capanno-utils
is a companion tool to manage metadata and workflow language files for bioinformatics tools in the capanno and similar repositories. Usage examples and additional documentation can be found in that repository. It is recommended to start with the Getting Started documentation.
schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/master/v1.0/CommonWorkflowLanguage.yml > capanno_utils/classes/cwl/common_workflow_language.py
or
curl https://raw.githubusercontent.com/common-workflow-language/cwl-utils/main/cwl_utils/parser/cwl_v1_2.py > capanno_utils/classes/cwl/common_workflow_language.py
perl -p -i -e 'print "from capanno_utils.classes.cwl.common_workflow_language_mixins import CommandLineToolMixin, \\
CommandInputParameterMixin, SchemaDefRequirementMixin, CommandLineBindingMixin, \\
CommandOutputParameterMixin, WorkflowMixin, InputParameterMixin, WorkflowOutputParameterMixin, \\
WorkflowStepMixin, WorkflowStepInputMixin\n" if $. == 1' capanno_utils/classes/cwl/common_workflow_language.py
perl -p -i -e 's/SchemaDefRequirement\(/SchemaDefRequirement(SchemaDefRequirementMixin,/; \
s/CommandLineBinding\(/CommandLineBinding(CommandLineBindingMixin,/; \
s/CommandInputParameter\(/CommandInputParameter(CommandInputParameterMixin,/; \
s/CommandOutputParameter\(/CommandOutputParameter(CommandOutputParameterMixin,/; \
s/CommandLineTool\(/CommandLineTool(CommandLineToolMixin,/; \
s/Workflow\(/Workflow(WorkflowMixin,/; \
s/class InputParameter\(/class InputParameter(InputParameterMixin,/; \
s/WorkflowOutputParameter\(/WorkflowOutputParameter(WorkflowOutputParameterMixin,/; \
s/class WorkflowStep\(/class WorkflowStep(WorkflowStepMixin,/; \
s/class WorkflowStepInput\(/class WorkflowStepInput(WorkflowStepInputMixin,/;' capanno_utils/classes/cwl/common_workflow_language.py
Usage:
capanno-add tool kallisto 0.45.x --biotoolsID kallisto #This will initialize a directory for kallisto
tools/
└── kallisto
└── 0.45.x
├── common
│ └── common-metadata.yaml
└── kallisto
├── instances
└── kallisto-metadata.yaml
If you don't provide a biotoolsID
, capanno-utils will just make a blank template.
capanno-add tool kallisto 0.45.x
tools/
└── kallisto
└── 0.45.x
└── common
└── common-metadata.yaml
#remote
capanno-add subtool kallisto 0.45.x index -u --init-cwl https://github.com/common-workflow-library/bio-cwl-tools/raw/release/Kallisto/Kallisto-Index.cwl
#local
capanno-add subtool kallisto 0.45.x index -u --init-cwl bio-cwl-tools-submodule/Kallisto/Kallisto-Index.cwl
tools/
└── kallisto
└── 0.45.x
├── common
│ └── common-metadata.yaml
├── kallisto
│ ├── instances
│ └── kallisto-metadata.yaml
└── kallisto_index
├── instances
├── kallisto-index-metadata.yaml
└── kallisto-index.cwl
If --init_cwl
is not provided, no cwl file is initialized and capanno-utils will make a blank template.
Can also initialize all subtool directories when first initialize the tool directory but haven't made a way to specify cwl urls to initialize each one doing it that way yet.
capanno-add subtool kallisto 0.45.x index -u
cwl-tools/
└── kallisto
└── 0.45.x
├── common
│ └── common-metadata.yaml
└── kallisto_index
├── instances
└── kallisto-index-metadata.yaml