annotate bland_altman_plot.xml @ 1:2e7d47c0b027 draft

"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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children caba07f41453
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1
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1 <tool id="secimtools_bland_altman_plot" name="Bland-Altman (BA) Plot" version="@WRAPPER_VERSION@">
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2 <description>- Create pairwise BA plots for outlier detection.</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 bland_altman_plot.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 $ba_plots
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13 --flag_dist $outlier_dist_plots
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14 --flag_sample $flag_sample
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15 --flag_feature $flag_feature
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16 --resid_cutoff $resid_cutoff
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17 --sample_flag_cutoff $sample_cutoff
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18 --feature_flag_cutoff $feature_cutoff
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19 --prop_feature $proportion_of_features
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20 --prop_sample $proportion_of_samples
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21
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22 #if $group
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23 --group $group
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24
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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25 #if $processOnly:
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26 --process_only "$processOnly"
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27 #end if
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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 is 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" size="30" type="text" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that contains unique feature identifiers."/>
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34 <param name="resid_cutoff" type="integer" size="30" value="3" label="Outlier Cutoff" help="Residual cutoff value, this value will flag samples with residuals ≥ this cutoff value."/>
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35 <param name="sample_cutoff" type="float" size="30" value="0.2" min="0" max="1" label="Sample Flag Cutoff" help="Flag a sample as 1 if the proportion of features within a sample that are outliers exceeds this cutoff. [Number between 0-1]."/>
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36 <param name="feature_cutoff" type="float" size="30" value="0.05" min="0" max="1" label="Feature Flag Cutoff" help="Flag a feature as 1 if the proportion of times this feature was identified as an outlier exceeds this cutoff. [Number between 0-1]."/>
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37 <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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38 <param name="processOnly" size="30" type="text" value="" optional="true" label="Group Name [Optional]" help="Name of the group(s) that you want to process. Separate multiple group names with spaces (e.g. RC,control,treatment). Leave blank to process all groups. Requires the group parameter."/>
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39 </inputs>
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40 <outputs>
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41 <data format="pdf" name="ba_plots" label= "${tool.name} on ${on_string}: BA plot" />
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42 <data format="pdf" name="outlier_dist_plots" label= "${tool.name} on ${on_string}: Distribution"/>
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43 <data format="tabular" name="flag_sample" label= "${tool.name} on ${on_string}: Flag Sample"/>
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44 <data format="tabular" name="flag_feature" label= "${tool.name} on ${on_string}: Flag Feature"/>
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45 <data format="tabular" name="proportion_of_features" label= "${tool.name} on ${on_string}: Proportion of Feature"/>
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46 <data format="tabular" name="proportion_of_samples" label= "${tool.name} on ${on_string}: Proportion of Samples"/>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input" value="ST000006_data.tsv"/>
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51 <param name="design" value="ST000006_design.tsv"/>
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52 <param name="uniqID" value="Retention_Index" />
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53 <param name="group" value="White_wine_type_and_source" />
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54 <output name="ba_plots" file="ST000006_bland_altman_plot_with_group_figure.pdf" compare="sim_size" delta="10000" />
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55 <output name="outlier_dist_plots" file="ST000006_bland_altman_plot_with_group_flag_distribution.pdf" compare="sim_size" delta="10000" />
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56 <output name="flag_sample" file="ST000006_bland_altman_plot_with_group_flag_sample.tsv" />
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57 <output name="flag_feature" file="ST000006_bland_altman_plot_with_group_flag_feature.tsv" />
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58 <output name="prop_feature" file="ST000006_bland_altman_plot_with_group_proportion_feature.tsv" />
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59 <output name="prop_sample" file="ST000006_bland_altman_plot_with_group_proportion_sample.tsv" />
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63
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64 @TIP_AND_WARNING@
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65
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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66 **Tool Description**
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67
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68 The Bland-Altman plot (BA-Plot) is used to look at the concordance of data between pairs of samples, particularly between replicates.
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69 The script generates BA-plots for all pairwise combinations of samples.
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70 If the Group/Treatment column and group name(s) in that column are provided then BA-Plots are generated only for pairwise combinations within the specified Group -- group name combination.
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71 In addition to generating the BA-plots, a linear regression fit is calculated between the values that correspond to the pair of samples to identify (flag) any unusual outlying values.
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72 The flags produced by the regression fit are used to generate distribution plots and text files for (i) each sample (column) and for (ii) each feature (row).
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73
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74
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75 --------------------------------------------------------------------------------
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76
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77 **Input**
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78
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79 - Two input datasets are required.
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80
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81 @WIDE@
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82
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83 **NOTE:** The sample IDs must match the sample IDs in the Design File
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84 (below). Extra columns will automatically be ignored.
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85
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86 @METADATA@
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87
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88 @UNIQID@
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89
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90
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91 **Outlier Cutoff – flagging values**
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92
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93 - Residual cutoff value, this value will flag samples with residuals ≥ than this cutoff value.
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94
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95 (1) If the magnitude of the residuals from the linear regression on the BA-plot exceeds the user-defined threshold, then a value is flagged as an outlier. This cutoff can be adjusted by the user, the default is 3.
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96
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97 (2) If a value is identified as a leverage point using Cook's D with a p-value cutoff of 0.5, then the value is flagged. This cannot be adjusted.
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98
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99 (3) If a value is identified as a leverage point using the DFFITS technique it is also flagged. This cannot be adjusted.
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100
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101 **Sample Flag Cutoff – flagging samples**
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102
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103 - Flag a sample as 1 if the proportion of features within a sample that are outliers exceeds this cutoff. [Number between 0-1].
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104
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105 **Feature Flag Cutoff – flagging features**
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106
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107 - Flag a feature as 1 if the proportion of times this feature was identified as an outlier exceeds this cutoff. [Number between 0-1].
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108
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109 @GROUP@
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110
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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111 **Group ID**
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112
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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113 - Name of the group(s) that you want to process. Separate multiple groupIDs with spaces. Leave blank to process all groups. Requires the group parameter.
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114
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115 --------------------------------------------------------------------------------
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116
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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117 **Output**
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118
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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119 This tool outputs four (or five) different files depending on the input settings:
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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120 (1) a PDF file containing BA-plots and scatterplots for each pair of samples
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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121 (2) a PDF file containing histograms of the most flagged features and samples
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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122 (3) two TSV files containing flags: one for samples and one for features
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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123 (4) if a grouping variable name is specified in the input, a TSV file containing flags for each group is also generated.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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124 (5) two TSV files containing (i) the proportion of features flagged per sample and (ii) the proportion of samples flagged per feature.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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125 If a sample (or feature) is flagged, the user should consider removing it from further analysis.
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126
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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127 ]]></help>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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128 <expand macro="citations"/>
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129 </tool>