Mercurial > repos > malex > secimtools
comparison multiple_testing_adjustment.xml @ 1:2e7d47c0b027 draft
"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author | malex |
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date | Mon, 08 Mar 2021 22:04:06 +0000 |
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0:b54326490b4d | 1:2e7d47c0b027 |
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1 <tool id="secimtools_multiple_testing_adjustment" name="Multiple Testing Adjustment (MTA)" version="@WRAPPER_VERSION@"> | |
2 <description>of p-values.</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command><![CDATA[ | |
8 multiple_testing_adjustment.py | |
9 --input $input | |
10 --uniqID $uniqID | |
11 --pval "$pval" | |
12 --alpha $alpha | |
13 --outadjusted $outadjusted | |
14 --flags $flags | |
15 ]]></command> | |
16 <inputs> | |
17 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/> | |
18 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique identifiers.."/> | |
19 <param name="pval" type="text" size="30" value="" label="p-value column" help="Name of the column in your wide dataset that contains the p-values."/> | |
20 <param name="alpha" type="float" size="6" value="0.05" label="α" help="Value of α to be used for multiple correction. Default α = 0.05."/> | |
21 </inputs> | |
22 <outputs> | |
23 <data format="tabular" name="outadjusted" label="${tool.name} on ${on_string}: Adjusted pval."/> | |
24 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags."/> | |
25 </outputs> | |
26 <tests> | |
27 <test> | |
28 <param name="input" value="ST000006_anova_fixed_with_group_summary.tsv"/> | |
29 <param name="uniqID" value="Retention_Index" /> | |
30 <param name="pval" value="prob_greater_than_t_for_diff_Chardonnay, Carneros, CA 2003 (CH01)-Chardonnay, Carneros, CA 2003 (CH02)" /> | |
31 <param name="alpha" value="0.05" /> | |
32 <output name="outadjusted" file="ST000006_multiple_testing_adjustment_outadjusted.tsv" /> | |
33 <output name="flags" file="ST000006_multiple_testing_adjustment_flags.tsv" /> | |
34 </test> | |
35 </tests> | |
36 <help><![CDATA[ | |
37 | |
38 @TIP_AND_WARNING@ | |
39 | |
40 **Tool Description** | |
41 | |
42 The tool is designed to adjust p-values for multiple comparisons using three different methods: | |
43 | |
44 (1) The Bonferroni method and two false discovery rate (FDR) methods, (2) the Benjamini-Hochberg method (BH) and (3) the Benjamini-Yekutieli method (BY). | |
45 The p-value correction can be carried out on p-values generated from the following tools: Analysis of Variance (ANOVA) Fixed Effects Model, Kruskal-Wallis Non-Parametric Test, T-test (Single Group) and T-test (Paired and/or Unpaired) in addition to p-values generated outside of these tools. | |
46 The user can specify the total type I error α value. | |
47 | |
48 More details about the PH and BY methods are available in the papers: | |
49 | |
50 Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the royal statistical society. Series B (Methodological), 289-300. | |
51 | |
52 Benjamini, Y., and Yekutieli, D. (2001). The control of the false discovery rate in multiple testing under dependency. Annals of statistics, 1165-1188. | |
53 | |
54 ------------------------------------------------------------------------------------------- | |
55 | |
56 **Input** | |
57 | |
58 - Two input datasets are required. | |
59 | |
60 @WIDE@ | |
61 | |
62 @UNIQID@ | |
63 | |
64 **Name for p-value column** | |
65 | |
66 - Name of the column in your Wide Dataset that contains the p-values. | |
67 | |
68 **α** | |
69 | |
70 - Value of α to be used for multiple correction. Default α = 0.05. | |
71 | |
72 ------------------------------------------------------------------------------------------- | |
73 | |
74 **Output** | |
75 | |
76 The tool produces two TSV files: | |
77 | |
78 (1) One TSV that contains the following five columns: | |
79 a column with unique feature IDs, | |
80 a column of the original p-values and | |
81 the last three columns contain the p-values adjusted using the 3 methods described above which are reflected in the column name. | |
82 (2) The second TSV file contains flags where all significant values are flagged as 1 and non-significant values are flagged as 0. | |
83 | |
84 ]]></help> | |
85 <expand macro="citations"/> | |
86 </tool> |