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annotate ttest_single_group.xml @ 1:2e7d47c0b027 draft

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"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author malex
date Mon, 08 Mar 2021 22:04:06 +0000
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2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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1 <tool id="secimtools_ttest_single_group" name="T-Test (Single Group)" version="@WRAPPER_VERSION@">
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2 <description>for the specified mean.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 ttest_single_group.py
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9 --input $input
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10 --design $design
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11 --uniqueID $uniqueID
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12 --mu $mu
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13 --summaries $summaries
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14 --flags $flags
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15 --volcano $volcano
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16 #if $group
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17 --group $group
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18 #end if
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19 ]]></command>
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20 <inputs>
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21 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
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22 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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23 <param name="uniqueID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
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24 <param name="mu" type="text" size="30" value = "0" label="Mu" help="The value of the mean under the null hypothesis. Default = 0. "/>
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25 <param name="group" type="text" size="30" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications."/>
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26 </inputs>
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27 <outputs>
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28 <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/>
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29 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01, 0.05 and 0.10 significance levels for the differences. "/>
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30 <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input" value="ST000006_data.tsv"/>
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35 <param name="design" value="ST000006_design.tsv"/>
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36 <param name="uniqueID" value="Retention_Index" />
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37 <param name="mu" value="0" />
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38 <output name="summaries" file="ST000006_ttest_single_group_no_group_summary.tsv" />
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39 <output name="flags" file="ST000006_ttest_single_group_no_group_flags.tsv" />
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40 <output name="volcano" file="ST000006_ttest_single_group_no_group_volcano.pdf" compare="sim_size" delta="10000"/>
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41 </test>
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42 <test>
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43 <param name="input" value="ST000006_data.tsv"/>
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44 <param name="design" value="ST000006_design.tsv"/>
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45 <param name="uniqueID" value="Retention_Index" />
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46 <param name="mu" value="0" />
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47 <param name="group" value="White_wine_type_and_source" />
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48 <output name="summaries" file="ST000006_ttest_single_group_with_group_summary.tsv" />
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49 <output name="flags" file="ST000006_ttest_single_group_with_group_flags.tsv" />
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50 <output name="volcano" file="ST000006_ttest_single_group_with_group_volcano.pdf" compare="sim_size" delta="10000"/>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54
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55 @TIP_AND_WARNING@
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56
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57 **Tool Description**
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58
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59 The tool performs a one sample t-test for each feature.
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60 Two options are available for the t-test: if the user provides the Group/Treatment variable, then the mean for each treatment condition is compared with Mu, the user-specified value of the true mean under the null hypothesis.
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61 If Group/Treatment is not provided, then the mean across all samples is compared to Mu.
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62
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63 --------------------------------------------------------------------------------
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64
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65 **Input**
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66
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67 - Two input datasets are required.
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68
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69
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70 @WIDE@
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71
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72 **NOTE:** The sample IDs must match the sample IDs in the Design File
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73 (below). Extra columns will automatically be ignored.
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74
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75 @METADATA@
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76
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77 @UNIQID@
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78
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79 **Group/Treatment [Optional]**
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80
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81 - Name of the column the Design File that contains group classifications.
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82
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83 **Mu**
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84
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85 - The value of the mean under the null hypothesis. Default = 0.
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86
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87
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88 --------------------------------------------------------------------------------
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89
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90 **Output**
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91
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92 The tool produces three outputs:
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93
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94 (1) a TSV file with the results table containing p-values for each test and the corresponding differences between the group means and the mu value under the null.
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95 (2) a TSV file containing indicator flags equal to 1 if the difference between the groups and the mean under the null is statistically significant using the indicated α levels.
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96 (3) a PDF file with volcano plots for visual inspection of the differences between the group means and p-values. The red dashed line in the volcano plot(s) corresponds to a p-value = 0.01 cutoff (2 on the negative log base 10 scale).
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97
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98 ]]></help>
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99 <expand macro="citations"/>
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100 </tool>