Galaxy | Pasteur | Published Workflow | Evo-Scope

Evo-Scope

Annotation:

Step	Annotation
Step 1: Input dataset tree select at runtime
Step 2: Input dataset tab select at runtime
Step 3: PastML Input tree(s) Output dataset 'output' from step 1 Do you have an annotation file? Yes annotation file with the first row containing the column names. Output dataset 'output' from step 2 Select the annotation table columns that contain characters to be analysed. Unavailable. Select a prediction method JOINT Add JOINT state? False
Step 4: Annotate pastml tree Input Newick tree Output dataset 'out_nhx' from step 3 PastML tabular output file Output dataset 'out_data' from step 3
Step 5: Epics p-value threshold for pairs 0.05 Matrix choice genealogically ordered pairs only will be computed (S matrix) (-S) Set outgroup Empty. Annotated phylogenetic tree Output dataset 'tree_ouput' from step 4 Output also monomorphic event sites? False Output also p-value of 0 inseparable/genealogically ordered pairs? False Use an event names file? False Set a first event id to be tested? False Set a second event id to be tested? False
Step 6: Epocs Annotated phylogenetic tree Output dataset 'tree_ouput' from step 4 Epics output file (optional) Output dataset 'output_mat' from step 5 Use an input events file? False Set a first event id to be tested? False Set a second event id to be tested? False Select a scenario mu1, mu2 (H0) (-Si) Set outgroup Empty. Maximum number of co-occurrences to consider in the analysis. 10 Evaluate the Initial State (otherwise, assume <0,0>)? False
Step 7: Epocs Annotated phylogenetic tree Output dataset 'tree_ouput' from step 4 Epics output file (optional) Output dataset 'output_mat' from step 5 Use an input events file? False Set a first event id to be tested? False Set a second event id to be tested? False Select a scenario mu1, mu2, mu2* (one-way induction: E1->E2) (-Sa) Set outgroup Empty. Maximum number of co-occurrences to consider in the analysis. 10 Evaluate the Initial State (otherwise, assume <0,0>)? False
Step 8: Epocs Annotated phylogenetic tree Output dataset 'tree_ouput' from step 4 Epics output file (optional) Output dataset 'output_mat' from step 5 Use an input events file? False Set a first event id to be tested? False Set a second event id to be tested? False Select a scenario mu1, mu1*, mu2 (one-way induction: E2->E1) (-Sb) Set outgroup Empty. Maximum number of co-occurrences to consider in the analysis. 10 Evaluate the Initial State (otherwise, assume <0,0>)? False
Step 9: Epocs Annotated phylogenetic tree Output dataset 'tree_ouput' from step 4 Epics output file (optional) Output dataset 'output_mat' from step 5 Use an input events file? False Set a first event id to be tested? False Set a second event id to be tested? False Select a scenario mu1, mu1, mu2, mu2 (induction both ways) (-Sl) Set outgroup Empty. Maximum number of co-occurrences to consider in the analysis. 10 Evaluate the Initial State (otherwise, assume <0,0>)? False
Step 10: Epocs output parser Parsing the result from epocs Parsing the result from epocs 1 Epocs output Output dataset 'output_mat' from step 6 Parsing the result from epocs 2 Epocs output Output dataset 'output_mat' from step 7 Parsing the result from epocs 3 Epocs output Output dataset 'output_mat' from step 8 Parsing the result from epocs 4 Epocs output Output dataset 'output_mat' from step 9 event names Output dataset 'eventID' from step 4

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maximeg

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