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WIP: Correlation work #511

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WIP: Correlation work #511

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af55803
style fixes
bgruening Aug 21, 2018
0ea2a6f
output is tabular
bgruening Aug 21, 2018
ec04770
remove tool dependencies
bgruening Aug 21, 2018
83c513f
corelation
bgruening Oct 25, 2018
d1d8fb2
rpy2 migration, demonstrate the column parameter feature request
bgruening Oct 25, 2018
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style fixes
@bgruening
bgruening committed Oct 25, 2018
commit af55803a56d6bd3575085e77b21ba85d3ea13a12
64 changes: 33 additions & 31 deletions tools/correlation/cor.xml
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Original file line number Diff line number Diff line change
@@ -1,33 +1,35 @@
<tool id="cor2" name="Correlation" version="1.0.0">
<description>for numeric columns</description>
<requirements>
<requirement type="package" version="1.0.3">rpy</requirement>
</requirements>
<command interpreter="python">cor.py $input1 $out_file1 $numeric_columns $method</command>
<inputs>
<param format="tabular" name="input1" type="data" label="Dataset" help="Dataset missing? See TIP below"/>
<param name="numeric_columns" label="Numerical columns" type="data_column" numerical="True" multiple="True" data_ref="input1" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
<param name="method" type="select" label="Method">
<option value="pearson">Pearson</option>
<option value="kendall">Kendall rank</option>
<option value="spearman">Spearman rank</option>
</param>
</inputs>
<outputs>
<data format="txt" name="out_file1" />
</outputs>
<tests>
<!--
Test a tabular input with the first line being a comment without a # character to start
-->
<test>
<param name="input1" value="cor.tabular" />
<param name="numeric_columns" value="2,3" />
<param name="method" value="pearson" />
<output name="out_file1" file="cor_out.txt" />
</test>
</tests>
<help>
<tool id="cor2" name="Correlation" version="1.0.1">
<description>for numeric columns</description>
<requirements>
<requirement type="package" version="1.0.3">rpy</requirement>
</requirements>
<command>
cor.py '$input1' '$out_file1' $numeric_columns $method
</command>
<inputs>
<param format="tabular" name="input1" type="data" label="Dataset" help="Dataset missing? See TIP below"/>
<param name="numeric_columns" label="Numerical columns" type="data_column" numerical="True" multiple="True" data_ref="input1" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
<param name="method" type="select" label="Method">
<option value="pearson">Pearson</option>
<option value="kendall">Kendall rank</option>
<option value="spearman">Spearman rank</option>
</param>
</inputs>
<outputs>
<data format="txt" name="out_file1" />
</outputs>
<tests>
<!--
Test a tabular input with the first line being a comment without a # character to start
-->
<test>
<param name="input1" value="cor.tabular" />
<param name="numeric_columns" value="2,3" />
<param name="method" value="pearson" />
<output name="out_file1" file="cor_out.txt" />
</test>
</tests>
<help>

.. class:: infomark

@@ -97,5 +99,5 @@ This tool computes the matrix of correlation coefficients between numeric column
0.730635686279 1.0

So the correlation for our twenty cases is .73, which is a fairly strong positive relationship.
</help>
</help>
</tool>