Mercurial > repos > bebatut > compute_wilcoxon_test

comparison compute_wilcoxon_test.xml @ 2:309fac5c91d8 draft default tip

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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 04:20:40 -0400
parents ff9e8750bb26
children
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1:ff9e8750bb26 2:309fac5c91d8
14 <version_command></version_command> 14 <version_command></version_command>
15 15
16 <command><![CDATA[ 16 <command><![CDATA[
17 Rscript $__tool_directory__/compute_wilcoxon_test.R 17 Rscript $__tool_directory__/compute_wilcoxon_test.R
18 --input_file $input_file 18 --input_file $input_file
19 --header $header
19 --output_file $output_file 20 --output_file $output_file
20 --column1_id $column1_id 21 --column1_id $column1_id
21 22
22 #if $add_data.test == 'true': 23 #if $add_column.add_column_test == "true":
23 --column2_id $add_data.column2_id 24 --column2_id $add_column.column2_id
24 --paired $add_data.paired 25 --paired $add_column.paired
25 #end if 26 #end if
26 27
27 --alternative "$alternative" 28 --alternative "$alternative"
28 --mu $mu 29 --mu $mu
29 30
33 ]]></command> 34 ]]></command>
34 35
35 <inputs> 36 <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 <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
39 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
40
38 <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/> 41 <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/>
39 42
40 <conditional name="add_data"> 43 <conditional name="add_column">
41 <param name="test" label="Add a new column?" type="select" help="(--alternative)"> 44 <param name="add_column_test" label="Add a new column?" type="select" help="(--alternative)">
42 <option value="true" selected="True">Yes</option> 45 <option value="true" selected="true">Yes</option>
43 <option value="false">No</option> 46 <option value="false">No</option>
44 </param> 47 </param>
45 <when value="true"> 48 <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)"/> 49 <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)"/> 50 <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/>
48 </when> 51 </when>
49 <when value="false" /> 52 <when value="false" />
50 </conditional> 53 </conditional>
51 54
52 <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)"> 55 <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)">
53 <option value="two.sided" selected="True">Two sided</option> 56 <option value="two.sided" selected="true">Two sided</option>
54 <option value="greater">Greater</option> 57 <option value="greater">Greater</option>
55 <option value="less">Less</option> 58 <option value="less">Less</option>
56 </param> 59 </param>
57 <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/> 60 <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/>
58 61
59 <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/> 62 <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)"/> 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)"/>
61 </inputs> 64 </inputs>
62 65
63 <outputs> 66 <outputs>
64 <data name="output_file" format="text" 67 <data name="output_file" format="txt" label="${tool.name} on ${on_string}: Wilcox test result" />
65 label="${tool.name} on ${on_string}: Wilcox test result" />
66 </outputs> 68 </outputs>
67 69
68 <tests> 70 <tests>
69 <param name="input_file" value="input_file.txt" /> 71 <test>
70 <param name="column1_id" value="2" /> 72 <param name="input_file" ftype="tabular" value="input_file.txt"/>
71 <param name="test" value="true" /> 73 <param name="header" value="TRUE"/>
72 <param name="column2_id" value="3" /> 74 <param name="column1_id" value="3"/>
73 <param name="paired" value="TRUE" /> 75 <param name="add_column_test" value="true"/>
74 <param name="alternative" value="two.sided" /> 76 <param name="column2_id" value="5"/>
75 <param name="mu" value="0" /> 77 <param name="paired" value="FALSE"/>
76 <param name="exact" value="FALSE" /> 78 <param name="alternative" value="two.sided"/>
77 <param name="correct" value="TRUE"/> 79 <param name="mu" value="0"/>
78 <output name="output_file" value="output_file.txt" /> 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>
79 </tests> 84 </tests>
80 85
81 <help><![CDATA[ 86 <help><![CDATA[
82 **What it does** 87 **What it does**
83 88
84 This tool compute a Wilcoxon test with R's wilcox.test function. 89 This tool compute a Wilcoxon test with R's wilcox.test function.
85
86 ]]></help> 90 ]]></help>
87 91
88 <citations> 92 <citations>
89 </citations> 93 </citations>
90 </tool> 94 </tool>