beta correlations #7
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josenavas
suggested changes
Jul 5, 2017
qp_qiime2/__init__.py
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| opt_params = {'m-metadata-category': ('string', ''), | ||
| 'p-method': ['choice:["spearman", "pearson"]', 'spearman'], | ||
| 'p-permutations': ('integer', 999)} | ||
| # outputs = {'qiime2-visualization': 'qiime2-visualization'} |
| @@ -9,6 +9,8 @@ | |||
| from os import mkdir | |||
| from os.path import join, exists | |||
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| import pandas as pd | |||
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qp_qiime2/__init__.py
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| # Define the beta_correlation command | ||
| req_params = {'i-distance-matrix': ('artifact', ['distance_matrix']), | ||
| 'm-metadata-file': ('artifact', ['BIOM'])} |
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I'm a bit confused about requesting a BIOM for the metadata-file. I would not request any metadata here, and I will ask the analysis of the artifact for the metadata.
qp_qiime2/qiime2.py
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| artifact_info = qclient.get("/qiita_db/artifacts/%s/" % artifact_id) | ||
| dm_fp = artifact_info['files']['plain_text'][0] | ||
| dm_qza = join(out_dir, 'q2-distance.qza') | ||
| analysis_id = parameters['m-metadata-file'] |
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Remove this, in the artifact_info dict above, there should be the entry "analysis" which contains the analysis id.
josenavas
approved these changes
Jul 5, 2017
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