From 197f0995f1c2d59e523246dc71d6a7c5a72a605f Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 31 Jan 2025 13:44:58 -0500 Subject: [PATCH] add annotations, validator for haplotype names inputs, and update pick value --- .../Assembly-Hifi-HiC-phasing-VGP4.ga | 146 +++++++++--------- .../CHANGELOG.md | 6 +- 2 files changed, 80 insertions(+), 72 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index 8f944ec55..2aadf88ff 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "", + "annotation": "Assemble Genome using PacBio HiFi and HiC data for phasing. Prerequisite: Run k-mer profiling workflow (VGP1). ", "comments": [], "creator": [ { @@ -73,7 +73,7 @@ "top": 149.4296875 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "46d0bd3a-f4fd-48ab-ba51-31838a288248", @@ -81,14 +81,14 @@ "workflow_outputs": [] }, "2": { - "annotation": "", + "annotation": "Collection of Hi-C forward reads.", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Collection of Hi-C forward reads.", "name": "Hi-C Forward reads" } ], @@ -108,14 +108,14 @@ "workflow_outputs": [] }, "3": { - "annotation": "", + "annotation": "Collection of Hi-C reverse reads.", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Collection of Hi-C reverse reads.", "name": "Hi-C Reverse reads" } ], @@ -189,14 +189,14 @@ "workflow_outputs": [] }, "6": { - "annotation": "", + "annotation": "Select the database to use for Busco lineages. ", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Select the database to use for Busco lineages. ", "name": "Database for Busco Lineage" } ], @@ -208,7 +208,7 @@ "top": 666.080035105452 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "245a5b51-c40d-4425-81ca-2baf3c157022", @@ -235,7 +235,7 @@ "top": 770.3740188995779 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", @@ -243,14 +243,14 @@ "workflow_outputs": [] }, "8": { - "annotation": "", + "annotation": "Name of the first haplotype without blank space. ", "content_id": null, "errors": null, "id": 8, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Name of the first haplotype without blank space. ", "name": "Name for Haplotype 1" } ], @@ -262,7 +262,7 @@ "top": 852.6092753452594 }, "tool_id": null, - "tool_state": "{\"default\": \"Hap1\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": \"Hap1\", \"multiple\": false, \"validators\": [{\"message\": \"Please do not use blank spaces\", \"expression\": \"^\\\\S+$\", \"negate\": false, \"type\": \"regex\"}], \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", @@ -270,14 +270,14 @@ "workflow_outputs": [] }, "9": { - "annotation": "", + "annotation": "Name of the second haplotype without blank space. ", "content_id": null, "errors": null, "id": 9, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Name of the second haplotype without blank space. ", "name": "Name for Haplotype 2" } ], @@ -289,7 +289,7 @@ "top": 939.8716854194543 }, "tool_id": null, - "tool_state": "{\"default\": \"Hap2\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": \"Hap2\", \"multiple\": false, \"validators\": [{\"message\": \"Please do not use blank spaces\", \"expression\": \"^\\\\S+$\", \"negate\": false, \"type\": \"regex\"}], \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", @@ -316,7 +316,7 @@ "top": 1033.0113085913417 }, "tool_id": null, - "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_state": "{\"default\": 37, \"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", @@ -324,14 +324,14 @@ "workflow_outputs": [] }, "11": { - "annotation": "", + "annotation": "Do not use. ", "content_id": null, "errors": null, "id": 11, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Do not use. ", "name": "SAK input file" } ], @@ -370,7 +370,7 @@ "top": 1228.4076056463502 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"integer\", \"optional\": true}", + "tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "b251eddc-49e6-4899-a893-a904c29b9e75", @@ -607,7 +607,7 @@ }, "18": { "annotation": "", - "content_id": "pick_value", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, "id": 18, "input_connections": { @@ -636,9 +636,15 @@ "output_name": "integer_param" } }, - "tool_id": "pick_value", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_default\", \"__current_case__\": 1, \"type_cond\": {\"param_type\": \"integer\", \"__current_case__\": 1, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}], \"default_value\": \"37\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0", + "tool_version": "0.2.0", "type": "tool", "uuid": "981127b6-37ac-4163-8036-da7aaacf83e7", "when": null, @@ -797,15 +803,15 @@ "uuid": "009e0075-cbca-449c-97ef-2b5d68ef5d00", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "Trimmed Hi-C Forward reads", - "output_name": "out1", - "uuid": "040f7265-5268-4047-bbde-778e48445e43" - }, { "label": "Trimmed Hi-C Reverse reads", "output_name": "out2", "uuid": "a9ac83eb-39ae-4df0-b547-ba240933167d" + }, + { + "label": "Trimmed Hi-C Forward reads", + "output_name": "out1", + "uuid": "040f7265-5268-4047-bbde-778e48445e43" } ] }, @@ -967,8 +973,8 @@ } ], "position": { - "left": 922.9453125, - "top": 817.02734375 + "left": 927.2411666226179, + "top": 823.8894389072996 }, "post_job_actions": { "HideDatasetActiondata_param": { @@ -1444,7 +1450,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"set\", \"__current_case__\": 1, \"h1\": {\"__class__\": \"RuntimeValue\"}, \"h2\": {\"__class__\": \"RuntimeValue\"}, \"seed\": null, \"n_weight\": null, \"n_perturb\": null, \"f_perturb\": null, \"l_msjoin\": \"500000\"}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"RuntimeValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"blank\", \"__current_case__\": 0}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"set\", \"__current_case__\": 1, \"cleaning_rounds\": \"4\", \"adapter_length\": \"0\", \"pop_contigs\": \"10000000\", \"pop_unitigs\": \"100000\", \"remove_tips\": \"3\", \"max_overlap\": \"0.8\", \"min_overlap\": \"0.2\", \"disable_post_join\": false, \"ignore_error_corrected\": false, \"hom_cov\": {\"__class__\": \"ConnectedValue\"}}, \"bins_out\": false, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"set\", \"__current_case__\": 1, \"h1\": {\"__class__\": \"ConnectedValue\"}, \"h2\": {\"__class__\": \"ConnectedValue\"}, \"seed\": null, \"n_weight\": null, \"n_perturb\": null, \"f_perturb\": null, \"l_msjoin\": \"500000\"}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}}, \"ont_integration\": {\"ont_integration_selector\": \"blank\", \"__current_case__\": 0}, \"purge_options\": {\"purge_selector\": \"blank\", \"__current_case__\": 0}, \"scaffolding_options\": {\"scaffold_selector\": \"blank\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.20.0+galaxy0", "type": "tool", "uuid": "0178b5a1-d244-43bc-85e4-e83d1360a94e", @@ -1555,7 +1561,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "001f8c0e-234a-4406-9d8b-a26b8e878c56", @@ -1613,7 +1619,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "fe43bf41-0e43-482e-99bb-7a855d4bcb2f", @@ -1667,7 +1673,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "723d5c3e-c0ec-4085-bccd-29d5d97ce3f8", @@ -1721,7 +1727,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"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\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"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+galaxy1", "type": "tool", "uuid": "4d4a30a0-d2e9-4814-afc2-74e4194ebdf5", @@ -1781,7 +1787,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "ed95e95b-68f3-47f4-ac03-eb4fb01d3020", @@ -1835,7 +1841,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"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\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"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+galaxy1", "type": "tool", "uuid": "2bf6f1be-461a-45e1-aa5f-0af394563a23", @@ -1890,7 +1896,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": true, \"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+galaxy1", "type": "tool", "uuid": "596ea56e-3c73-402a-b1ae-e2be1bb91227", @@ -1939,7 +1945,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": true, \"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+galaxy1", "type": "tool", "uuid": "cd65bf95-931d-4514-8851-6652198c7ab7", @@ -3094,7 +3100,7 @@ "top": 296.3210144042969 }, "tool_id": null, - "tool_state": "{\"default\": \"Primary\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": \"Primary\", \"validators\": [], \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "6118c82a-61da-4856-9e25-1f0d93297527", @@ -3127,7 +3133,7 @@ "top": 440.4403076171875 }, "tool_id": null, - "tool_state": "{\"default\": \"Alternate\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": \"Alternate\", \"validators\": [], \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "3204b6e0-bd83-4a8d-8ddb-3b0dd89dbd04", @@ -3494,15 +3500,15 @@ "uuid": "1b8e2d4e-3380-4414-bdb0-b356383c0ee2", "when": null, "workflow_outputs": [ - { - "label": "Nx Plot", - "output_name": "Nx Plot", - "uuid": "781f8511-c3fe-4954-afa8-d21c94c996a4" - }, { "label": "Size Plot", "output_name": "Size Plot", "uuid": "03a0d2a8-c2d5-4ca7-80fe-7d04d1c4894a" + }, + { + "label": "Nx Plot", + "output_name": "Nx Plot", + "uuid": "781f8511-c3fe-4954-afa8-d21c94c996a4" } ] }, @@ -3598,7 +3604,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.8.0+galaxy0", "type": "tool", "uuid": "08066bc3-0992-4606-844d-16be3c56691a", @@ -3609,15 +3615,15 @@ "output_name": "summary_image", "uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1" }, - { - "label": "Busco Gff File - Hap2", - "output_name": "busco_gff", - "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" - }, { "label": "Busco Summary Hap2", "output_name": "busco_sum", "uuid": "bf7e959c-5252-467e-bb58-2b8cabbd0f3b" + }, + { + "label": "Busco Gff File - Hap2", + "output_name": "busco_gff", + "uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2" } ] }, @@ -3738,16 +3744,6 @@ "uuid": "9985e575-3113-4c2c-bc2c-78faab3a1291", "when": null, "workflow_outputs": [ - { - "label": "Merqury QV", - "output_name": "qv_files", - "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" - }, - { - "label": "Merqury Stats", - "output_name": "stats_files", - "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" - }, { "label": "Merqury images", "output_name": "png_files", @@ -3757,6 +3753,16 @@ "label": "Merqury Histograms", "output_name": "hist_files", "uuid": "67d9d45d-989d-43c0-9ebd-0da9cc35763a" + }, + { + "label": "Merqury QV", + "output_name": "qv_files", + "uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814" + }, + { + "label": "Merqury Stats", + "output_name": "stats_files", + "uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3" } ] }, @@ -3852,22 +3858,22 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.8.0+galaxy0", "type": "tool", "uuid": "a4957dee-45cc-4f34-ae2e-e07f93b9fcc4", "when": null, "workflow_outputs": [ - { - "label": "Busco Gff File - Hap1", - "output_name": "busco_gff", - "uuid": "ba26cb24-25d4-4669-982c-abe4816753a6" - }, { "label": "Busco Summary Image Hap1", "output_name": "summary_image", "uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757" }, + { + "label": "Busco Gff File - Hap1", + "output_name": "busco_gff", + "uuid": "ba26cb24-25d4-4669-982c-abe4816753a6" + }, { "label": "Busco Summary Hap1", "output_name": "busco_sum", @@ -4261,6 +4267,6 @@ "VGP", "Reviewed" ], - "uuid": "442c1ce7-a2b8-4d19-a19b-a3c47dcf674d", - "version": 2 + "uuid": "a4513aba-433a-46a0-84cc-f675a29b205b", + "version": 4 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index 6f8dee847..e729a8cb5 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,11 +1,13 @@ # Changelog -## [0.2.3] 2024-12-13 +## [0.2.3] 2025-01-13 ### Changes - Hi-C inputs are now entered as collections instead of single datasets - Add optional trimming of Hi-C reads +- Add inputs annotations +- Add validator for haplotype names: No blank spaces ### Automatic update - `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` @@ -14,7 +16,7 @@ - `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0` - `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2` - `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0` - +- `toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.1.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0` ## [0.2.2] 2024-08-07