-hicup-cooler/{hic_fastq_to_cool_hicup_cooler.ga => hic-fastq-to-cool-hicup-cooler.ga} (100%) rename workflows/epigenetics/hic-hicup-cooler/{hic_fastq_to_pairs_hicup-tests.yml => hic-fastq-to-pairs-hicup-tests.yml} (100%) rename workflows/epigenetics/hic-hicup-cooler/{hic_fastq_to_pairs_hicup.ga => hic-fastq-to-pairs-hicup.ga} (100%) rename workflows/epigenetics/hic-hicup-cooler/{hic_juicermediumtabix_to_cool_cooler-tests.yml => hic-juicermediumtabix-to-cool-cooler-tests.yml} (100%) rename workflows/epigenetics/hic-hicup-cooler/{hic_juicermediumtabix_to_cool_cooler.ga => hic-juicermediumtabix-to-cool-cooler.ga} (100%) diff --git a/workflows/epigenetics/hic-hicup-cooler/.dockstore.yml b/workflows/epigenetics/hic-hicup-cooler/.dockstore.yml index 7c6c4b9a8..6d9404165 100644 --- a/workflows/epigenetics/hic-hicup-cooler/.dockstore.yml +++ b/workflows/epigenetics/hic-hicup-cooler/.dockstore.yml @@ -3,36 +3,36 @@ workflows: - name: hic-fastq-to-cool-hicup-cooler subclass: Galaxy publish: true - primaryDescriptorPath: /hic_fastq_to_cool_hicup_cooler.ga + primaryDescriptorPath: /hic-fastq-to-cool-hicup-cooler.ga testParameterFiles: - - /hic_fastq_to_cool_hicup_cooler-tests.yml + - /hic-fastq-to-cool-hicup-cooler-tests.yml authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 - name: chic-fastq-to-cool-hicup-cooler subclass: Galaxy publish: true - primaryDescriptorPath: /chic_fastq_to_cool_hicup_cooler.ga + primaryDescriptorPath: /chic-fastq-to-cool-hicup-cooler.ga testParameterFiles: - - /chic_fastq_to_cool_hicup_cooler-tests.yml + - /chic-fastq-to-cool-hicup-cooler-tests.yml authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 -- name: hic-juicermediumtabix-to_cool-cooler +- name: hic-juicermediumtabix-to-cool-cooler subclass: Galaxy publish: true - primaryDescriptorPath: /hic_juicermediumtabix_to_cool_cooler.ga + primaryDescriptorPath: /hic-juicermediumtabix-to-cool-cooler.ga testParameterFiles: - - /hic_juicermediumtabix_to_cool_cooler-tests.yml + - /hic-juicermediumtabix-to-cool-cooler-tests.yml authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 - name: hic-fastq-to-pairs-hicup subclass: Galaxy publish: true - primaryDescriptorPath: /hic_fastq_to_pairs_hicup.ga + primaryDescriptorPath: /hic-fastq-to-pairs-hicup.ga testParameterFiles: - - /hic_fastq_to_pairs_hicup-tests.yml + - /hic-fastq-to-pairs-hicup-tests.yml authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 diff --git a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler-tests.yml rename to workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml diff --git a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga rename to workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler-tests.yml rename to workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga rename to workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup-tests.yml similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup-tests.yml rename to workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup-tests.yml diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup.ga similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga rename to workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup.ga diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler-tests.yml similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler-tests.yml rename to workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler-tests.yml diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga rename to workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga From cc38f0e66773d30f55a6f234c518d7cd7ea17e0a Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Tue, 12 Sep 2023 12:31:34 +0200 Subject: [PATCH 4/7] cooler 0.9.2 to 0.9.3 --- .../epigenetics/hic-hicup-cooler/CHANGELOG.md | 2 +- .../chic-fastq-to-cool-hicup-cooler.ga | 32 ++++++++-------- .../hic-fastq-to-cool-hicup-cooler.ga | 38 +++++++++---------- .../hic-juicermediumtabix-to-cool-cooler.ga | 24 ++++++------ 4 files changed, 48 insertions(+), 48 deletions(-) diff --git a/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md b/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md index 113c0665d..86f34616a 100644 --- a/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md +++ b/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md @@ -3,7 +3,7 @@ ## [0.3] 2023-09-08 ### Update tools -- all cooler tools were updated from 0.8.11 to 0.9.2 +- all cooler tools were updated from 0.8.11 to 0.9.3 - pyGenomeTracks was updated from 3.7 to 3.8 ## [0.2.1] 2023-09-01 Bug fix diff --git a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga index 460c36292..903a8e783 100644 --- a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga @@ -933,7 +933,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.2+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1", "errors": null, "id": 14, "input_connections": { @@ -975,15 +975,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.2+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "5cb855a2dc9e", + "changeset_revision": "8c3cba559c99", "name": "cooler_csort_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "bbb479cd-c67c-4347-9c1d-ac8095d90aa9", "when": null, @@ -1170,7 +1170,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -1203,15 +1203,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "f67664a4e1d6", + "changeset_revision": "ebd2a52eb245", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -1219,7 +1219,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -1258,15 +1258,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "c639f60ae76a", + "changeset_revision": "0641e1c892c6", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "d411eea7-7996-44f2-af2a-feecb854a067", "when": null, @@ -1280,7 +1280,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -1320,15 +1320,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", + "tool_id": 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b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga index 5d493126c..71ea93dc9 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga @@ -687,7 +687,7 @@ } }, "tags": "", - "uuid": "66a6daaa-028b-43e0-99ab-772dc13feab9" + "uuid": "f6bb48d4-0392-4c89-825e-01b8523b0943" }, "tool_id": null, "type": "subworkflow", @@ -718,7 +718,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.2+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -760,15 +760,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.2+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "5cb855a2dc9e", + "changeset_revision": "8c3cba559c99", "name": "cooler_csort_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "bbb479cd-c67c-4347-9c1d-ac8095d90aa9", "when": null, @@ -955,7 +955,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -988,15 +988,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "f67664a4e1d6", + "changeset_revision": "ebd2a52eb245", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -1004,7 +1004,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -1043,15 +1043,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "c639f60ae76a", + "changeset_revision": "0641e1c892c6", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "d411eea7-7996-44f2-af2a-feecb854a067", "when": null, @@ -1065,7 +1065,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -1105,15 +1105,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "9655af207032", + "changeset_revision": "8f9fe0667b89", "name": "cooler_balance", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"cistrans\": {\"__class__\": \"ConnectedValue\"}, \"convergencepolicy\": \"error\", \"ignorediags\": \"2\", \"ignoredist\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"madmax\": \"5\", \"maxiters\": \"200\", \"mincount\": \"0\", \"minnnz\": \"10\", \"name\": \"weight\", \"tol\": \"1e-05\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "44270887-1c96-4ede-8bb9-3db2a07eeb6e", "when": null, @@ -1127,7 +1127,7 @@ } }, "tags": "", - "uuid": "a6b80258-0411-4f80-8f4f-2646647c3cea" + "uuid": "d7fb120d-41f4-4a67-a6fe-2885dcd33ebf" }, "tool_id": null, "type": "subworkflow", @@ -1209,4 +1209,4 @@ ], "uuid": "2196fbff-317e-437d-a022-696a1f95a850", "version": 4 -} +} \ No newline at end of file diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga index 31a012080..408e5ca35 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga @@ -123,7 +123,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -156,15 +156,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "f67664a4e1d6", + "changeset_revision": "ebd2a52eb245", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -172,7 +172,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -211,15 +211,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.2+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "c639f60ae76a", + "changeset_revision": "0641e1c892c6", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "d411eea7-7996-44f2-af2a-feecb854a067", "when": null, @@ -233,7 +233,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -273,15 +273,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "9655af207032", + "changeset_revision": "8f9fe0667b89", "name": "cooler_balance", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"cistrans\": {\"__class__\": \"ConnectedValue\"}, \"convergencepolicy\": \"error\", \"ignorediags\": \"2\", \"ignoredist\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"madmax\": \"5\", \"maxiters\": \"200\", \"mincount\": \"0\", \"minnnz\": \"10\", \"name\": \"weight\", \"tol\": \"1e-05\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9.2+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "44270887-1c96-4ede-8bb9-3db2a07eeb6e", "when": null, From fba00e760cd57811a6eeb15f0ad677ec40fc8c8b Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Sep 2023 23:38:34 +0200 Subject: [PATCH 5/7] test with canon --- .../hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml index ab9ed27a5..1800ddd20 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml @@ -16,7 +16,7 @@ identifier: reverse location: https://github.com/bgruening/galaxytools/raw/master/tools/hicup/test-data/dataset2.fastq filetype: fastqsanger - genome name: hg19 + genome name: hg19canon Restriction enzyme: A^AGCTT,HindIII No fill-in: 'false' minimum MAPQ: 30 From 9015332c8c8b4a688516b36ae83c56c51aeb207a Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 14 Sep 2023 14:39:17 +0200 Subject: [PATCH 6/7] try balance genome wide --- .../hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml index 1800ddd20..2d8253e45 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml @@ -16,12 +16,12 @@ identifier: reverse location: https://github.com/bgruening/galaxytools/raw/master/tools/hicup/test-data/dataset2.fastq filetype: fastqsanger - genome name: hg19canon + genome name: hg19 Restriction enzyme: A^AGCTT,HindIII No fill-in: 'false' minimum MAPQ: 30 Bin size in bp: 1000000 - Interactions to consider to calculate weights in normalization step: --cis-only + Interactions to consider to calculate weights in normalization step: "" region for matrix plotting: chr2:175,689,620-178,604,461 outputs: HiCUP report (html): From 7f525af7dfaae900b2b047d77e2e206a9514d4be Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Fri, 15 Sep 2023 07:17:14 +0200 Subject: [PATCH 7/7] update results --- .../hic-fastq-to-cool-hicup-cooler-tests.yml | 2 +- .../hic-hicup-cooler/test-data/plot_hic.png | Bin 16354 -> 19576 bytes 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml index 2d8253e45..95a438d6b 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml @@ -76,7 +76,7 @@ test_dataset: 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