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"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
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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_coefficient_variation_flags" name="Coefficient of Variation (CV) Flags" version="@WRAPPER_VERSION@">
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2 <description>- Calculate the coefficient of variation and flag potential outliers.</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 coefficient_variation_flags.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 --figure $CVplot
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13 --flag $CVflag
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14 #if $group:
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15 --group $group
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16 #end if
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17 #if $CVcutoff:
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18 --CVcutoff $CVcutoff
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
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23 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note: you need a 'sampleID' column. If not tab separated see TIP below."/>
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24 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that contains unique feature identifiers."/>
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25 <param name="group" type="text" size="30" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications." />
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26 <param name="CVcutoff" type="float" optional="true" size="4" value="0.1" label="CV Cutoff [Optional]" help="The cutoff (in decimals) that specifies the proportion of features to flag. The default CV cutoff is 0.1 which implies that 10% of the features with the largest CV-s will be flagged."/>
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27 </inputs>
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28 <outputs>
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29 <data format="pdf" name="CVplot" label="${tool.name} on ${on_string}: Plot" />
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30 <data format="tabular" name="CVflag" label="${tool.name} on ${on_string}: Flag" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input" value="ST000006_data.tsv"/>
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35 <param name="design" value="ST000006_design.tsv"/>
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36 <param name="uniqID" value="Retention_Index" />
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37 <param name="group" value="White_wine_type_and_source" />
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38 <output name="CVplot" file="ST000006_coefficient_variation_flags_with_group_figure.pdf" compare="sim_size" delta="100000"/>
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39 <output name="CVflag" file="ST000006_coefficient_variation_flags_with_group_flag.tsv" />
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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
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46 **Tool Description**
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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 This tool calculates the coefficient of variation (standard deviation as a percentage of the mean) and is often used to look at the consistency of features across samples.
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49 The user can define what percent of features with the highest CV to flag.
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50 If no percentage is selected, then the top 10% of features with the highest CV are flagged (default value of 0.1).
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51 The CV value corresponding to the percentage is given in the resulting histogram plot.
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52
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53 --------------------------------------------------------------------------------
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54
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55 **Input**
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56
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57 - Two input datasets are required.
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58
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59 @WIDE@
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60
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61 **NOTE:** The sample IDs must match the sample IDs in the Design File (below).
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62 Extra columns will automatically be ignored.
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63
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64 @METADATA@
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65
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66 @UNIQID@
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67
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68 **CV cutoff [Optional]**
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69
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70 - The cutoff point (in decimals) that specifies the proportion of the features to flag. The default CV cutoff is 0.1 which implies that 10% of the features with the largest CV will be flagged. If the Group/Treatment variable is provided, then the analysis is performed independently for each group. If no Group/Treatment variable is provided, the analysis is performed on the entire dataset.
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72 @GROUP_OPTIONAL@
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74
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75 --------------------------------------------------------------------------------
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76
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77 **Output**
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78
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79 This tool outputs two different files:
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80
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81 (1) a TSV file containing the CV Flags for each feature for each group (if group variable is specified). A flag value of one (1) corresponds to features with large CV values as specified by the CV cutoff.
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82 (2) a PDF file containing histograms with overlayed density plots of the coefficients of variation for each group (optional) and a summary density plot containing the densities for each group without the histograms.
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83 ]]></help>
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84 <expand macro="citations"/>
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85 </tool>