Mercurial > repos > bebatut > compute_wilcoxon_test

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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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2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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1 <tool id="compute_wilcoxon_test" name="Compute Wilcoxon test" version="0.1.0">
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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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>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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6 <requirement type="package" version="1.20.0">r-getopt</requirement>
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7 </requirements>
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2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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9 <stdio>
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10 <exit_code range="1:" />
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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11 <exit_code range=":-1" />
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12 </stdio>
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2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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14 <version_command></version_command>
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2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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16 <command><![CDATA[
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17 Rscript $__tool_directory__/compute_wilcoxon_test.R
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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18 --input_file $input_file
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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19 --header $header
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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20 --output_file $output_file
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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21 --column1_id $column1_id
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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23 #if $add_column.add_column_test == "true":
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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24 --column2_id $add_column.column2_id
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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25 --paired $add_column.paired
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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26 #end if
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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27
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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28 --alternative "$alternative"
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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29 --mu $mu
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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30
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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31 --exact $exact
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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32 --correct $correct
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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33
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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34 ]]></command>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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36 <inputs>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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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)"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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38
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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39 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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40
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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41 <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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42
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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43 <conditional name="add_column">
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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44 <param name="add_column_test" label="Add a new column?" type="select" help="(--alternative)">
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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45 <option value="true" selected="true">Yes</option>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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46 <option value="false">No</option>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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47 </param>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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48 <when value="true">
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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49 <param name="column2_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column2_id)"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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50 <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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51 </when>
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52 <when value="false" />
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53 </conditional>
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54
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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55 <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)">
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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56 <option value="two.sided" selected="true">Two sided</option>
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57 <option value="greater">Greater</option>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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58 <option value="less">Less</option>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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59 </param>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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60 <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/>
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61
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62 <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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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)"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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64 </inputs>
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65
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66 <outputs>
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67 <data name="output_file" format="txt" label="${tool.name} on ${on_string}: Wilcox test result" />
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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68 </outputs>
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69
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70 <tests>
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71 <test>
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72 <param name="input_file" ftype="tabular" value="input_file.txt"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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73 <param name="header" value="TRUE"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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74 <param name="column1_id" value="3"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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75 <param name="add_column_test" value="true"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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76 <param name="column2_id" value="5"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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77 <param name="paired" value="FALSE"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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78 <param name="alternative" value="two.sided"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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79 <param name="mu" value="0"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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80 <param name="exact" value="FALSE"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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81 <param name="correct" value="TRUE"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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82 <output name="output_file" file="two_sided_two_columns_test_output.txt"/>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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83 </test>
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84 </tests>
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85
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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86 <help><![CDATA[
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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87 **What it does**
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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88
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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89 This tool compute a Wilcoxon test with R's wilcox.test function.
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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90 ]]></help>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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91
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92 <citations>
2a8acb4c0afc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
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93 </citations>
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94 </tool>