diff --git a/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/CHANGELOG.md b/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/CHANGELOG.md index cdd050d464..2d255d7347 100644 --- a/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/CHANGELOG.md +++ b/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.3] - 2026-01-19 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.11+galaxy0` + ## [0.2] - 2025-03-10 ### Automatic update diff --git a/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga b/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga index fa48373b88..8f1c5aeb3d 100644 --- a/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga +++ b/workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga @@ -51,7 +51,6 @@ "format-version": "0.1", "license": "MIT", "name": "MAPseq to ampvis2", - "release": "0.2", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -76,7 +75,7 @@ "top": 282.53420657186683 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", "tool_version": null, "type": "data_collection_input", "uuid": "d273ae7f-de2e-4f1f-a6ea-582804a31dc5", @@ -154,6 +153,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"save_db\": false, \"sqlquery\": \"SELECT \\n c1,\\n c2,\\n c3,\\n c3 * 100 / SUM(c3) OVER() AS relative_abundance\\nFROM \\n t1;\\n\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"comment\", \"__current_case__\": 1, \"comment_char\": \"35\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"prepend_dataset_name\", \"__current_case__\": 4}}]}, \"tbl_opts\": {\"table_name\": \"\", \"column_names_from_first_line\": false, \"col_names\": \"\", \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "3.3.2", "type": "tool", "uuid": "ee2e3ed8-e95e-4c6f-8898-f417916dbeb4", @@ -162,7 +162,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "errors": null, "id": 3, "input_connections": { @@ -191,15 +191,16 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "3dc70b59608c", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"code\": \"NR > 2 {\\n # Extract OTU ID and add \\\"OTU_\\\" prefix\\n otu_id = \\\"OTU_\\\" $1\\n\\n # Initialize variables for taxonomic levels\\n superkingdom = kingdom = phylum = class = order = family = genus = species = \\\"\\\"\\n\\n # Split the taxonomy column by \\\";\\\"\\n split($3, taxonomy, \\\";\\\")\\n\\n # Extract taxonomic levels\\n for (i in taxonomy) {\\n if (taxonomy[i] ~ /^sk__/) {\\n superkingdom = taxonomy[i]\\n }else if (taxonomy[i] ~ /^k__/) {\\n kingdom = taxonomy[i]\\n }else if (taxonomy[i] ~ /^p__/) {\\n phylum = taxonomy[i]\\n } else if (taxonomy[i] ~ /^c__/) {\\n class = taxonomy[i]\\n } else if (taxonomy[i] ~ /^o__/) {\\n order = taxonomy[i]\\n } else if (taxonomy[i] ~ /^f__/) {\\n family = taxonomy[i]\\n } else if (taxonomy[i] ~ /^g__/) {\\n genus = taxonomy[i]\\n } else if (taxonomy[i] ~ /^s__/) {\\n species = taxonomy[i]\\n }\\n }\\n\\n # Print the row with extracted values\\n print otu_id \\\"\\\\t\\\" superkingdom \\\"\\\\t\\\" kingdom \\\"\\\\t\\\" phylum \\\"\\\\t\\\" class \\\"\\\\t\\\" order \\\"\\\\t\\\" family \\\"\\\\t\\\" genus \\\"\\\\t\\\" species\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.5+galaxy0", + "tool_state": "{\"code\": \"NR > 2 {\\n # Extract OTU ID and add \\\"OTU_\\\" prefix\\n otu_id = \\\"OTU_\\\" $1\\n\\n # Initialize variables for taxonomic levels\\n superkingdom = kingdom = phylum = class = order = family = genus = species = \\\"\\\"\\n\\n # Split the taxonomy column by \\\";\\\"\\n split($3, taxonomy, \\\";\\\")\\n\\n # Extract taxonomic levels\\n for (i in taxonomy) {\\n if (taxonomy[i] ~ /^sk__/) {\\n superkingdom = taxonomy[i]\\n }else if (taxonomy[i] ~ /^k__/) {\\n kingdom = taxonomy[i]\\n }else if (taxonomy[i] ~ /^p__/) {\\n phylum = taxonomy[i]\\n } else if (taxonomy[i] ~ /^c__/) {\\n class = taxonomy[i]\\n } else if (taxonomy[i] ~ /^o__/) {\\n order = taxonomy[i]\\n } else if (taxonomy[i] ~ /^f__/) {\\n family = taxonomy[i]\\n } else if (taxonomy[i] ~ /^g__/) {\\n genus = taxonomy[i]\\n } else if (taxonomy[i] ~ /^s__/) {\\n species = taxonomy[i]\\n }\\n }\\n\\n # Print the row with extracted values\\n print otu_id \\\"\\\\t\\\" superkingdom \\\"\\\\t\\\" kingdom \\\"\\\\t\\\" phylum \\\"\\\\t\\\" class \\\"\\\\t\\\" order \\\"\\\\t\\\" family \\\"\\\\t\\\" genus \\\"\\\\t\\\" species\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"variables\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "542e2486-608c-48c3-949f-bf693f35e503", "when": null, @@ -207,7 +208,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "errors": null, "id": 4, "input_connections": { @@ -236,15 +237,16 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "3dc70b59608c", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"code\": \"BEGIN {\\n FS = \\\"\\\\t\\\";\\n OFS = \\\"\\\\t\\\";\\n}\\n\\nNR == 1 {\\n # Extract the prefix before the first underscore from the filename in the first row, first column\\n split($1, filename_parts, \\\"_\\\");\\n filename_prefix = filename_parts[1];\\n print \\\"OTU\\\", filename_prefix;\\n}\\n\\n{\\n # Print the OTU ID with 'OTU_' prefix and the relative_abundance\\n print \\\"OTU_\\\" $2, $4;\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.5+galaxy0", + "tool_state": "{\"code\": \"BEGIN {\\n FS = \\\"\\\\t\\\";\\n OFS = \\\"\\\\t\\\";\\n}\\n\\nNR == 1 {\\n # Extract the prefix before the first underscore from the filename in the first row, first column\\n split($1, filename_parts, \\\"_\\\");\\n filename_prefix = filename_parts[1];\\n print \\\"OTU\\\", filename_prefix;\\n}\\n\\n{\\n # Print the OTU ID with 'OTU_' prefix and the relative_abundance\\n print \\\"OTU_\\\" $2, $4;\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"variables\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "b3a78171-289c-40dc-95c7-f1ea65b12167", "when": null, @@ -289,6 +291,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "5.1.0", "type": "tool", "uuid": "cbdaeb1f-a7ad-4a7a-afd4-20a5567732c1", @@ -334,6 +337,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"fill_char\": \"0\", \"has_header\": \"0\", \"identifier_column\": \"1\", \"include_outputs\": null, \"input_tabular\": {\"__class__\": \"ConnectedValue\"}, \"old_col_in_header\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "0.0.3", "type": "tool", "uuid": "653811aa-3f19-4f7c-84d4-be3d091a4550", @@ -342,7 +346,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "errors": null, "id": 7, "input_connections": { @@ -371,15 +375,16 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "3dc70b59608c", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"code\": \"BEGIN {\\n # Print the header\\n print \\\"OTU\\\\tSuperkingdom\\\\tKingdom\\\\tPhylum\\\\tClass\\\\tOrder\\\\tFamily\\\\tGenus\\\\tSpecies\\\"\\n}\\n\\n# Print each line as it is\\n{\\n print\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.5+galaxy0", + "tool_state": "{\"code\": \"BEGIN {\\n # Print the header\\n print \\\"OTU\\\\tSuperkingdom\\\\tKingdom\\\\tPhylum\\\\tClass\\\\tOrder\\\\tFamily\\\\tGenus\\\\tSpecies\\\"\\n}\\n\\n# Print each line as it is\\n{\\n print\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"variables\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "25d25ac8-20a2-491e-8847-d49874922821", "when": null, @@ -387,7 +392,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "errors": null, "id": 8, "input_connections": { @@ -418,15 +423,16 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "3dc70b59608c", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"code\": \"NR==2 {for(i=2; i<=NF; i++) if (index($i, \\\".\\\") > 0) $i = substr($i, 1, index($i, \\\".\\\")-1)} NR>1 {print}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.5+galaxy0", + "tool_state": "{\"code\": \"NR==2 {for(i=2; i<=NF; i++) if (index($i, \\\".\\\") > 0) $i = substr($i, 1, index($i, \\\".\\\")-1)} NR>1 {print}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"variables\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "8ada9fc3-1ec1-4ec8-995e-b2f6411c777f", "when": null, @@ -484,6 +490,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"save_db\": false, \"sqlquery\": \"SELECT c1,\\n GROUP_CONCAT(DISTINCT c2) AS c2,\\n GROUP_CONCAT(DISTINCT c3) AS c3,\\n GROUP_CONCAT(DISTINCT c4) AS c4,\\n GROUP_CONCAT(DISTINCT c5) AS c5,\\n GROUP_CONCAT(DISTINCT c6) AS c6,\\n GROUP_CONCAT(DISTINCT c7) AS c7,\\n GROUP_CONCAT(DISTINCT c8) AS c8,\\n GROUP_CONCAT(DISTINCT c9) AS c9\\nFROM t1\\nGROUP BY c1;\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"\", \"column_names_from_first_line\": false, \"col_names\": \"\", \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "3.3.2", "type": "tool", "uuid": "fb4a4528-4617-4416-94fa-c3e1a2ddea0e", @@ -498,7 +505,7 @@ }, "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.11+galaxy0", "errors": null, "id": 10, "input_connections": { @@ -568,15 +575,16 @@ "output_name": "taxonomy_list_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.11+galaxy0", "tool_shed_repository": { - "changeset_revision": "738474880da8", + "changeset_revision": "9b3e1acc3ad0", "name": "ampvis2_load", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"asv_otu_col_empty\": false, \"asv_sequences\": false, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"guess_column_types\": true, \"metadata\": {\"__class__\": \"ConnectedValue\"}, \"otutable\": {\"__class__\": \"ConnectedValue\"}, \"pruneSingletons\": false, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}, \"tree\": {\"__class__\": \"RuntimeValue\"}, \"write_lists\": [\"tax\", \"metadata\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.8.9+galaxy0", + "tool_uuid": null, + "tool_version": "2.8.11+galaxy0", "type": "tool", "uuid": "283c89ea-5c69-4ad0-9905-146d721621b8", "when": null, @@ -600,6 +608,7 @@ } }, "tags": [], - "uuid": "e24060a0-1cfe-40f1-9251-48e96f7e1121", - "version": 40 + "uuid": "b51aa9cd-7048-44e3-ab40-cdad80961dd1", + "version": 1, + "release": "0.3" } \ No newline at end of file