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planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
author artbio
date Wed, 07 Feb 2024 19:49:56 +0000
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1 <tool id="ez_histograms" name="ez_histograms" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <macros>
3 <token name="@TOOL_VERSION@">3.4.4</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">23.0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="3.4.4">r-ggplot2</requirement>
9 <requirement type="package" version="1.4.4">r-reshape2</requirement>
10 <requirement type="package" version="1.1.4">r-dplyr</requirement>
11 <requirement type="package" version="1.3.0">r-scales</requirement>
12 <requirement type="package" version="1.4.6">r-vtable</requirement>
13 <requirement type="package" version="1.7.4">r-optparse</requirement>
14 </requirements>
15
16 <stdio>
17 <exit_code range="1:" level="fatal" />
18 </stdio>
19
20 <command detect_errors="exit_code"><![CDATA[
21 Rscript $__tool_directory__/ez_histograms.R
22 --file '$file'
23 --profile '$plot_options.plot_options_selector'
24 --xscale '$plot_options.xscale'
25 #if str($plot_options.plot_options_selector) == "count":
26 --yscale '$plot_options.yscale'
27 #end if
28 --pdf '$pdf'
29 --summary '$summary'
30 ]]></command>
31
32 <inputs>
33 <param name="file" type="data" format="tabular" label="Input tabular dataset"
34 help="Only numeric columns will be plotted"/>
35 <conditional name="plot_options">
36 <param name="plot_options_selector" type="select" label="Set plot types">
37 <option value="count" selected="true">Count Histograms</option>
38 <option value="density">Density Plots</option>
39 </param>
40 <when value="density">
41 <param name="xscale" type="select" label="Set x-axis scale">
42 <option value="cartesian" selected="true">Cartesian</option>
43 <option value="log2">log2</option>
44 <option value="log10">log10</option>
45 </param>
46 </when>
47 <when value="count">
48 <param name="xscale" type="select" label="Set x-axis scale">
49 <option value="cartesian" selected="true">Cartesian</option>
50 <option value="log2">log2</option>
51 <option value="log10">log10</option>
52 </param>
53 <param name="yscale" type="select" label="Set y-axis scale">
54 <option value="cartesian" selected="true">Cartesian</option>
55 <option value="log2">log2</option>
56 <option value="log10">log10</option>
57 </param>
58 </when>
59 </conditional>
60 </inputs>
61 <outputs>
62 <data name="pdf" format="pdf" label="${tool.name} plots from ${on_string}"/>
63 <data name="summary" format="tabular" label="Statistics Summary from ${on_string}"/>
64 </outputs>
65 <tests>
66 <test expect_num_outputs="2">
67 <param name="file" value="classic.tsv"/>
68 <param name="plot_options_selector" value="count"/>
69 <param name="xscale" value="cartesian"/>
70 <param name="yscale" value="cartesian"/>
71 <output name="pdf" file="classic.pdf"/>
72 <output name="summary" file="summary_1.tsv"/>
73 </test>
74 <test expect_num_outputs="2">
75 <param name="file" value="counts.tsv"/>
76 <param name="plot_options_selector" value="count"/>
77 <param name="xscale" value="log2"/>
78 <param name="yscale" value="cartesian"/>
79 <output name="pdf" file="count.pdf"/>
80 <output name="summary" file="summary_2.tsv"/>
81 </test>
82 <test expect_num_outputs="2">
83 <param name="file" value="headless.tsv"/>
84 <param name="plot_options_selector" value="count"/>
85 <param name="xscale" value="log10"/>
86 <param name="yscale" value="log2"/>
87 <output name="pdf" file="headless.pdf"/>
88 <output name="summary" file="summary_3.tsv"/>
89 </test>
90 <test expect_num_outputs="2">
91 <param name="file" value="large.tsv"/>
92 <param name="plot_options_selector" value="density"/>
93 <param name="xscale" value="log2"/>
94 <output name="pdf" file="large.pdf"/>
95 <output name="summary" file="summary_4.tsv"/>
96 </test>
97 <test expect_num_outputs="2">
98 <param name="file" value="rowheadless.tsv"/>
99 <param name="plot_options_selector" value="density"/>
100 <param name="xscale" value="cartesian"/>
101 <output name="pdf" file="rowheadless.pdf"/>
102 <output name="summary" file="summary_5.tsv"/>
103 </test>
104 <test expect_num_outputs="2">
105 <param name="file" value="single_headed_col.tsv"/>
106 <param name="plot_options_selector" value="density"/>
107 <param name="xscale" value="log10"/>
108 <output name="pdf" file="single_headed_col.pdf"/>
109 <output name="summary" file="summary_6.tsv"/>
110 </test>
111 </tests>
112 <help><![CDATA[
113 **What it does**
114
115 The tool generates faceted histograms or density plots using the ggplot2 functions
116 geom_histogram() or geom_density(), respectively.
117
118 **Inputs**
119
120 Any regular tabular data, provided that the number of columns (tabulations) is unchanged
121 for any row.
122
123 Except for the first one, any column will be considered as one variable with n_rows
124 observations. However, non-numeric columns will be filtered and will not be considered
125 variables.
126
127 If the first column is not numeric, it will be taken as row names (ie observation identifiers),
128 otherwise, it will be considered as the first numerical variable of the table.
129
130 If the first row is not numerical, it will be considered as a header, ie as describing the
131 variable names.
132
133 If you provide a table without header, variable names will be assigned to each column
134 following the R default rule: (V1), V2, ..., Vn
135
136 **Parameters**
137
138 For Count Histograms, both x- and y-axis can have linear (cartesian), log2 or log10 scales.
139
140 For Density Plots, only x-axis can be customized with linear (cartesian), log2, or log10
141 scales
142
143 **Outputs**
144
145 The ez_histograms Galaxy tool returns
146
147 - A pdf file with plots faceted on three columns
148 - A tsv file with statistics summary of the variables generated by the R package vtables
149
150 ]]></help>
151 <citations>
152 <citation type="bibtex">
153 @BOOK{Wickham2016-ic,
154 title = "Ggplot2: Elegant graphics for data analysis",
155 author = "Wickham, Hadley",
156 publisher = "Springer International Publishing",
157 series = "Use R!",
158 edition = 2,
159 month = jun,
160 year = 2016,
161 address = "Cham, Switzerland",
162 language = "en",
163 isbn = "9783319242774"
164 } </citation>
165 </citations>
166 </tool>