From cc38f0e66773d30f55a6f234c518d7cd7ea17e0a Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Tue, 12 Sep 2023 12:31:34 +0200 Subject: [PATCH] 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": "", - 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"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": "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, 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 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": { - 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