mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
67 lines
2.4 KiB
XML
67 lines
2.4 KiB
XML
<tool id="BestSubsetsRegression1" name="Perform Best-subsets Regression">
|
|
<description> </description>
|
|
<command interpreter="python">
|
|
best_regression_subsets.py
|
|
$input1
|
|
$response_col
|
|
$predictor_cols
|
|
$out_file1
|
|
$out_file2
|
|
1>/dev/null
|
|
2>/dev/null
|
|
</command>
|
|
<inputs>
|
|
<param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
|
|
<param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" />
|
|
<param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true" >
|
|
<validator type="no_options" message="Please select at least one column."/>
|
|
</param>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="input" name="out_file1" metadata_source="input1" />
|
|
<data format="pdf" name="out_file2" />
|
|
</outputs>
|
|
<requirements>
|
|
<requirement type="python-module">rpy</requirement>
|
|
</requirements>
|
|
<tests>
|
|
<!-- Testing this tool will not be possible because this tool produces a pdf output file.
|
|
-->
|
|
</tests>
|
|
<help>
|
|
|
|
.. class:: infomark
|
|
|
|
**TIP:** If your data is not TAB delimited, use *Edit Queries->Convert characters*
|
|
|
|
-----
|
|
|
|
.. class:: infomark
|
|
|
|
**What it does**
|
|
|
|
This tool uses the 'regsubsets' function from R statistical package for regression subset selection. It outputs two files, one containing a table with the best subsets and the corresponding summary statistics, and the other containing the graphical representation of the results.
|
|
|
|
-----
|
|
|
|
.. class:: warningmark
|
|
|
|
**Note**
|
|
|
|
- This tool currently treats all predictor and response variables as continuous variables.
|
|
|
|
- Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis.
|
|
|
|
- The 6 columns in the output are described below:
|
|
|
|
- Column 1 (Vars): denotes the number of variables in the model
|
|
- Column 2 ([c2 c3 c4...]): represents a list of the user-selected predictor variables (full model). An asterix denotes the presence of the corresponding predictor variable in the selected model.
|
|
- Column 3 (R-sq): the fraction of variance explained by the model
|
|
- Column 4 (Adj. R-sq): the above R-squared statistic adjusted, penalizing for higher number of predictors (p)
|
|
- Column 5 (Cp): Mallow's Cp statistics
|
|
- Column 6 (bic): Bayesian Information Criterion.
|
|
|
|
|
|
</help>
|
|
</tool>
|