Closed dleehr closed 4 years ago
Bug Description q2cwl template conda fails to generate cwl for qiime2.plugins.sample_classifier.visualizers.confusion_matrix
q2cwl template conda
Steps to reproduce the behavior
535 wget https://data.qiime2.org/distro/core/qiime2-2019.10-py36-osx-conda.yml 536 conda env create -n qiime2-2019.10 --file qiime2-2019.10-py36-osx-conda.yml 537 conda activate qiime2-2019.10 538 pip install cwltool 539 pip install . 540 mkdir output 541 q2cwl template conda output/
Expected behavior Expected all plugins to produce CWL tools
Screenshots
$ q2cwl template conda output/ output/qiime2.plugins.vsearch.methods.cluster_features_de_novo.cwl : created successfully. output/qiime2.plugins.vsearch.methods.cluster_features_closed_reference.cwl : created successfully. output/qiime2.plugins.vsearch.methods.dereplicate_sequences.cwl : created successfully. output/qiime2.plugins.vsearch.methods.join_pairs.cwl : created successfully. output/qiime2.plugins.vsearch.methods.uchime_ref.cwl : created successfully. output/qiime2.plugins.vsearch.methods.uchime_denovo.cwl : created successfully. output/qiime2.plugins.vsearch.pipelines.cluster_features_open_reference.cwl : created successfully. output/qiime2.plugins.taxa.methods.collapse.cwl : created successfully. output/qiime2.plugins.taxa.methods.filter_table.cwl : created successfully. output/qiime2.plugins.taxa.methods.filter_seqs.cwl : created successfully. output/qiime2.plugins.taxa.visualizers.barplot.cwl : created successfully. output/qiime2.plugins.sample_classifier.methods.regress_samples_ncv.cwl : created successfully. output/qiime2.plugins.sample_classifier.methods.classify_samples_ncv.cwl : created successfully. output/qiime2.plugins.sample_classifier.methods.fit_classifier.cwl : created successfully. output/qiime2.plugins.sample_classifier.methods.fit_regressor.cwl : created successfully. output/qiime2.plugins.sample_classifier.methods.predict_classification.cwl : created successfully. output/qiime2.plugins.sample_classifier.methods.predict_regression.cwl : created successfully. output/qiime2.plugins.sample_classifier.methods.split_table.cwl : created successfully. output/qiime2.plugins.sample_classifier.visualizers.scatterplot.cwl : created successfully. Traceback (most recent call last): File "/Users/dcl9/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cwl/template.py", line 250, in template tool = make_tool(plugin, action, directory, extra_req_factory) File "/Users/dcl9/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cwl/template.py", line 137, in make_tool tool['inputs'].update(template_parameters(name, spec)) File "/Users/dcl9/opt/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cwl/template.py", line 210, in template_parameters raise Exception("Unknown type: %r" % qiime_type) Exception: Unknown type: Float | Str % Choices('auto') <visualizer qiime2.plugins.sample_classifier.visualizers.confusion_matrix> : Unknown type: Float | Str % Choices('auto') See above for error details.
Computation Environment
Thanks @dleehr, this seems like a reasonable issue for it to have (it is a newer feature of our type-system). I'll see what it takes to get it working!
Fixed (we believe) in #11
Bug Description
q2cwl template conda
fails to generate cwl for qiime2.plugins.sample_classifier.visualizers.confusion_matrixSteps to reproduce the behavior
Expected behavior Expected all plugins to produce CWL tools
Screenshots
Computation Environment