Mercurial > repos > malex > secimtools
comparison ttest_perm.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 |
parents | |
children | caba07f41453 |
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0:b54326490b4d | 1:2e7d47c0b027 |
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1 <tool id="secimtools_ttest_perm" name="Group Comparison by Permutation" version="@WRAPPER_VERSION@"> | |
2 <description>on features.</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 ttest_perm.py | |
9 --input $input | |
10 --design $design | |
11 --uniqueID $uniqueID | |
12 --group $group | |
13 --reps $reps | |
14 --summaries $summaries | |
15 --flags $flags | |
16 --volcano $volcano | |
17 </command> | |
18 <inputs> | |
19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/> | |
20 <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/> | |
21 <param name="uniqueID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/> | |
22 <param name="group" type="text" size="30" label="Group/Treatment" help="Name of the column in your Design File that contains group classifications."/> | |
23 <param name="reps" type="text" size="30" value="" label ="Iteration Number." help="Enter the number of iterations you want to carry out."/> | |
24 </inputs> | |
25 <outputs> | |
26 <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/> | |
27 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01, 0.05 and 0.10 significance levels for the differences. "/> | |
28 <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/> | |
29 </outputs> | |
30 <tests> | |
31 <test> | |
32 <param name="input" value="fly_test_sbys.tsv"/> | |
33 <param name="design" value="fly_test_design.tsv"/> | |
34 <param name="uniqueID" value="rowID" /> | |
35 <param name="group" value="mating_source" /> | |
36 <param name="reps" value="1000" /> | |
37 <output name="summaries" file="fly_ttest_permuted_summary.tsv" /> | |
38 <output name="flags" file="fly_ttest_permuted_flags.tsv" /> | |
39 <output name="volcano" file="fly_ttest_permuted_volcano.pdf" compare="sim_size" delta="10000"/> | |
40 </test> | |
41 </tests> | |
42 <help><![CDATA[ | |
43 | |
44 @TIP_AND_WARNING@ | |
45 | |
46 **Tool Description** | |
47 | |
48 The tool performs a permuted two-sided t-test for multiple (two or more) groups of independent sample (unpaired or independent t-test). | |
49 The user selects the number of iterations to perform. | |
50 | |
51 In an unpaired t-test the samples within and between groups are independent. The p-value is calculated by permutation of the data. | |
52 The permutation test is performed for all pairs of conditions specified using the Group/Treatment field and for the number of specified iterations. | |
53 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. | |
54 Note that this will give slightly different results than the contrast in an ANOVA because the ANOVA uses all groups to estimate the error. | |
55 | |
56 -------------------------------------------------------------------------------- | |
57 | |
58 **Input** | |
59 | |
60 - Two input datasets are required. | |
61 | |
62 | |
63 @WIDE@ | |
64 | |
65 **NOTE:** The sample IDs must match the sample IDs in the Design File | |
66 (below). Extra columns will automatically be ignored. | |
67 | |
68 @METADATA@ | |
69 | |
70 @UNIQID@ | |
71 | |
72 **Group/Treatment** | |
73 | |
74 - List with the name of the column the Design File that contains group classifications. | |
75 | |
76 ** Reps** | |
77 | |
78 - Number of iterations (permutations) to carry out | |
79 | |
80 -------------------------------------------------------------------------------- | |
81 | |
82 **Output** | |
83 | |
84 The tool outputs 3 files: | |
85 | |
86 (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. | |
87 (2) a TSV file with an indicator flag = 1 if the difference between the groups is statistically significant using provided α levels. | |
88 (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). | |
89 | |
90 ]]></help> | |
91 <expand macro="citations"/> | |
92 </tool> |