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annotate ttest_perm.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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children caba07f41453
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2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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1 <tool id="secimtools_ttest_perm" name="Group Comparison by Permutation" 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[
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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8 ttest_perm.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 --reps $reps
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14 --summaries $summaries
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15 --flags $flags
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16 --volcano $volcano
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17 </command>
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18 <inputs>
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19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
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20 <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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21 <param name="uniqueID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
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22 <param name="group" type="text" size="30" label="Group/Treatment" help="Name of the column in your Design File that contains group classifications."/>
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23 <param name="reps" type="text" size="30" value="" label ="Iteration Number." help="Enter the number of iterations you want to carry out."/>
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24 </inputs>
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25 <outputs>
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26 <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/>
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27 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01, 0.05 and 0.10 significance levels for the differences. "/>
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28 <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input" value="fly_test_sbys.tsv"/>
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33 <param name="design" value="fly_test_design.tsv"/>
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34 <param name="uniqueID" value="rowID" />
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35 <param name="group" value="mating_source" />
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36 <param name="reps" value="1000" />
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37 <output name="summaries" file="fly_ttest_permuted_summary.tsv" />
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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"
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39 <output name="volcano" file="fly_ttest_permuted_volcano.pdf" compare="sim_size" delta="10000"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43
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44 @TIP_AND_WARNING@
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45
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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46 **Tool Description**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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47
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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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"
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49 The user selects the number of iterations to perform.
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50
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51 In an unpaired t-test the samples within and between groups are independent. The p-value is calculated by permutation of the data.
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52 The permutation test is performed for all pairs of conditions specified using the Group/Treatment field and for the number of specified iterations.
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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"
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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.
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55
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56 --------------------------------------------------------------------------------
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57
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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58 **Input**
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59
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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60 - Two input datasets are required.
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61
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62
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63 @WIDE@
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64
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65 **NOTE:** The sample IDs must match the sample IDs in the Design File
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66 (below). Extra columns will automatically be ignored.
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67
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68 @METADATA@
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69
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70 @UNIQID@
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71
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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72 **Group/Treatment**
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73
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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74 - List with the name of the column the Design File that contains group classifications.
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75
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76 ** Reps**
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77
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78 - Number of iterations (permutations) to carry out
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79
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80 --------------------------------------------------------------------------------
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81
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82 **Output**
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83
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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84 The tool outputs 3 files:
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85
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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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.
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87 (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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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).
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89
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90 ]]></help>
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91 <expand macro="citations"/>
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92 </tool>