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annotate standardized_euclidean_distance.xml @ 2:caba07f41453 draft default tip

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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_standardized_euclidean_distance" name="Standardized Euclidean Distance (SED)" 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 standardized_euclidean_distance.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 --fig $plot
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13 --SEDtoMean $out1
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14 --SEDpairwise $out2
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15
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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16 #if $group
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17 --group $group
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18 #end if
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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19 #if $levels
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20 --levels $levels
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21 #end if
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22 #if $p
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23 --per $p
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24 #end if
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25
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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26 #if $order
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27 --order $order
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28 #end if
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29 ]]></command>
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30 <inputs>
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31 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file not tab separated see TIP below."/>
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32 <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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33 <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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34 <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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35 <param name="order" type="text" size="30" label="Input Run Order Name [Optional]" help="Enter the name of the column containing the order samples were run. Spelling and capitalization must be exact." />
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36 <param name="levels" type="text" size="30" label="Additional groups to separate by [Optional]" help="Enter additional group(s) name(s). Spelling and capitalization must be exact. If more than one group separate with a ','." />
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37 <param name="p" type="float" value= "0.95" size="6" label="Threshold" help="Threshold for standard distribution, specified as percentile. Default = 0.95." />
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38 </inputs>
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39 <outputs>
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40 <data format="pdf" name="plot" label="${tool.name} on ${on_string}: Plot" />
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41 <data format="tabular" name="out1" label="${tool.name} on ${on_string}: SEDtoMean" />
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42 <data format="tabular" name="out2" label="${tool.name} on ${on_string}: SEDpairwise" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input" value="ST000006_data.tsv"/>
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47 <param name="design" value="ST000006_design.tsv"/>
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48 <param name="uniqID" value="Retention_Index" />
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49 <param name="group" value="White_wine_type_and_source" />
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50 <output name="plot" value="ST000006_standardized_euclidean_distance_figure.pdf" compare="sim_size" delta="50000" />
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51 <output name="out1" file="ST000006_standardized_euclidean_distance_to_mean.tsv" />
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52 <output name="out2" file="ST000006_standardized_euclidean_distance_pairwise.tsv" />
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56
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57 @TIP_AND_WARNING@
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58
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59 **Tool Description**
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60
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61 The tool is designed to identify samples that are different using the standardized Euclidian distance (SED) between samples.
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62 The tool estimates the variance of features and calculates the SED between each pair of samples in addition to the SED between each sample and the estimated mean.
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63 If a group or treatment variable is provided, then the same distance plots are generated for each group and for all samples together.
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64
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65 **NOTE:** Groups with less than three samples will be excluded from the analysis.
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66
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67
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68
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69 **Input**
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70
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71 - Two input datasets are required.
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72
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73 @WIDE@
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74
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75 **NOTE:** The sample IDs must match the sample IDs in the Design File
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76 (below). Extra columns will automatically be ignored.
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77
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78 @METADATA@
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79
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80 @UNIQID@
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81
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82 @GROUP_OPTIONAL@
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83
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84 - **Warning:** All groups must contain 3 or more samples.
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85
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86
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87 @RUNORDER_OPTIONAL@
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88
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89 **Additional groups to separate by [Optional]**
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90
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91 - Enter group(s) name(s). Spelling and capitalization must be exact. If more than one group, separate with commas.
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92 - **Warning:** All groups must contain 3 or more samples.
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93 - **NOTE:** Groups with one element will be excluded from the analysis.
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94
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95
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96 **Percentile cutoff**
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97
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98 - The percentile cutoff for standard distributions. The default is 0.95.
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99
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100 --------------------------------------------------------------------------------
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101
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102 **Output**
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103
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104 The tool outputs three different files:
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105
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106 (1) a TSV file that contains a n x n matrix (where n is the number computed samples) of the pairwise distances between the samples.
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107 If the Group/Treatment [Optional] variable is specified, the distances will be computed within groups.
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108
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109 (2) A PDF file containing:
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110 (i) Boxplots of the distribution of distances. The distances are computed between samples in the group and summarized as boxplots.
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111 The outliers (blue dots), means (red squares) and median (blue bars) of the distances are presented for each sample within the group.
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112 (ii) 2D scatter plots that show distances computed pairwise within the group
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113
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114 ]]></help>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
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115 <expand macro="citations"/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
malex
parents:
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116 </tool>