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annotate scatter_plot_3D.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
children
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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_scatter_plot_3D" name="Scatter Plot 3D" version="@WRAPPER_VERSION@">
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2 <description>- A standalone tool.</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 scatter_plot_3D.py
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9 --input $input
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10 --ID $uniqID
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11
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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12 --X $x
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13 --Y $y
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14 --Z $z
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15 --figure $figure
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16
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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17 #if $design
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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18 --design $design
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19 #end if
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20
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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21 #if $group
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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22 --group $group
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23 #end if
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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 $color
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26 --color $color
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27 #end if
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28
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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29 #if $palette
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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30 --palette $palette
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31 #end if
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32
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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33 #if $rotation
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34 --rotation $rotation
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35 #end if
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36
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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37 #if $elevation
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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38 --elevation $elevation
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39 #end if
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40 ]]></command>
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41 <inputs>
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42 <param name="input" type="data" format="tabular" label="Long Dataset" help="Input dataset in tab-separated long format. Please see the description of the file format below. If the file is 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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43 <param name="uniqID" type="text" size="30" value="" label="SampleID" help="Name of the column in your long dataset with unique sample identifiers (sampleID). If coloring by group, sampleIDs must match sampleIDs in the Design File."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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44 <param name="x" type="text" size="30" value="" label="X Group Title" help="Name of the column in long format dataset for X values."/>
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45 <param name="y" type="text" size="30" value="" label="Y Group Title" help="Name of the column in long format dataset for Y values."/>
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46 <param name="z" type="text" size="30" value="" label="Z Group Title" help="Name of the column in long format dataset for Z values."/>
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47 <param name="rotation" type="text" size="30" value="" label="Azimuth (Rotation) Angle for Viewing [Optional]" help="The azimuth (rotation) angle for viewing in degrees. Default = 45 degrees. The ideal azimuth (rotation) angle may be a process of trial and error."/>
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48 <param name="elevation" type="text" size="30" value="" label="Elevation Angle for Viewing [Optional]" help="The elevation angle for viewing in degrees. Default = 45 degrees. The ideal elevation angle may be a process of trial and error."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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49 <param name="design" type="data" format="tabular" optional="true" label="Design File [Optional]" help="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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50 <param name="group" type="text" size="30" value="" label="Group/Treatment [Optional]" help="Name of the column in your Design File that contains group classification that will be used for coloring."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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51 <param name="palette" type="text" size="30" label="Palette [Optional]" help="Select color palette. Default = tableau. Other options include diverging, qualitative, sequential, cubehelix, and wesanderson. Please see the descriptions for the palettes below."/>
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52 <param name="color" type="text" size="30" label="Color Scheme [Optional]" help="Select color scheme within the palette. The default color scheme for palette tableau = Tableau_20. User must specify Color Scheme if the Palette field has been filled. Please see the descriptions for the color schemes below."/>
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53 </inputs>
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54 <outputs>
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55 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: scatter plots"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="input" value="ST000006_principal_component_analysis_score_out.tsv"/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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60 <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
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61 <param name="uniqID" value="sampleID" />
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62 <param name="group" value="White_wine_type_and_source" />
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63 <param name="x" value="PC1" />
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64 <param name="y" value="PC2" />
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65 <param name="z" value="PC3" />
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66 <output name="figure" file="ST000006_scatter_plot_3D_default_figure.pdf" compare="sim_size" delta="10000" />
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67 </test>
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68 <test>
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69 <param name="input" value="ST000006_principal_component_analysis_score_out.tsv"/>
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70 <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
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71 <param name="uniqID" value="sampleID" />
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72 <param name="group" value="White_wine_type_and_source" />
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73 <param name="x" value="PC1" />
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74 <param name="y" value="PC2" />
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75 <param name="z" value="PC3" />
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76 <param name="rotation" value="30" />
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77 <param name="elevation" value="23" />
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78 <param name="palette" value="sequential" />
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79 <param name="color" value="Blues_3" />
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80 <output name="figure" file="ST000006_scatter_plot_3D_palette_color_figure.pdf" compare="sim_size" delta="10000" />
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84
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85 @TIP_AND_WARNING@
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86
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87
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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88 **Tool Description**
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89
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90 The tool provides a 3D scatter plot of values in a Long Format file. Please see the description of the Long Format below.
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91 If coloring by group is desired, the column with the sample names in the Long Format dataset has to have the name "sampleID" to match the name in the Design File.
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92 Scatter plot 2D allows the user to plot any pair of values from the Principal Component Analysis (PCA) output or plot other data.
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93
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94 NOTE: The user should ensure that the input datasets have no missing values.
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95
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96 The user has an option to specify the palette and the color scheme within the palette.
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97 If the palette is specified by the user, the color scheme must to be specified.
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98 The list of available palettes are:
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99
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100 diverging,
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101 qualitative,
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102 sequential,
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103 cubehelix,
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104 tableau (default), and
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105 wesanderson.
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106
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107 The lists of corresponding color schemes for each palattes are available via the links below:
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108
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109 https://jiffyclub.github.io/palettable/tableau/
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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 https://jiffyclub.github.io/palettable/colorbrewer/diverging/
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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 https://jiffyclub.github.io/palettable/colorbrewer/qualitative/
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114
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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115 https://jiffyclub.github.io/palettable/colorbrewer/sequential/
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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 https://jiffyclub.github.io/palettable/cubehelix/
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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 https://jiffyclub.github.io/palettable/wesanderson/
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120
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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121
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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122 **NOTE:** The user should ensure that the Long Format and Design File datasets have no missing values.
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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
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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125 --------------------------------------------------------------------------------
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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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 **Input**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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128
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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129 - Two input datasets are required.
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130
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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131 @LONG@
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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132
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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133
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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134 **Sample ID**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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135
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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136 - Name of the column in your Long Dataset that has the unique sample IDs. If coloring by group is desired based on the Design File sample IDs have to be saved in a column with the name sampleID to match the name in the Design File
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137
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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138
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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139 **X Group Title**
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140
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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141 - Name of the column in the Long Format dataset for X values.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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142
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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143 **Y Group Title**
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144
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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145 - Name of the column in the Long Format dataset for Y values.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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146
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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147 **Z Group Title**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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148
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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149 - Name of the column in the Long Format dataset for Z values.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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150
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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151 **Azimuth (Rotation) Angle for Viewing [Optional]:**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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152
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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153 - The azimuth (rotation) angle for viewing in degrees. The default value = 45 degrees. The ideal azimuth (rotation) angle for viewing may involve trial and error.
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154
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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155 **Elevation Angle for Viewing [Optional]:**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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156
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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157 - The elevation angle for viewing in degrees. The default value = 45 degrees. The ideal elevation angle for viewing may involve trial and error.
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158
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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159 @DF@
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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160
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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161 **Group/Treatment [Optional]**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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162
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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163 - Name of the column in your Design File that contains group classification for coloring.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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164
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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165 **Palette [Optional]**
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166
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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167 - Choice of the palette. Default = tableau. The other options include: diverging, qualitative, sequential, cubehelix, tableau, and wesanderson.
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168
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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169 **Color Scheme [Optional]**
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170
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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171 - Choice of the color scheme within the palette. The default color scheme for palette tableau is Tableau_20. User has to specify Color Scheme if the Palette field has been filled.
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172
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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173 --------------------------------------------------------------------------------
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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174
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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175 **Output**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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176
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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177 The tool produces a PDF file containing a 3D scatter plot.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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178 The coloring of the features by group and the corresponding legend will be included in the plot if the user provides the Design File and Palette.
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179
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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180 ]]></help>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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181 <expand macro="citations"/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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182 </tool>