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110 lines
2.9 KiB
Python
110 lines
2.9 KiB
Python
import pytest
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from galaxy.model.unittest_utils import GalaxyDataTestApp
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from galaxy.tool_util.parser import get_tool_source
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from galaxy.tool_util.parser.cwl import CwlToolSource
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from galaxy.tools import create_tool_from_source
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XML_TOOL = """
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<tool id="tool_id" name="xml tool" version="1"/>
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"""
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CWL_TOOL = """
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: echo
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inputs:
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message:
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type: string
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inputBinding:
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position: 1
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outputs: []
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"""
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YAML_TOOL = """
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id: simple_constructs_y
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name: simple_constructs_y
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version: 1.0
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command:
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>
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echo "$booltest" >> $out_file1;
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inputs:
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- name: booltest
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type: boolean
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truevalue: booltrue
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falsevalue: boolfalse
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checked: false
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- name: data_input
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type: data
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extensions:
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- tabular
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- csv
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outputs:
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out_file1:
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format: txt
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"""
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USER_DEFINED_TOOL = """
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class: GalaxyUserTool
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id: samtools-reference
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version: "0.3"
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name: samtools reference
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description: Extract or fetch reference sequences from CRAM files
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container: quay.io/biocontainers/samtools:1.22.1--h96c455f_0
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shell_command: |
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set -euo pipefail; samtools reference '$(inputs.alignment.path)'| bgzip > fasta.gz
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inputs:
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- name: alignment
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type: data
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extensions:
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- cram
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outputs:
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- name: output1
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type: data
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format: fasta.gz
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from_work_dir: fasta.gz
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"""
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class ToolApp(GalaxyDataTestApp):
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name = "galaxy"
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biotools_metadata_source = None
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job_search = None
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is_webapp = True
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@pytest.fixture
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def tool_app():
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return ToolApp()
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def _deserialize(app, tool_source_class, raw_tool_source):
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tool_source = get_tool_source(tool_source_class=tool_source_class, raw_tool_source=raw_tool_source)
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assert type(tool_source).__name__ == tool_source_class
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return create_tool_from_source(app, tool_source=tool_source)
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def test_deserialize_xml_tool(tool_app):
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tool = _deserialize(tool_app, tool_source_class="XmlToolSource", raw_tool_source=XML_TOOL)
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assert tool.id == "tool_id"
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assert tool.name == "xml tool"
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def test_deserialize_yaml_tool(tool_app):
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tool = _deserialize(tool_app, tool_source_class="YamlToolSource", raw_tool_source=YAML_TOOL)
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assert tool.id == "simple_constructs_y"
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assert tool.name == "simple_constructs_y"
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assert tool.inputs["data_input"].extensions == ["tabular", "csv"]
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def test_deserialize_user_defined_tool(tool_app):
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tool = _deserialize(tool_app, tool_source_class="YamlToolSource", raw_tool_source=USER_DEFINED_TOOL)
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assert tool.tool_type == "user_defined"
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assert tool.id == "samtools-reference"
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assert tool.name == "samtools reference"
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assert tool.inputs["alignment"].type == "data"
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assert tool.outputs["output1"].format == "fasta.gz"
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def test_deserialize_cwl_tool(tool_app):
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# Can't verify much about cwl tools at this point
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tool_source = get_tool_source(tool_app, tool_source_class="CwlToolSource", raw_tool_source=CWL_TOOL)
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assert isinstance(tool_source, CwlToolSource)
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