From 930d8f993f5d65d5fa2deccec1282e02ccecd2af Mon Sep 17 00:00:00 2001 From: xuebingjie1990 Date: Wed, 14 Apr 2021 15:13:16 -0400 Subject: [PATCH 1/6] update bed and bedset schema --- bbconf/schemas/bedfiles_schema.yaml | 14 ++++++++++++++ bbconf/schemas/bedsets_schema.yaml | 25 +++++++++++++------------ 2 files changed, 27 insertions(+), 12 deletions(-) diff --git a/bbconf/schemas/bedfiles_schema.yaml b/bbconf/schemas/bedfiles_schema.yaml index dfb7fe8..7ec5e03 100644 --- a/bbconf/schemas/bedfiles_schema.yaml +++ b/bbconf/schemas/bedfiles_schema.yaml @@ -6,9 +6,11 @@ md5sum: description: BED file checksum bedfile: type: file + label: bed description: BED file bigbedfile: type: file + label: bigBed description: bigBed file regions_no: type: integer @@ -66,31 +68,43 @@ promotercore_percentage: description: Promoter core percentage tssdist: type: image + label: TSS_distance description: Region-TSS distance plot chrombins: type: image + label: Chromosome_bins description: Regions distribution over chromosomes plot gccontent: type: image + label: GC_content description: GC content plot paritions: type: image + label: Regions_dist_partitions description: Regions distribution over genomic partitions plot expected_partitions: type: image + label: Expected_partitions description: Expected distribution over genomic partitions plot cumulative_partitions: type: image + label: Cumulative_partitions description: Cumulative distribution over genomic partitions plot widths_histogram: type: image + label: Widths_histogram description: Quantile-trimmed histogram of widths neighbor_distances: type: image + label: Neighbor_distance description: Distance between neighbor regions open_chromatin: type: image + label: Open_chromatin description: Cell specific enrichment for open chromatin plot +genome: + type: object + description: genome assembly and it's refgenie digest other: type: object description: Other, not categorized BED file metadata diff --git a/bbconf/schemas/bedsets_schema.yaml b/bbconf/schemas/bedsets_schema.yaml index 5fb015e..075e829 100644 --- a/bbconf/schemas/bedsets_schema.yaml +++ b/bbconf/schemas/bedsets_schema.yaml @@ -6,24 +6,28 @@ md5sum: description: BED set checksum bedset_tar_archive_path: type: file - label: BED set archive + label: BED_set_archive description: Relative path to the TAR archive with BED files in this BED set bedset_igd_database_path: type: file - label: BED set iGD database + label: iGD_database description: Relative path to the iGD database bedset_pep: type: file - label: BED set PEP + label: PEP description: Relative path to PEP bedset_bedfiles_gd_stats: - type: object - label: BED files statistics + type: file + label: BED_statistics description: Statistics of BED files in this BED set bedset_gd_stats: - type: object - label: BED set statistics + type: file + label: BED_set_statistics description: BED set statistics +hubfile_path: + type: file + label: Hub_file + description: Path to the hub.txt files for the BED set bedset_means: type: object description: Mean statistics of the BED files in this BED set @@ -32,12 +36,9 @@ bedset_standard_deviation: description: Standard deviations of statistics of the BED files in this BED set region_commonality: type: image + label: Region_commonality description: Region commonality plot -hubfile_path: - type: file - label: BED set hub file - description: Path to the hub.txt files for the BED set genome: - type: string + type: object description: genome assembly of the BED set From e216d2b4893d242f5ca0033ecf285e6b4144f1c6 Mon Sep 17 00:00:00 2001 From: Bingjie Xue Date: Thu, 15 Apr 2021 11:07:42 -0400 Subject: [PATCH 2/6] Update _version.py --- bbconf/_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bbconf/_version.py b/bbconf/_version.py index 3dc1f76..485f44a 100644 --- a/bbconf/_version.py +++ b/bbconf/_version.py @@ -1 +1 @@ -__version__ = "0.1.0" +__version__ = "0.1.1" From bedcdf9a7f353a6fa35bdc06c290f9a2cb4edf0d Mon Sep 17 00:00:00 2001 From: Bingjie Xue Date: Thu, 15 Apr 2021 11:10:49 -0400 Subject: [PATCH 3/6] Update changelog.md --- docs/changelog.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/changelog.md b/docs/changelog.md index 2b6d781..cbefeb9 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -2,6 +2,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. +## [0.1.1] - 2021-04-15 +### added +- added new feilds in the bedfiles and bedsets schema + ## [0.1.0] - 2021-02-22 **This release introduces backwards incompatible changes** ### Changed @@ -23,4 +27,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ## [0.0.1] - 2020-02-05 ### Added -- initial project release \ No newline at end of file +- initial project release From 539126e288a1f7d0dfd8e211d1492c2546e8af39 Mon Sep 17 00:00:00 2001 From: Bingjie Xue Date: Thu, 15 Apr 2021 11:35:53 -0400 Subject: [PATCH 4/6] Update bedsets_schema.yaml --- bbconf/schemas/bedsets_schema.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bbconf/schemas/bedsets_schema.yaml b/bbconf/schemas/bedsets_schema.yaml index 075e829..cbbc1f8 100644 --- a/bbconf/schemas/bedsets_schema.yaml +++ b/bbconf/schemas/bedsets_schema.yaml @@ -39,6 +39,6 @@ region_commonality: label: Region_commonality description: Region commonality plot genome: - type: object + type: string description: genome assembly of the BED set From 3806a39e2211a4d128370c35c555ea42a66adfa2 Mon Sep 17 00:00:00 2001 From: Bingjie Xue Date: Thu, 15 Apr 2021 11:43:35 -0400 Subject: [PATCH 5/6] Update changelog.md --- docs/changelog.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/changelog.md b/docs/changelog.md index cbefeb9..7c2e810 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -4,7 +4,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ## [0.1.1] - 2021-04-15 ### added -- added new feilds in the bedfiles and bedsets schema +- added new fields in the bedfiles and bedsets schema ## [0.1.0] - 2021-02-22 **This release introduces backwards incompatible changes** From 3fdca1ec40ed2e8f00c62b33e373f053dcaa1f42 Mon Sep 17 00:00:00 2001 From: Bingjie Xue Date: Thu, 15 Apr 2021 11:58:28 -0400 Subject: [PATCH 6/6] Update bedfiles_schema.yaml --- bbconf/schemas/bedfiles_schema.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/bbconf/schemas/bedfiles_schema.yaml b/bbconf/schemas/bedfiles_schema.yaml index 7ec5e03..b019b4c 100644 --- a/bbconf/schemas/bedfiles_schema.yaml +++ b/bbconf/schemas/bedfiles_schema.yaml @@ -102,9 +102,6 @@ open_chromatin: type: image label: Open_chromatin description: Cell specific enrichment for open chromatin plot -genome: - type: object - description: genome assembly and it's refgenie digest other: type: object description: Other, not categorized BED file metadata