Mercurial > repos > laurenmarazzi > netisce_test
diff tools/myTools/9_class_and_consensus.xml @ 1:7e5c71b2e71f draft default tip
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author | laurenmarazzi |
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date | Wed, 22 Dec 2021 16:00:34 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/myTools/9_class_and_consensus.xml Wed Dec 22 16:00:34 2021 +0000 @@ -0,0 +1,45 @@ +<tool id="netisce9" name="Netisce step 9" version="0.1.0" python_template_version="3.5"> +<description>classifies perturbation attractors to k clusters with SVM, Naive Bayes and Random Forest + and then extracts the perturbation attractors that shifted to the cluster associated to the desired phenotype by to 2/3 classification methods.</description> + + <requirements> + <requirement type="package" version="1.1.5">pandas</requirement> + <requirement type="package" version="3.5.0">collections</requirement> + <requirement type="package" version="3.5.0">sys</requirement> + <requirement type="package" version="1.0.1">sklearn.naive_bayes</requirement> + <requirement type="package" version="1.0.1">sklearn.svm</requirement> + <requirement type="package" version="1.0.1">sklearn.ensemble</requirement> + </requirements> + + <command> python3 '$__tool_directory__/bin/class_and_consensus.py' '$experimental_attractors','$random_attractors' '$pert_attrs' '$kmeans' </command> + + <inputs> + <param name="experimental_attractors" type="data" format="tabular" label="Attractors Generated from Experimental Samples"/> + <param name="random_attractors" type="data" format="tabular" label="Attractors Generated from randomly generated initial states."/> + <param name="pert_attrs" type="data" format="tabular" label="Attractors when FVS set is randomly perturbed"/> + <param name="kmeans" type="data" format="txt" label="K-means clustering of experimental and insilico attractors"/> + </inputs> + + <outputs> + <data name="output" format="txt" from_work_dir="crit1perts.txt" label="Names of perturbations whose attractors shifted to a the cluster associated with the desired phenotype"/> + </outputs> + + <tests> + <test> + <param name="train_attrs" value="attrs_exp.tsv,attrs_insilico.tsv"/> + <param name="test_attrs" value="pert_logss.tsv"/> + <param name="kmeans" value="kmeans.txt"/> + <output name="output" value="crit1perts.txt" ftype="txt"/> + </test> + </tests> + + <help> + Classifies perturbation attractors to k clusters with SVM, Naive Bayes and Random Forest + and then extracts the perturbation attractors that shifted to the cluster associated to the desired phenotype by to 2/3 classification methods. + Required Inputs: + 1. Training Set: Experimental and Insilico Attractors + 2. Test Set: Perturbation Attractors + 3. K-mean classifications of training set attractors + </help> + +</tool> \ No newline at end of file