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comparison compute_wilcoxon_test.xml @ 0:bba4cafe21a8 draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author bebatut
date Tue, 12 Apr 2016 02:56:51 -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">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 --output_file $output_file
20 --column1_id $column1_id
21
22 #if $add_data.test == 'true':
23 --column2_id $add_data.column2_id
24 --paired $add_data.paired
25 #end if
26
27 --alternative "$alternative"
28 --mu $mu
29
30 --exact $exact
31 --correct $correct
32
33 ]]></command>
34
35 <inputs>
36 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
37
38 <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/>
39
40 <conditional name="add_data">
41 <param name="test" label="Add a new column?" type="select" help="(--alternative)">
42 <option value="true" selected="True">Yes</option>
43 <option value="false">No</option>
44 </param>
45 <when value="true">
46 <param name="column2_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column2_id)"/>
47 <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/>
48 </when>
49 <when value="false" />
50 </conditional>
51
52 <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)">
53 <option value="two.sided" selected="True">Two sided</option>
54 <option value="greater">Greater</option>
55 <option value="less">Less</option>
56 </param>
57 <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/>
58
59 <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/>
60 <param name="correct" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Apply a continuity correction in the normal approximation for the p-value?" checked="true" help="(--correct)"/>
61 </inputs>
62
63 <outputs>
64 <data name="output_file" format="text"
65 label="${tool.name} on ${on_string}: Wilcox test result" />
66 </outputs>
67
68 <tests>
69 <param name="input_file" value="input_file.txt" />
70 <param name="column1_id" value="2" />
71 <param name="test" value="true" />
72 <param name="column2_id" value="3" />
73 <param name="paired" value="TRUE" />
74 <param name="alternative" value="two.sided" />
75 <param name="mu" value="0" />
76 <param name="exact" value="FALSE" />
77 <param name="correct" value="TRUE"/>
78 <output name="output_file" value="output_file.txt" />
79 </tests>
80
81 <help><![CDATA[
82 **What it does**
83
84 This tool compute a Wilcoxon test with R's wilcox.test function.
85
86 ]]></help>
87
88 <citations>
89 </citations>
90 </tool>