Mercurial > repos > malex > secimtools

annotate mahalanobis_distance.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_mahalanobis_distance" name="Penalized Mahalanobis Distance (PMD)" version="@WRAPPER_VERSION@">
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2 <description>to compare groups</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 <stdio>
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8 <exit_code range="1:" level="warning" description="RuntimeWarning"/>
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9 </stdio>
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10 <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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11 mahalanobis_distance.py
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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12 --input $input
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13 --design $design
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14 --ID $uniqID
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15 --figure $plot
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16 --distanceToMean $out1
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17 --distancePairwise $out2
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18
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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19 #if $group
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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20 --group $group
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21 #end if
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22
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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23 #if $levels
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24 --levels $levels
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25 #end if
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26
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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27 #if $p
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28 --per $p
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29 #end if
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30
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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31 #if $order
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32 --order $order
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33 #end if
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34
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35 #if $penalty
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36 --penalty $penalty
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37 #end if
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38 ]]></command>
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39 <inputs>
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40 <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."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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41 <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."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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42 <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.."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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43 <param name="group" type="text" size="30" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications." />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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44 <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." />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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45 <param name="levels" type="text" size="30" label="Additional groups to separate by [Optional]" help="Enter additional group(s) name(s) to include. Spelling and capitalization must be exact. If more than one group separate with ','." />
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46 <param name="p" type="float" value= ".95" size="6" label="Threshold" help="Threshold for standard distribution, specified as a percentile. Default = 0.95." />
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47 <param name="penalty" type="float" value= "0.5" size="6" label="λ Penalty" help="λ Penalty to use in the distance. The default is λ=0.5." />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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48 </inputs>
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49 <outputs>
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50 <data format="pdf" name="plot" label="${tool.name} on ${on_string}: plot" />
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51 <data format="tabular" name="out1" label="${tool.name} on ${on_string}: toMean" />
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52 <data format="tabular" name="out2" label="${tool.name} on ${on_string}: pairwise" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input" value="ST000006_data.tsv"/>
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57 <param name="design" value="ST000006_design.tsv"/>
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58 <param name="uniqID" value="Retention_Index" />
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59 <param name="group" value="White_wine_type_and_source" />
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60 <param name="penalty" value="0.5" />
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61 <output name="plot" file="ST000006_mahalanobis_distance_figure.pdf" compare="sim_size" delta="10000" />
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62 <output name="out1" file="ST000006_mahalanobis_distance_to_mean.tsv" />
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63 <output name="out2" file="ST000006_mahalanobis_distance_pairwise.tsv" />
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67
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68 @TIP_AND_WARNING@
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69
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70 **Tool Description**
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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 The Penalized Mahalanobis distance (PMD) tool can be used to compare samples within a group and accounts for the correlation structure between metabolites.
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73 In contrast, Standardized Euclidian distance (SED) relies solely on geometric distance and ignores any dependency structures between features.
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74 PMD incorporates the correlation structure inside the distance measurement.
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75
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76 When correlation structure and dependency between metabolites is ignored, the features inverse variance-covariance matrix simplifies to a diagonal matrix with diagonal values - in this case, MD simplifies to SED.
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77 When the number of features is greater than the number of samples, the inverse of the features variance-covariance matrix does not exist.
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78 This is the case for most -omic data. Here, the inverse is estimated using a regularization method (Archambeau et al. 2004).
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79 The details of the regularization algorithm can be found in Supplementary file 3 in Kirpich et al. 2017.
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80
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81 Archambeau C, Vrins F, Verleysen M. Flexible and Robust Bayesian Classification by Finite Mixture Models. InESANN 2004 (pp. 75-80).​
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82
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83 **NOTE:** Because of the nature of the tool, groups with less than 3 samples will be discarded from the analysis.
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84
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85
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86 **Input**
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87
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88 - Two input datasets are required.
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89
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90 @WIDE@
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91
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92 **NOTE:** The sample IDs must match the sample IDs in the Design File
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93 (below). Extra columns will automatically be ignored.
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94
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95 @METADATA@
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96
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97 @UNIQID@
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98
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99 @GROUP_OPTIONAL@
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100
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101 - **Warning:** All groups must contain 3 or more samples.
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102
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103
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104 @RUNORDER_OPTIONAL@
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105
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106 **Additional groups to separate by [Optional]**
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107
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108 - Enter additional group(s) name(s) to include. Spelling and capitalization must be exact. If more than one group, separate them with a comma
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109 - **Warning:** All groups must contain 3 or more samples.
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110
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111
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112 **Percentile cutoff**
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113
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114 - The percentile cutoff for standard distributions. The default is 0.95.
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115
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116 **λ Penalty**
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117
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118 - λ Penalty to use in the distance. The default is λ=0.5.
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119
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120 --------------------------------------------------------------------------------
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121
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122 **Output**
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123
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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124 The tool outputs three different files:
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125
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126 (1) a PDF file containing 2D scatter plots and boxplots for the distances
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127
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128 (2) a TSV file containing distances from the sample to the estimated mean
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129
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130 (3) a TSV file containing distances from the sample to other samples.
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131
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132 If the grouping variable is specified by the user, the distances are computed both within the groups and for the entire dataset.
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133
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134 ]]></help>
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135 <expand macro="citations"/>
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136 </tool>