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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
author bebatut
date Thu, 21 Apr 2016 04:21:13 -0400
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1 <tool id="compute_wilcoxon_test" name="Compute Wilcoxon test" version="0.1.0">
2 <description>with R</description>
3
4 <requirements>
5 <requirement type="package" version="3.2.1">R</requirement>
6 <requirement type="package" version="1.20.0">r-getopt</requirement>
7 </requirements>
8
9 <stdio>
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 </stdio>
13
14 <version_command></version_command>
15
16 <command><![CDATA[
17 Rscript $__tool_directory__/compute_wilcoxon_test.R
18 --input_file $input_file
19 --header $header
20 --output_file $output_file
21 --column1_id $column1_id
22
23 #if $add_column.add_column_test == "true":
24 --column2_id $add_column.column2_id
25 --paired $add_column.paired
26 #end if
27
28 --alternative "$alternative"
29 --mu $mu
30
31 --exact $exact
32 --correct $correct
33
34 ]]></command>
35
36 <inputs>
37 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
38
39 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
40
41 <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/>
42
43 <conditional name="add_column">
44 <param name="add_column_test" label="Add a new column?" type="select" help="(--alternative)">
45 <option value="true" selected="true">Yes</option>
46 <option value="false">No</option>
47 </param>
48 <when value="true">
49 <param name="column2_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column2_id)"/>
50 <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/>
51 </when>
52 <when value="false" />
53 </conditional>
54
55 <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)">
56 <option value="two.sided" selected="true">Two sided</option>
57 <option value="greater">Greater</option>
58 <option value="less">Less</option>
59 </param>
60 <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/>
61
62 <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/>
63 <param name="correct" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Apply a continuity correction in the normal approximation for the p-value?" checked="true" help="(--correct)"/>
64 </inputs>
65
66 <outputs>
67 <data name="output_file" format="txt" label="${tool.name} on ${on_string}: Wilcox test result" />
68 </outputs>
69
70 <tests>
71 <test>
72 <param name="input_file" ftype="tabular" value="input_file.txt"/>
73 <param name="header" value="TRUE"/>
74 <param name="column1_id" value="3"/>
75 <param name="add_column_test" value="true"/>
76 <param name="column2_id" value="5"/>
77 <param name="paired" value="FALSE"/>
78 <param name="alternative" value="two.sided"/>
79 <param name="mu" value="0"/>
80 <param name="exact" value="FALSE"/>
81 <param name="correct" value="TRUE"/>
82 <output name="output_file" file="two_sided_two_columns_test_output.txt"/>
83 </test>
84 </tests>
85
86 <help><![CDATA[
87 **What it does**
88
89 This tool compute a Wilcoxon test with R's wilcox.test function.
90 ]]></help>
91
92 <citations>
93 </citations>
94 </tool>