Skip to content

Commit 1fc7fd8

Browse files
authored
Merge pull request #672 from planemo-autoupdate/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b
Updating workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b from 0.7.2 to 0.7.3
2 parents 6c91869 + d97dedc commit 1fc7fd8

File tree

2 files changed

+45
-39
lines changed

2 files changed

+45
-39
lines changed

workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,11 @@
11
# Changelog
22

3+
## [0.7.3] 2025-02-10
4+
5+
### Automatic update
6+
- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1`
7+
- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2`
8+
39
## [0.7.2] 2025-01-30
410

511
### Automatic update

workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga

Lines changed: 39 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@
1515
],
1616
"format-version": "0.1",
1717
"license": "CC-BY-4.0",
18-
"release": "0.7.2",
18+
"release": "0.7.3",
1919
"name": "Purging duplicates in one haplotype VGP6b",
2020
"report": {
2121
"markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Merqury results\n\nMerqury QV:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_QV\")\n```\n\nMerqury completeness:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\nMerqury plots:\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\n\nspectra-asm:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n\n\n\n## BUSCO results (Vertebrata database)\n\nPurged Assembly\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco on Purged Primary assembly: summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -203,7 +203,7 @@
203203
"top": 1674.0155168754275
204204
},
205205
"tool_id": null,
206-
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
206+
"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
207207
"tool_version": null,
208208
"type": "parameter_input",
209209
"uuid": "1562a9b8-e3b5-473f-9f77-e09693d1a98f",
@@ -230,7 +230,7 @@
230230
"top": 1810.0027445448727
231231
},
232232
"tool_id": null,
233-
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
233+
"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
234234
"tool_version": null,
235235
"type": "parameter_input",
236236
"uuid": "f95d611e-99bd-43a3-8455-b87df2071d01",
@@ -257,7 +257,7 @@
257257
"top": 831.9098633921083
258258
},
259259
"tool_id": null,
260-
"tool_state": "{\"default\": \"Primary\", \"validators\": [], \"parameter_type\": \"text\", \"optional\": true}",
260+
"tool_state": "{\"default\": \"Primary\", \"parameter_type\": \"text\", \"optional\": true}",
261261
"tool_version": null,
262262
"type": "parameter_input",
263263
"uuid": "2bb6f78a-3a49-4cd4-87d1-29b7900b7950",
@@ -284,7 +284,7 @@
284284
"top": 949.2459649024566
285285
},
286286
"tool_id": null,
287-
"tool_state": "{\"default\": \"Alternate\", \"validators\": [], \"parameter_type\": \"text\", \"optional\": true}",
287+
"tool_state": "{\"default\": \"Alternate\", \"parameter_type\": \"text\", \"optional\": true}",
288288
"tool_version": null,
289289
"type": "parameter_input",
290290
"uuid": "c04ef45a-c035-4470-9fe1-87ded0e8bafb",
@@ -338,7 +338,7 @@
338338
},
339339
"11": {
340340
"annotation": "",
341-
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
341+
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
342342
"errors": null,
343343
"id": 11,
344344
"input_connections": {
@@ -378,15 +378,15 @@
378378
"output_name": "alignment_output"
379379
}
380380
},
381-
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
381+
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
382382
"tool_shed_repository": {
383-
"changeset_revision": "5cc34c3f440d",
383+
"changeset_revision": "66367287b4e6",
384384
"name": "minimap2",
385385
"owner": "iuc",
386386
"tool_shed": "toolshed.g2.bx.psu.edu"
387387
},
388388
"tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"asm5\"}, \"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\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"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}",
389-
"tool_version": "2.28+galaxy0",
389+
"tool_version": "2.28+galaxy1",
390390
"type": "tool",
391391
"uuid": "b6259cc9-6c33-48ff-bc0f-c7fcd0643809",
392392
"when": null,
@@ -439,7 +439,7 @@
439439
},
440440
"13": {
441441
"annotation": "",
442-
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
442+
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
443443
"errors": null,
444444
"id": 13,
445445
"input_connections": {
@@ -468,15 +468,15 @@
468468
"output_name": "stats"
469469
}
470470
},
471-
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
471+
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
472472
"tool_shed_repository": {
473-
"changeset_revision": "764f2516d837",
473+
"changeset_revision": "7729cd89aaf7",
474474
"name": "gfastats",
475475
"owner": "bgruening",
476476
"tool_shed": "toolshed.g2.bx.psu.edu"
477477
},
478478
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
479-
"tool_version": "1.3.9+galaxy1",
479+
"tool_version": "1.3.9+galaxy2",
480480
"type": "tool",
481481
"uuid": "2bde750d-f225-498f-bd3c-b954e71b5bdd",
482482
"when": null,
@@ -608,7 +608,7 @@
608608
},
609609
"17": {
610610
"annotation": "",
611-
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
611+
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
612612
"errors": null,
613613
"id": 17,
614614
"input_connections": {
@@ -643,15 +643,15 @@
643643
"output_name": "alignment_output"
644644
}
645645
},
646-
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
646+
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1",
647647
"tool_shed_repository": {
648-
"changeset_revision": "5cc34c3f440d",
648+
"changeset_revision": "66367287b4e6",
649649
"name": "minimap2",
650650
"owner": "iuc",
651651
"tool_shed": "toolshed.g2.bx.psu.edu"
652652
},
653653
"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}",
654-
"tool_version": "2.28+galaxy0",
654+
"tool_version": "2.28+galaxy1",
655655
"type": "tool",
656656
"uuid": "6f009c42-6298-4db3-999e-b408c4ebedd6",
657657
"when": null,
@@ -1026,7 +1026,7 @@
10261026
}
10271027
},
10281028
"tags": [],
1029-
"uuid": "0d4d6822-81e5-46e8-b8b7-0b3094fb6195"
1029+
"uuid": "42e35c17-51a5-4b9e-8c5f-1a5da19e8276"
10301030
},
10311031
"tool_id": null,
10321032
"type": "subworkflow",
@@ -1036,7 +1036,7 @@
10361036
},
10371037
"19": {
10381038
"annotation": "",
1039-
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
1039+
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
10401040
"errors": null,
10411041
"id": 19,
10421042
"input_connections": {
@@ -1069,15 +1069,15 @@
10691069
"output_name": "stats"
10701070
}
10711071
},
1072-
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
1072+
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
10731073
"tool_shed_repository": {
1074-
"changeset_revision": "764f2516d837",
1074+
"changeset_revision": "7729cd89aaf7",
10751075
"name": "gfastats",
10761076
"owner": "bgruening",
10771077
"tool_shed": "toolshed.g2.bx.psu.edu"
10781078
},
10791079
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
1080-
"tool_version": "1.3.9+galaxy1",
1080+
"tool_version": "1.3.9+galaxy2",
10811081
"type": "tool",
10821082
"uuid": "a7237fd4-e2ee-4b33-bdb7-975e49ccc16c",
10831083
"when": null,
@@ -1691,7 +1691,7 @@
16911691
},
16921692
"28": {
16931693
"annotation": "",
1694-
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
1694+
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
16951695
"errors": null,
16961696
"id": 28,
16971697
"input_connections": {
@@ -1727,15 +1727,15 @@
17271727
"output_name": "stats"
17281728
}
17291729
},
1730-
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
1730+
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
17311731
"tool_shed_repository": {
1732-
"changeset_revision": "764f2516d837",
1732+
"changeset_revision": "7729cd89aaf7",
17331733
"name": "gfastats",
17341734
"owner": "bgruening",
17351735
"tool_shed": "toolshed.g2.bx.psu.edu"
17361736
},
17371737
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
1738-
"tool_version": "1.3.9+galaxy1",
1738+
"tool_version": "1.3.9+galaxy2",
17391739
"type": "tool",
17401740
"uuid": "ce91b60e-4bcf-45ff-8334-329f885cc145",
17411741
"when": null,
@@ -1853,7 +1853,7 @@
18531853
},
18541854
"30": {
18551855
"annotation": "",
1856-
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
1856+
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
18571857
"errors": null,
18581858
"id": 30,
18591859
"input_connections": {
@@ -1891,15 +1891,15 @@
18911891
"output_name": "output"
18921892
}
18931893
},
1894-
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
1894+
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
18951895
"tool_shed_repository": {
1896-
"changeset_revision": "764f2516d837",
1896+
"changeset_revision": "7729cd89aaf7",
18971897
"name": "gfastats",
18981898
"owner": "bgruening",
18991899
"tool_shed": "toolshed.g2.bx.psu.edu"
19001900
},
1901-
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"1000\"}}, \"discover_paths\": false, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
1902-
"tool_version": "1.3.9+galaxy1",
1901+
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"1000\"}, \"no_sequence\": false}, \"discover_paths\": false, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
1902+
"tool_version": "1.3.9+galaxy2",
19031903
"type": "tool",
19041904
"uuid": "90cfbc84-a100-4795-a376-f93ffe2dbd0b",
19051905
"when": null,
@@ -1913,7 +1913,7 @@
19131913
},
19141914
"31": {
19151915
"annotation": "",
1916-
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
1916+
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
19171917
"errors": null,
19181918
"id": 31,
19191919
"input_connections": {
@@ -1948,15 +1948,15 @@
19481948
"output_name": "stats"
19491949
}
19501950
},
1951-
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
1951+
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2",
19521952
"tool_shed_repository": {
1953-
"changeset_revision": "764f2516d837",
1953+
"changeset_revision": "7729cd89aaf7",
19541954
"name": "gfastats",
19551955
"owner": "bgruening",
19561956
"tool_shed": "toolshed.g2.bx.psu.edu"
19571957
},
19581958
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
1959-
"tool_version": "1.3.9+galaxy1",
1959+
"tool_version": "1.3.9+galaxy2",
19601960
"type": "tool",
19611961
"uuid": "ff2b02d1-f6dc-4cd6-bd4a-a70e4d97492c",
19621962
"when": null,
@@ -2635,7 +2635,7 @@
26352635
}
26362636
},
26372637
"tags": [],
2638-
"uuid": "f5a2834d-1f19-45a3-81b3-830886f85f5f"
2638+
"uuid": "f05b8b1b-67b2-42fd-adf2-36b90c6d7b11"
26392639
},
26402640
"tool_id": null,
26412641
"type": "subworkflow",
@@ -2814,7 +2814,7 @@
28142814
"top": 296.3210144042969
28152815
},
28162816
"tool_id": null,
2817-
"tool_state": "{\"default\": \"Primary\", \"validators\": [], \"parameter_type\": \"text\", \"optional\": true}",
2817+
"tool_state": "{\"default\": \"Primary\", \"parameter_type\": \"text\", \"optional\": true}",
28182818
"tool_version": null,
28192819
"type": "parameter_input",
28202820
"uuid": "76f3bd32-bf3e-42be-9e79-cee9e401a28b",
@@ -2847,7 +2847,7 @@
28472847
"top": 440.4403076171875
28482848
},
28492849
"tool_id": null,
2850-
"tool_state": "{\"default\": \"Alternate\", \"validators\": [], \"parameter_type\": \"text\", \"optional\": true}",
2850+
"tool_state": "{\"default\": \"Alternate\", \"parameter_type\": \"text\", \"optional\": true}",
28512851
"tool_version": null,
28522852
"type": "parameter_input",
28532853
"uuid": "cd232b7f-e618-4548-a1da-55e5be6b3f32",
@@ -3207,7 +3207,7 @@
32073207
}
32083208
},
32093209
"tags": [],
3210-
"uuid": "74578271-8fc3-4280-b568-c86da90df140"
3210+
"uuid": "a5b9a0e1-4e4f-4889-beec-7432446a5aac"
32113211
},
32123212
"tool_id": null,
32133213
"type": "subworkflow",

0 commit comments

Comments
 (0)