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Updating workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2 from 0.2 to 0.3 #884

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Updating workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2 from 0.2 to 0.3 #884

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5 changes: 5 additions & 0 deletions workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/CHANGELOG.md
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@@ -1,5 +1,10 @@
# Changelog

## [0.3] - 2025-06-09

### 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+galaxy2`

## [0.2] - 2025-03-10

### Automatic update
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48 changes: 24 additions & 24 deletions workflows/amplicon/amplicon-mgnify/mapseq-to-ampvis2/mapseq-to-ampvis2.ga
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Expand Up @@ -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"
},
Expand Down Expand Up @@ -162,7 +161,7 @@
},
"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+galaxy2",
"errors": null,
"id": 3,
"input_connections": {
Expand Down Expand Up @@ -191,23 +190,23 @@
"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+galaxy2",
"tool_shed_repository": {
"changeset_revision": "3dc70b59608c",
"changeset_revision": "c41d78ae5fee",
"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_version": "9.5+galaxy2",
"type": "tool",
"uuid": "542e2486-608c-48c3-949f-bf693f35e503",
"when": null,
"workflow_outputs": []
},
"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+galaxy2",
"errors": null,
"id": 4,
"input_connections": {
Expand Down Expand Up @@ -236,15 +235,15 @@
"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+galaxy2",
"tool_shed_repository": {
"changeset_revision": "3dc70b59608c",
"changeset_revision": "c41d78ae5fee",
"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_version": "9.5+galaxy2",
"type": "tool",
"uuid": "b3a78171-289c-40dc-95c7-f1ea65b12167",
"when": null,
Expand Down Expand Up @@ -342,7 +341,7 @@
},
"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+galaxy2",
"errors": null,
"id": 7,
"input_connections": {
Expand Down Expand Up @@ -371,23 +370,23 @@
"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+galaxy2",
"tool_shed_repository": {
"changeset_revision": "3dc70b59608c",
"changeset_revision": "c41d78ae5fee",
"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_version": "9.5+galaxy2",
"type": "tool",
"uuid": "25d25ac8-20a2-491e-8847-d49874922821",
"when": null,
"workflow_outputs": []
},
"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+galaxy2",
"errors": null,
"id": 8,
"input_connections": {
Expand Down Expand Up @@ -418,15 +417,15 @@
"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+galaxy2",
"tool_shed_repository": {
"changeset_revision": "3dc70b59608c",
"changeset_revision": "c41d78ae5fee",
"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_version": "9.5+galaxy2",
"type": "tool",
"uuid": "8ada9fc3-1ec1-4ec8-995e-b2f6411c777f",
"when": null,
Expand Down Expand Up @@ -570,7 +569,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0",
"tool_shed_repository": {
"changeset_revision": "738474880da8",
"changeset_revision": "5029fd9d572e",
"name": "ampvis2_load",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -600,6 +599,7 @@
}
},
"tags": [],
"uuid": "e24060a0-1cfe-40f1-9251-48e96f7e1121",
"version": 40
"uuid": "f76fb305-1a60-4711-96cd-713de4070e79",
"version": 1,
"release": "0.3"
}