Package: capanno-utils
Generalcapanno-utilsis a companion tool to manage metadata and workflow language files for bioinformatics tools in thecapannoand similar repositories. Usage examples and additional documentation can be found in that repository. It is recommended to start with theGetting Starteddocumentation.Create the parser using the latest and greatest CWL and schema-salad versionsschema-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.pyorcurl https://raw.githubusercontent.com/common-workflow-language/cwl-utils/main/cwl_utils/parser/cwl_v1_2.py > capanno_utils/classes/cwl/common_workflow_language.pyAdd the 10 mixins by handperl -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.pyAdding a toolUsage: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.yamlIf you don't provide abiotoolsID, capanno-utils will just make a blank template.capanno-add tool kallisto 0.45.x
tools/
└── kallisto
    └── 0.45.x
        └── common
            └── common-metadata.yamlAdding 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.cwlIf--init_cwlis 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