Mercurial > repos > bebatut > compute_wilcoxon_test

annotate 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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bba4cafe21a8 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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1 <tool id="compute_wilcoxon_test" name="Compute Wilcoxon test" version="0.1.0">
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2 <description>with R</description>
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4 <requirements>
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5 <requirement type="package" version="3.2.1">R</requirement>
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6 <requirement type="package" version="1.20.0">getopt</requirement>
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7 </requirements>
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8
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 </stdio>
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14 <version_command></version_command>
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16 <command><![CDATA[
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17 Rscript $__tool_directory__/compute_wilcoxon_test.R
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18 --input_file $input_file
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19 --output_file $output_file
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20 --column1_id $column1_id
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21
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22 #if $add_data.test == 'true':
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23 --column2_id $add_data.column2_id
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24 --paired $add_data.paired
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25 #end if
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26
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27 --alternative "$alternative"
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28 --mu $mu
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29
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30 --exact $exact
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31 --correct $correct
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32
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33 ]]></command>
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34
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35 <inputs>
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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)"/>
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37
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38 <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/>
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39
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40 <conditional name="add_data">
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41 <param name="test" label="Add a new column?" type="select" help="(--alternative)">
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42 <option value="true" selected="True">Yes</option>
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43 <option value="false">No</option>
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44 </param>
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45 <when value="true">
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46 <param name="column2_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column2_id)"/>
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47 <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/>
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48 </when>
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49 <when value="false" />
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50 </conditional>
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51
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52 <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)">
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53 <option value="two.sided" selected="True">Two sided</option>
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54 <option value="greater">Greater</option>
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55 <option value="less">Less</option>
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56 </param>
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57 <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/>
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58
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59 <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/>
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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)"/>
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61 </inputs>
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62
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63 <outputs>
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64 <data name="output_file" format="text"
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65 label="${tool.name} on ${on_string}: Wilcox test result" />
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66 </outputs>
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67
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68 <tests>
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69 <param name="input_file" value="input_file.txt" />
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70 <param name="column1_id" value="2" />
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71 <param name="test" value="true" />
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72 <param name="column2_id" value="3" />
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73 <param name="paired" value="TRUE" />
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74 <param name="alternative" value="two.sided" />
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75 <param name="mu" value="0" />
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76 <param name="exact" value="FALSE" />
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77 <param name="correct" value="TRUE"/>
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78 <output name="output_file" value="output_file.txt" />
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79 </tests>
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80
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81 <help><![CDATA[
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82 **What it does**
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83
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84 This tool compute a Wilcoxon test with R's wilcox.test function.
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85
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86 ]]></help>
bba4cafe21a8 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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88 <citations>
bba4cafe21a8 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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89 </citations>
bba4cafe21a8 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
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90 </tool>