Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_sample-classifier_classify-samples.xml @ 9:f190567fe3f6 draft
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author | florianbegusch |
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date | Wed, 14 Aug 2019 15:12:48 -0400 |
parents | a025a4a89e07 |
children | a0a8d77a991c |
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8:d66c7509e8f9 | 9:f190567fe3f6 |
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1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
2 <tool id="qiime_sample-classifier_classify-samples" name="qiime sample-classifier classify-samples" version="2019.4"> | 2 <tool id="qiime_sample-classifier_classify-samples" name="qiime sample-classifier classify-samples" version="2019.7"> |
3 <description> - Train and test a cross-validated supervised learning classifier.</description> | 3 <description> - Train and test a cross-validated supervised learning classifier.</description> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="2019.4">qiime2</requirement> | 5 <requirement type="package" version="2019.7">qiime2</requirement> |
6 </requirements> | 6 </requirements> |
7 <command><![CDATA[ | 7 <command><![CDATA[ |
8 qiime sample-classifier classify-samples | 8 qiime sample-classifier classify-samples |
9 | 9 |
10 --i-table=$itable | 10 --i-table=$itable |
62 --m-metadata-file=$metadatafile | 62 --m-metadata-file=$metadatafile |
63 #end if | 63 #end if |
64 | 64 |
65 | 65 |
66 | 66 |
67 --o-probabilities=oprobabilities | |
67 --o-sample-estimator=osampleestimator | 68 --o-sample-estimator=osampleestimator |
68 --o-feature-importance=ofeatureimportance | 69 --o-feature-importance=ofeatureimportance |
69 --o-predictions=opredictions | 70 --o-predictions=opredictions |
70 --o-model-summary=omodelsummary | 71 --o-model-summary=omodelsummary |
71 --o-accuracy-results=oaccuracyresults | 72 --o-accuracy-results=oaccuracyresults |
72 ; | 73 ; |
74 cp oprobabilities.qza $oprobabilities; | |
73 cp osampleestimator.qza $osampleestimator; | 75 cp osampleestimator.qza $osampleestimator; |
74 cp ofeatureimportance.qza $ofeatureimportance; | 76 cp ofeatureimportance.qza $ofeatureimportance; |
75 cp opredictions.qza $opredictions; | 77 cp opredictions.qza $opredictions; |
76 qiime tools export --input-path omodelsummary.qzv --output-path out && mkdir -p '$omodelsummary.files_path' | 78 qiime tools export --input-path omodelsummary.qzv --output-path out && mkdir -p '$omodelsummary.files_path' |
77 && cp -r out/* '$omodelsummary.files_path' | 79 && cp -r out/* '$omodelsummary.files_path' |
141 | 143 |
142 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" /> | 144 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" /> |
143 | 145 |
144 </inputs> | 146 </inputs> |
145 <outputs> | 147 <outputs> |
148 <data format="qza" label="${tool.name} on ${on_string}: probabilities.qza" name="oprobabilities"/> | |
146 <data format="qza" label="${tool.name} on ${on_string}: sampleestimator.qza" name="osampleestimator"/> | 149 <data format="qza" label="${tool.name} on ${on_string}: sampleestimator.qza" name="osampleestimator"/> |
147 <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance"/> | 150 <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance"/> |
148 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/> | 151 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/> |
149 <data format="html" label="${tool.name} on ${on_string}: modelsummary.qzv" name="omodelsummary"/> | 152 <data format="html" label="${tool.name} on ${on_string}: modelsummary.qzv" name="omodelsummary"/> |
150 <data format="html" label="${tool.name} on ${on_string}: accuracyresults.qzv" name="oaccuracyresults"/> | 153 <data format="html" label="${tool.name} on ${on_string}: accuracyresults.qzv" name="oaccuracyresults"/> |
211 model_summary : Visualization | 214 model_summary : Visualization |
212 Summarized parameter and (if enabled) feature selection information for | 215 Summarized parameter and (if enabled) feature selection information for |
213 the trained estimator. | 216 the trained estimator. |
214 accuracy_results : Visualization | 217 accuracy_results : Visualization |
215 Accuracy results visualization. | 218 Accuracy results visualization. |
219 probabilities : SampleData[Probabilities] | |
220 Predicted class probabilities for each input sample. | |
216 ]]></help> | 221 ]]></help> |
217 <macros> | 222 <macros> |
218 <import>qiime_citation.xml</import> | 223 <import>qiime_citation.xml</import> |
219 </macros> | 224 </macros> |
220 <expand macro="qiime_citation"/> | 225 <expand macro="qiime_citation"/> |