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annotate anova_fixed.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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2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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1 <tool id="secimtools_anova_fixed" name="Analysis of Variance (ANOVA) Fixed Effects Model" version="@WRAPPER_VERSION@">
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2 <description>- Perform a multi-way ANOVA with covariates and fixed effects.</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[
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8 anova_fixed.py
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9 --input $input
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10 --design $design
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11 --ID $uniqID
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12 --factors "$factor"
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13 --factorTypes $factorTypes
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14 --out $results_table
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15 --flags $flags_table
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16 --fig $qq_plots
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17 --fig2 $volcano_plots
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18 #if $interactions
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19 --interactions
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20 #end if
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21 ]]></command>
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22 <inputs>
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23 <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."/>
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24 <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."/>
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25 <param name="uniqID" type="text" size="30" value="" label="Unique Feature Identifier" help="Name of the column in your wide dataset that contains unique feature identifiers."/>
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26 <param name="factor" type="text" size="30" value="" label="Group(s)/Treatment(s)" help="Name of the column(s) (comma separated) in your design file that you want to use for ANOVA (ie. treatment1,treatment2,weight)."/>
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27 <param name="factorTypes" type="text" size="30" value="" label=" Type of Group(s)/Treatment(s)" help="Type of data in your treatment columns: 'C' for Categorical and 'N' for numerical. Match the order the groups used. (ie. C,C,N)."/>
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28 <param name="interactions" type="boolean" label="Calculate ANOVA with interactions" help="If 'Yes', the ANOVA program will output the interactions."/>
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29 </inputs>
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30 <outputs>
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31 <data format="tabular" name="results_table" label="${tool.name} on ${on_string}: Results Table"/>
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32 <data format="tabular" name="flags_table" label="${tool.name} on ${on_string}: Flags Table"/>
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33 <data format="pdf" name="qq_plots" label="${tool.name} on ${on_string}: QQ Plots"/>
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34 <data format="pdf" name="volcano_plots" label="${tool.name} on ${on_string}: Volcano Plots"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" value="ST000006_data.tsv"/>
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39 <param name="design" value="ST000006_design.tsv"/>
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40 <param name="uniqID" value="Retention_Index" />
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41 <param name="factor" value="White_wine_type_and_source" />
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42 <param name="factorTypes" value="C" />
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43 <output name="results_table" file="ST000006_anova_fixed_with_group_summary.tsv" />
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44 <output name="flags_table" file="ST000006_anova_fixed_with_group_flags.tsv" />
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45 <output name="qq_plots" file="ST000006_anova_fixed_with_group_qq_plots.pdf" compare="sim_size" delta="10000" />
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46 <output name="volcano_plots" file="ST000006_anova_fixed_with_group_volcano.pdf" compare="sim_size" delta="10000" />
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50
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51 @TIP_AND_WARNING@
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52
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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53 **Tool Description**
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54
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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55 The tool fits analysis of variance (ANOVA) fixed effects model with multiple grouping variables, their interactions and numerical characteristics.
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56 The analysis is performed row wise, independently for each feature.
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57 The user can choose whether to include interactions between grouping variables in the model or to use a pure additive model.
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58 Numerical characteristics of the samples can be included for both scenarios.
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59
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60 --------------------------------------------------------------------------------
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61
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62 **Input**
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63
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64 - Two input datasets are required.
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65
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66
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67 @WIDE@
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68
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69 **NOTE:** The sample IDs must match the sample IDs in the Design File
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70 (below). Extra columns will automatically be ignored.
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71
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72 @METADATA@
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73
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74 @UNIQID@
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75
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76 **Group(s)/Treatment(s)**
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77
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78 - Name of the column(s) (comma separated) in your Design File that you want to use for ANOVA.(ie. treatment1,treatment2,weight).
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79
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80 **Type of Group(s)/Treatment(s)**
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81
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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82 - Type of data in your treatment column(s): 'C' for Categorical and 'N' for numerical. Match the order the groups are used. (ie. C,C,N).
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83
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84 **Calculate ANOVA with interactions**
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85
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86 - If 'Yes', the ANOVA program will output interactions.
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87
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88 --------------------------------------------------------------------------------
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89
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90 **Output**
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91
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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92 The user will get four different outputs from the fixed effects ANOVA tool:
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93
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94 (1) a TSV file with the results table containing the fixed effects ANOVA results for each variable, the corresponding contrast and analysis of the means.
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95 (2) a TSV file with the flags for significant p-values. The flags in the TSV file are equal to 1 if the difference between the groups is statistically significant using the specified α level.
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96 (3) a PDF file with QQ (quantile-quantile) plots displaying the expected quantiles of a normal distribution on x-axis versus the observed quantiles on y-axis.
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97 (4) and a Volcano plot with the fold change displayed on the x-axis and the -log 10 of the p-value from the test of the null hypothesis is displayed on the y-axis. The red dashed line corresponds to p=0.01.
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98
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99 ]]></help>
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100 <expand macro="citations"/>
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101 </tool>