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comparison scatter_plot_2D.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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0:b54326490b4d 1:2e7d47c0b027
1 <tool id="secimtools_scatter_plot_2D" name="Scatter Plot 2D" version="@WRAPPER_VERSION@">
2 <description>- A standalone tool.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 scatter_plot_2D.py
9 --input $input
10 --ID $uniqID
11
12 --X $x
13 --Y $y
14 --figure $figure
15
16 #if $design
17 --design $design
18 #end if
19
20 #if $group
21 --group $group
22 #end if
23
24 #if $color
25 --color $color
26 #end if
27
28 #if $palette
29 --palette $palette
30 #end if
31 ]]></command>
32 <inputs>
33 <param name="input" type="data" format="tabular" label="Long Dataset" help="Input dataset in tab-separated long format. Please see the description of the file format below. If the file is not tab separated see TIP below."/>
34 <param name="uniqID" type="text" size="30" value="" label="SampleID" help="Name of the column in your long dataset that has the unique sample idenifiers (sampleID)."/>
35 <param name="x" type="text" size="30" value="" label="X Group Title" help="Name of the column in your long format dataset for X values."/>
36 <param name="y" type="text" size="30" value="" label="Y Group Title" help="Name of the column in your long format dataset for Y values."/>
37 <param name="design" type="data" format="tabular" optional="true" label="Design File [Optional]" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
38 <param name="group" type="text" size="30" value="" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classification to be used for coloring."/>
39 <param name="palette" type="text" size="30" label="Palette [Optional]" help="Select color palette. Default = tableau. Other options are diverging, qualitative, sequential, cubehelix, tableau, and wesanderson. Please see the descriptions for the palettes below."/>
40 <param name="color" type="text" size="30" label="Color Scheme [Optional]" help="Select color scheme within the palette. Default color scheme for palette tableau = Tableau_20. User must specify a color scheme if the palette field has been filled. Please see the descriptions for the color schemes below."/>
41 </inputs>
42 <outputs>
43 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: scatter plots"/>
44 </outputs>
45 <tests>
46 <test>
47 <param name="input" value="ST000006_principal_component_analysis_score_out.tsv"/>
48 <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
49 <param name="uniqID" value="sampleID" />
50 <param name="group" value="White_wine_type_and_source" />
51 <param name="x" value="PC1" />
52 <param name="y" value="PC2" />
53 <output name="figure" file="ST000006_scatter_plot_2D_default_figure.pdf" compare="sim_size" delta="10000"/>
54 </test>
55 <test>
56 <param name="input" value="ST000006_principal_component_analysis_score_out.tsv"/>
57 <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
58 <param name="uniqID" value="sampleID" />
59 <param name="group" value="White_wine_type_and_source" />
60 <param name="x" value="PC1" />
61 <param name="y" value="PC2" />
62 <param name="palette" value="sequential" />
63 <param name="color" value="Blues_3" />
64 <output name="figure" file="ST000006_scatter_plot_2D_palette_color_figure.pdf" compare="sim_size" delta="10000"/>
65 </test>
66 </tests>
67 <help><![CDATA[
68
69 @TIP_AND_WARNING@
70
71
72
73 **Tool Description**
74
75 The tool provides a 2D scatter plot of values in a Long Format file. Please see the description of the Long Format below.
76 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.
77 Scatter plot 2D allows the user to plot any pair of values from the Principal Component Analysis (PCA) output or plot other data.
78
79 NOTE: The user should ensure that the input datasets have no missing values.
80
81 The user has an option to specify the palette and the color scheme within the palette.
82 If the palette is specified by the user, the color scheme must to be specified.
83 The list of available palettes are:
84
85 diverging,
86 qualitative,
87 sequential,
88 cubehelix,
89 tableau (default), and
90 wesanderson.
91
92 The lists of corresponding color schemes for each palattes are available via the links below:
93
94
95 https://jiffyclub.github.io/palettable/tableau/
96
97 https://jiffyclub.github.io/palettable/colorbrewer/diverging/
98
99 https://jiffyclub.github.io/palettable/colorbrewer/qualitative/
100
101 https://jiffyclub.github.io/palettable/colorbrewer/sequential/
102
103 https://jiffyclub.github.io/palettable/cubehelix/
104
105 https://jiffyclub.github.io/palettable/wesanderson/
106
107
108 --------------------------------------------------------------------------------
109
110 **Input**
111
112 - Two input datasets are required.
113
114 @LONG@
115
116
117 **Sample ID**
118
119 - Name of the column in your Long Dataset that has unique sample IDs. If coloring by group, the sampleIDs must match the sampleIDs in the Design File (below).
120
121
122 **X Group Title**
123
124 - Name of the column in the Long Format dataset for X values.
125
126 **Y Group Title**
127
128 - Name of the column in the Long Format dataset for Y values.
129
130 @DF@
131
132 **Group/Treatment [Optional]**
133
134 - Name of the column in your Design File that contains group classification to be used for coloring.
135
136
137 **Palette [Optional]**
138
139 - Choice of the palette. Default = tableau. Other options include: diverging, qualitative, sequential, cubehelix, and wesanderson.
140
141 **Color Scheme [Optional]**
142
143 - Choice of the color scheme within the palette. The default color scheme for palette tableau is Tableau_20. The user must specify the color scheme if the Palette field has been filled.
144
145 --------------------------------------------------------------------------------
146
147 **Output**
148
149 The tool produces a PDF file with the 2D scatter plot.
150 Coloring of the features by group and the corresponding legend will be included in the plot if the user provides a Design file and Palette.
151
152 ]]></help>
153 <expand macro="citations"/>
154 </tool>