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1 <tool id="secimtools_ttest" name="T-Test (Paired or Unpaired)" version="@WRAPPER_VERSION@">
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2 <description>on features.</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.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 --group $group
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13 --pairing $pairing
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14 --summaries $summaries
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15 --flags $flags
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16 --volcano $volcano
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17 #if $order
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18 --order $order
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
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23 <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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24 <param name="uniqueID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
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25 <param name="group" type="text" size="30" label="Group/Treatment" help="Name of the column in your Design File that contains group classifications."/>
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26 <param name="pairing" size="30" display="radio" type="select" value="unpaired" label="Select Test" help="Select either paired (dependent samples) or unpaired (independent samples) tests.">
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27 <option value="unpaired" selected="true">Unpaired (Independent Samples)</option>
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28 <option value="paired" selected="true">Paired (Dependent Samples)</option>
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29 </param>
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30 <param name="order" type="text" value="" size="30" label="Pairing ID" help="Name of the column in your Design File that contains Pairing IDs. Ignored for Unpaired (Independent Samples) test."/>
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31 </inputs>
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32 <outputs>
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33 <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/>
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34 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01, 0.05 and 0.10 significance levels for the differences. "/>
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35 <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" value="ST000006_data.tsv"/>
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40 <param name="design" value="ST000006_design.tsv"/>
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41 <param name="uniqueID" value="Retention_Index" />
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42 <param name="group" value="White_wine_type_and_source" />
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43 <param name="pairing" value="unpaired" />
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44 <output name="summaries" file="ST000006_ttest_select_unpaired_summary.tsv" />
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45 <output name="flags" file="ST000006_ttest_select_unpaired_flags.tsv" />
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46 <output name="volcano" file="ST000006_ttest_select_unpaired_volcano.pdf" compare="sim_size" delta="10000"/>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50
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51 @TIP_AND_WARNING@
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52
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53 **Tool Description**
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54
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55 The tool performs a two-sided t-test for two groups of dependent samples (paired or dependent t-test) or multiple (two or more) groups of independent samples (unpaired or independent t-test).
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56 The user selects which test (paired or unpaired) to perform.
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57
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58 In an unpaired t-test, the samples within and between groups are independent.
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59 The test is performed for all pairs of conditions specified using the Group/Treatment field.
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60 For example, if there are three treatment conditions (Control, Time1 and Time2) then t-tests will be performed for: (i) Control vs Time1, (ii) Control vs Time2, and (iii) Time1 vs Time2.
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61 Note that this will give slightly different results than the contrast in an ANOVA because the ANOVA uses all groups to estimate the error.
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62
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63 A paired t-test can be performed for pairs of treatment conditions where sample pairs are known and specified by the user in the Pairing ID field.
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64 Here, the difference between the measurements for the pairs is calculated.
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65 To ensure that the differences are taken in the same order across all pairs, the Group/Treatment variable is required.
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66 The differences will be calculated beween the groups in the order that the groups appear in the Design File.
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67 The Pairing ID specifies which samples are paired. A two sided t-test will be performed for the test that the difference is zero.
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68
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69 --------------------------------------------------------------------------------
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70
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71 **Input**
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72
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73 - Two input datasets are required.
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74
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75
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76 @WIDE@
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77
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78 **NOTE:** The sample IDs must match the sample IDs in the Design File
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79 (below). Extra columns will automatically be ignored.
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80
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81 @METADATA@
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82
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83 @UNIQID@
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84
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85 **Group/Treatment**
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86
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87 - List with the name of the column the Design File that contains group classifications.
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88
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89 **Pairing ID**
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90
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91 - Name of the column in your Design File that contains Pairing IDs. An example is given below:
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92
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93 +----------+--------+--------+
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94 | sampleID | group | pairID |
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95 +==========+========+========+
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96 | sample1 | g1 | p1 |
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97 +----------+--------+--------+
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98 | sample2 | g1 | p2 |
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99 +----------+--------+--------+
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100 | sample3 | g1 | p3 |
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101 +----------+--------+--------+
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102 | sample4 | g2 | p1 |
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103 +----------+--------+--------+
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104 | sample5 | g2 | p2 |
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105 +----------+--------+--------+
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106 | sample6 | g2 | p3 |
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107 +----------+--------+--------+
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108 | ... | ... | ... |
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109 +----------+--------+--------+
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110
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111
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112
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113 --------------------------------------------------------------------------------
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114
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115 **Output**
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116
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117 The tool outputs 3 files:
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118
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119 (1) a TSV file with the results table containing p-values for each test and the corresponding differences between the means for comparisons between the groups.
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120 (2) a TSV file with an indicator flag = 1 if the difference between the groups is statistically significant using provided α levels.
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121 (3) a PDF file with volcano plots visual inspection of the differences between group means and p-values. The red dashed line in volcano plot(s) corresponds to a p-value = 0.01 cutoff (2 on the negative log base 10 scale).
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122
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123 ]]></help>
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124 <expand macro="citations"/>
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125 </tool>
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