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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_distribution_samples" name="Generate Distribution of Features within Samples." version="@WRAPPER_VERSION@">
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2 <description></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 distribution_samples.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 $figure
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13
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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
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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18 #if $order
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19 --order $order
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20 #end if
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21 ]]></command>
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22 <inputs>
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23 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
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24 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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25 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique identifiers."/>
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26 <param name="group" type="text" size="30" value="" optional="true" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications."/>
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27 <param name="order" type="text" size="30" value="" optional="true" label="Run Order [Optional]" help="The column name in your design file that contains the order samples were run."/>
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28 </inputs>
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29 <outputs>
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30 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: Plot"/>
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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="figure" file="ST000006_distribution_samples_with_group_figure.pdf" compare="sim_size" delta="10000"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42
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43 @TIP_AND_WARNING@
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44
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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45 **Tool Description**
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46
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47 The tool plots the distribution of features within each sample.
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48 All samples are colored by group and are plotted on the same graph for comparison purposes.
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49 The distributions of the features within each sample are presented as estimated densities and box-and-whiskers plots with potential outliers.
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50 If the order samples were run is specified in the input, box plots will be displayed according to the run order.
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51
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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52 **NOTE:** This script works best with log transformed data.
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53
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54
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55 --------------------------------------------------------------------------------
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56
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57 **Input**
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58
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59 - Two input datasets are required.
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60
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61 @WIDE@
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62
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63 **NOTE:** The sample IDs must match the sample IDs in the Design File
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64 (below). Extra columns will automatically be ignored.
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65
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66 @METADATA@
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67
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68 @UNIQID@
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69
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70 @GROUP_OPTIONAL@
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71
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72 @RUNORDER_OPTIONAL@
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73
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74 --------------------------------------------------------------------------------
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75
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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76 **Output**
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77
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78 PDF file containing two plots:
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79
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80 (1) Density plots illustrating the distribution of features within a given sample
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81 (2) Boxplots of the distribution of features within each sample
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82
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83 ]]></help>
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84 <expand macro="citations"/>
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85 </tool>