diff --git a/.planemo.yml b/.planemo.yml new file mode 100644 index 0000000..e69de29 diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 92618ac..02a917e 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -1,6 +1,5 @@ { "recommendations": [ - "davelopez.galaxy-tools", "mechatroner.rainbow-csv", "redhat.vscode-xml", "ms-vscode.live-server" diff --git a/.vscode/tasks.json b/.vscode/tasks.json index 3c96974..dbb3a29 100644 --- a/.vscode/tasks.json +++ b/.vscode/tasks.json @@ -8,6 +8,12 @@ "type": "shell", "command": "planemo lint", "problemMatcher": [] + }, + { + "label": "serve", + "type": "shell", + "command": "planemo serve", + "problemMatcher": [] } ] } \ No newline at end of file diff --git a/autobigs-cli.xml b/autobigs-cli.xml index 49787bd..17866d6 100644 --- a/autobigs-cli.xml +++ b/autobigs-cli.xml @@ -1,7 +1,7 @@ Automated MLST typing from PubMLST and InstitutPasteur. - 0.4.3 + 0.5.0 0 autobigs-cli_macros.xml @@ -12,52 +12,56 @@ - + - + - + - + - - - + + + - + + - mode == "st" + mode.operation == "st" + + + mode.operation == "info" - + @@ -89,7 +93,6 @@ positional arguments: options: -h, --help show this help message and exit - --exact, -ex Should run exact matching rather than returning all similar ones --stop-on-fail, -sof Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches). @@ -98,8 +101,8 @@ options: @book{Deng2025RealYHD, -title = {RealYHD/autoBIGS.cli}, -url = {https://github.com/RealYHD/autoBIGS.cli}, +title = {Syph-and-VPD-Lab/autoBIGS.cli}, +url = {https://github.com/Syph-and-VPD-Lab/autoBIGS.cli}, author = {Deng, Harrison}, date = {2025-01-24}, year = {2025}, diff --git a/test-data/results.csv b/test-data/results.csv index a138d7e..9a83ce5 100644 --- a/test-data/results.csv +++ b/test-data/results.csv @@ -1,2 +1,2 @@ -id,st,clonal-complex,tyrB,icd,pepA,adk,pgm,fumC,glyA -BX470248.1,1,ST-2 complex,1,1,1,1,1,1,1 \ No newline at end of file +id,st,clonal-complex,adk,fumC,glyA,icd,pepA,pgm,tyrB +BX470248.1,1,ST-2 complex,1,1,1,1,1,1,1