diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index 5e8481557..07b4ca87a 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -482,7 +482,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 15, "input_connections": { @@ -509,15 +509,15 @@ "top": 0 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"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}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "47c9d134-9895-4055-a3cf-98a77dc6a0b7", "when": null, @@ -1233,7 +1233,7 @@ }, "29": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 29, "input_connections": { @@ -1275,15 +1275,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"scaffolding\", \"__current_case__\": 2, \"agp_to_path\": {\"__class__\": \"ConnectedValue\"}, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "c9168832-ba68-4d06-bbba-86e6b1b82d5f", "when": null, @@ -1297,7 +1297,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 30, "input_connections": { @@ -1332,15 +1332,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"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}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "d59cf1b1-67dd-4b31-856a-28061e27e0b7", "when": null, @@ -1354,7 +1354,7 @@ }, "31": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 31, "input_connections": { @@ -1389,15 +1389,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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}", - "tool_version": "1.3.9+galaxy0", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "80bbd119-3f2b-4bdf-86ca-c1c1871031c8", "when": null, @@ -1411,7 +1411,7 @@ }, "32": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 32, "input_connections": { @@ -1442,15 +1442,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "f4a3eff8ab85", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"s\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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