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comparison 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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0:b54326490b4d 1:2e7d47c0b027
1 <tool id="secimtools_ttest_single_group" name="T-Test (Single Group)" version="@WRAPPER_VERSION@">
2 <description>for the specified mean.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 ttest_single_group.py
9 --input $input
10 --design $design
11 --uniqueID $uniqueID
12 --mu $mu
13 --summaries $summaries
14 --flags $flags
15 --volcano $volcano
16 #if $group
17 --group $group
18 #end if
19 ]]></command>
20 <inputs>
21 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
22 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
23 <param name="uniqueID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
24 <param name="mu" type="text" size="30" value = "0" label="Mu" help="The value of the mean under the null hypothesis. Default = 0. "/>
25 <param name="group" type="text" size="30" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications."/>
26 </inputs>
27 <outputs>
28 <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/>
29 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01, 0.05 and 0.10 significance levels for the differences. "/>
30 <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/>
31 </outputs>
32 <tests>
33 <test>
34 <param name="input" value="ST000006_data.tsv"/>
35 <param name="design" value="ST000006_design.tsv"/>
36 <param name="uniqueID" value="Retention_Index" />
37 <param name="mu" value="0" />
38 <output name="summaries" file="ST000006_ttest_single_group_no_group_summary.tsv" />
39 <output name="flags" file="ST000006_ttest_single_group_no_group_flags.tsv" />
40 <output name="volcano" file="ST000006_ttest_single_group_no_group_volcano.pdf" compare="sim_size" delta="10000"/>
41 </test>
42 <test>
43 <param name="input" value="ST000006_data.tsv"/>
44 <param name="design" value="ST000006_design.tsv"/>
45 <param name="uniqueID" value="Retention_Index" />
46 <param name="mu" value="0" />
47 <param name="group" value="White_wine_type_and_source" />
48 <output name="summaries" file="ST000006_ttest_single_group_with_group_summary.tsv" />
49 <output name="flags" file="ST000006_ttest_single_group_with_group_flags.tsv" />
50 <output name="volcano" file="ST000006_ttest_single_group_with_group_volcano.pdf" compare="sim_size" delta="10000"/>
51 </test>
52 </tests>
53 <help><![CDATA[
54
55 @TIP_AND_WARNING@
56
57 **Tool Description**
58
59 The tool performs a one sample t-test for each feature.
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.
61 If Group/Treatment is not provided, then the mean across all samples is compared to Mu.
62
63 --------------------------------------------------------------------------------
64
65 **Input**
66
67 - Two input datasets are required.
68
69
70 @WIDE@
71
72 **NOTE:** The sample IDs must match the sample IDs in the Design File
73 (below). Extra columns will automatically be ignored.
74
75 @METADATA@
76
77 @UNIQID@
78
79 **Group/Treatment [Optional]**
80
81 - Name of the column the Design File that contains group classifications.
82
83 **Mu**
84
85 - The value of the mean under the null hypothesis. Default = 0.
86
87
88 --------------------------------------------------------------------------------
89
90 **Output**
91
92 The tool produces three outputs:
93
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.
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.
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).
97
98 ]]></help>
99 <expand macro="citations"/>
100 </tool>