Tool for managing bioinformatics content repositories.
Project description
Tools actively under development. Documentation will be updated when ready for outside use!
Create the parser using the latest and greatest CWL and schema-salad versions
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_v1_2.py > capanno_utils/classes/cwl/common_workflow_language.py
Add the mixins by hand
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
WorkflowMixin InputParameterMixin WorkflowOutputParameterMixin WorkflowStepMixin WorkflowStepInputMixin
Adding a tool
Usage:
capanno-add tool kallisto 0.45.x --biotoolsID kallisto #This will initialize a directory for kallisto
cwl-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
cwl-tools/
└── kallisto
└── 0.45.x
└── common
└── common-metadata.yaml
Adding a subtool
#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
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
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