capanno-utils 0.11.2

Tool for managing bioinformatics content repositories.

General

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.

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/cwl_v1_2.py > capanno_utils/classes/cwl/common_workflow_language.py

Add the 10 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

Adding a tool

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

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 
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