Skip to content

Commit

Permalink
Merge pull request galaxyproject#205 from planemo-autoupdate/workflow…
Browse files Browse the repository at this point in the history 
…s/epigenetics/hic-hicup-cooler

Updating workflows/epigenetics/hic-hicup-cooler from 0.2.1 to 0.3
  • Loading branch information
@mvdbeek
mvdbeek authored Sep 15, 2023
2 parents ea2c65f + 7f525af commit 0689b57
Show file tree
Hide file tree
Showing 11 changed files with 96 additions and 99 deletions.
18 changes: 9 additions & 9 deletions workflows/epigenetics/hic-hicup-cooler/.dockstore.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
6 changes: 6 additions & 0 deletions workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# Changelog

## [0.3] 2023-09-08

### Update tools
- 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

Fix dockstore (workflows are the same)
Expand Down
0 ...chic_fastq_to_cool_hicup_cooler-tests.yml → ...chic-fastq-to-cool-hicup-cooler-tests.yml
View file
File renamed without changes.
82 changes: 41 additions & 41 deletions ...cooler/chic_fastq_to_cool_hicup_cooler.ga → ...cooler/chic-fastq-to-cool-hicup-cooler.ga
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down Expand Up @@ -319,7 +319,7 @@
"outputs": [],
"position": {
"left": 520,
"top": 0.0
"top": 0
},
"subworkflow": {
"a_galaxy_workflow": "true",
Expand Down Expand Up @@ -741,23 +741,13 @@
}
},
"tags": "",
"uuid": "4a815412-cadd-4df9-9559-15b365715f05"
"uuid": "9df7c037-6fe4-47e9-8311-e40bc5101b58"
},
"tool_id": null,
"type": "subworkflow",
"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",
Expand All @@ -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"
}
]
},
Expand Down Expand Up @@ -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/0.9.3+galaxy1",
"errors": null,
"id": 14,
"input_connections": {
Expand Down Expand Up @@ -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/0.9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "d56db0e1555d",
"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": "0.8.11+galaxy1",
"tool_version": "0.9.3+galaxy1",
"type": "tool",
"uuid": "bbb479cd-c67c-4347-9c1d-ac8095d90aa9",
"when": null,
Expand Down Expand Up @@ -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/0.9.3+galaxy0",
"errors": null,
"id": 4,
"input_connections": {
Expand Down Expand Up @@ -1203,23 +1203,23 @@
"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/0.9.3+galaxy0",
"tool_shed_repository": {
"changeset_revision": "c3dc51297bf8",
"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": "0.8.11+galaxy0",
"tool_version": "0.9.3+galaxy0",
"type": "tool",
"uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6",
"when": null,
"workflow_outputs": []
},
"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/0.9.3+galaxy1",
"errors": null,
"id": 5,
"input_connections": {
Expand Down Expand Up @@ -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/0.9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "3ff6eeca667e",
"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": "0.8.11+galaxy1",
"tool_version": "0.9.3+galaxy1",
"type": "tool",
"uuid": "d411eea7-7996-44f2-af2a-feecb854a067",
"when": null,
Expand All @@ -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/0.9.3+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
Expand Down Expand Up @@ -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/0.9.3+galaxy0",
"tool_shed_repository": {
"changeset_revision": "8f71aaf6e59d",
"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": "0.8.11+galaxy0",
"tool_version": "0.9.3+galaxy0",
"type": "tool",
"uuid": "44270887-1c96-4ede-8bb9-3db2a07eeb6e",
"when": null,
Expand All @@ -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": {
Expand Down Expand Up @@ -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,
Expand All @@ -1422,6 +1422,6 @@
"tags": [
"Hi-C"
],
"uuid": "f310abac-4a50-41fa-a59a-84c51816a462",
"version": 1
"uuid": "2a89cbe4-a69f-4bff-9465-2e04b0217e35",
"version": 4
}
4 changes: 2 additions & 2 deletions .../hic_fastq_to_cool_hicup_cooler-tests.yml → .../hic-fastq-to-cool-hicup-cooler-tests.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
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):
Expand Down Expand Up @@ -76,7 +76,7 @@
test_dataset:
asserts:
has_size:
value: 123613
value: 149349
delta: 10000
plot with pyGenomeTracks:
class: File
Expand Down
Loading

0 comments on commit 0689b57

Please sign in to comment.