Mercurial > repos > malex > secimtools

annotate ttest_perm.xml @ 2:caba07f41453 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
author malex
date Thu, 10 Jun 2021 15:41:17 +0000
parents 2e7d47c0b027
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
1 <tool id="secimtools_ttest_perm" name="Group Comparison by Permutation" version="@WRAPPER_VERSION@">
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
2 <description>on features.</description>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
3 <macros>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
4 <import>macros.xml</import>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
5 </macros>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
6 <expand macro="requirements" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
8 ttest_perm.py
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
9 --input $input
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
10 --design $design
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
11 --uniqueID $uniqueID
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
12 --group $group
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
13 --reps $reps
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
14 --summaries $summaries
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
15 --flags $flags
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
16 --volcano $volcano
2
caba07f41453 "planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
malex
parents: 1
diff changeset
17 ]]></command>
1
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
18 <inputs>
2
caba07f41453 "planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
malex
parents: 1
diff changeset
19 <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."/>
caba07f41453 "planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
malex
parents: 1
diff changeset
20 <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."/>
caba07f41453 "planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
malex
parents: 1
diff changeset
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 identifiers."/>
caba07f41453 "planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
malex
parents: 1
diff changeset
22 <param name="group" type="text" size="30" label="Group/Treatment" help="Name of the column in your design file that contains group classifications."/>
1
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
23 <param name="reps" type="text" size="30" value="" label ="Iteration Number." help="Enter the number of iterations you want to carry out."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
24 </inputs>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
25 <outputs>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
26 <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
27 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01, 0.05 and 0.10 significance levels for the differences. "/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
28 <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
29 </outputs>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
30 <tests>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
31 <test>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
32 <param name="input" value="fly_test_sbys.tsv"/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
33 <param name="design" value="fly_test_design.tsv"/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
34 <param name="uniqueID" value="rowID" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
35 <param name="group" value="mating_source" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
36 <param name="reps" value="1000" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
37 <output name="summaries" file="fly_ttest_permuted_summary.tsv" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
38 <output name="flags" file="fly_ttest_permuted_flags.tsv" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
39 <output name="volcano" file="fly_ttest_permuted_volcano.pdf" compare="sim_size" delta="10000"/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
40 </test>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
41 </tests>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
42 <help><![CDATA[
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
43
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
44 @TIP_AND_WARNING@
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
45
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
46 **Tool Description**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
47
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
48 The tool performs a permuted two-sided t-test for multiple (two or more) groups of independent sample (unpaired or independent t-test).
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
49 The user selects the number of iterations to perform.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
50
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
51 In an unpaired t-test the samples within and between groups are independent. The p-value is calculated by permutation of the data.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
52 The permutation test is performed for all pairs of conditions specified using the Group/Treatment field and for the number of specified iterations.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
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.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
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.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
55
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
56 --------------------------------------------------------------------------------
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
57
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
58 **Input**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
59
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
60 - Two input datasets are required.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
61
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
62
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
63 @WIDE@
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
64
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
65 **NOTE:** The sample IDs must match the sample IDs in the Design File
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
66 (below). Extra columns will automatically be ignored.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
67
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
68 @METADATA@
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
69
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
70 @UNIQID@
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
71
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
72 **Group/Treatment**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
73
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
74 - List with the name of the column the Design File that contains group classifications.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
75
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
76 ** Reps**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
77
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
78 - Number of iterations (permutations) to carry out
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
79
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
80 --------------------------------------------------------------------------------
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
81
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
82 **Output**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
83
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
84 The tool outputs 3 files:
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
85
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
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.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
87 (2) a TSV file with an indicator flag = 1 if the difference between the groups is statistically significant using provided α levels.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
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).
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
89
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
90 ]]></help>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
91 <expand macro="citations"/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
diff changeset
92 </tool>