Mercurial > repos > recetox > rcx_boxplot

comparison rcx_boxplot.xml @ 0:92325ed91115 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools commit 68159a987b0597222625834e235441b95e8c3a5e
author recetox
date Mon, 03 Feb 2025 16:18:52 +0000
parents
children ebb0730f6175
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-1:000000000000 0:92325ed91115
1 <tool id="rcx_boxplot" name="recetox-boxplot" version="@TOOL_VERSION@+galaxy0" profile="23.0">
2 <description>Boxplot visualization tool using ggplot2</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>help.xml</import>
6 </macros>
7
8 <expand macro="creator" />
9 <expand macro="requirements" />
10
11 <command detect_errors="exit_code"><![CDATA[
12 Rscript '${run_script}'
13 #if $export_R_script
14 && cat ${run_script} >> $script
15 #end if
16 ]]></command>
17
18 <configfiles>
19 <configfile name="run_script"><![CDATA[
20
21 #if $input_data.ext == "csv"
22 data_input <- read.csv("$input_data", check.names = "false")
23 #else if $input_data.ext in ["tsv", "txt", "tabular"]
24 data_input <- read.delim("$input_data", sep="\t", check.names = "false")
25 #else if $input_data.ext == "parquet"
26 data_input <- arrow::read_parquet("$input_data")
27 #end if
28
29 #if $has_rownames
30 rownames(data_input) <- data_input[, 1]
31 data_input <- data_input[ ,-1]
32 #end if
33
34 y_colname <- "intensity"
35 data_long <- tidyr::pivot_longer(data_input,
36 cols = c(1:ncol(data_input)),
37 names_to = "samples",
38 values_to = y_colname)
39
40 #if $transform_data == "replace_zero"
41 data_long[data_long == 0] <- NA
42 #else if $transform_data == "log2"
43 data_long[[y_colname]] <- log2(data_long[[y_colname]])
44 #else if $transform_data == "log10"
45 data_long[[y_colname]] <- log10(data_long[[y_colname]])
46 #end if
47
48 #if $grouping_boxplot.use_grouping == "yes"
49 metadata_input <- read.delim("$grouping_boxplot.input_metadata", sep="\t", check.names = "false")
50 sampleID_column <- colnames(metadata_input)[$grouping_boxplot.sampleID]
51 plotting_column <- colnames(metadata_input)[$grouping_boxplot.groupingCol]
52 metadata_input <- data.frame(lapply(metadata_input, as.factor))
53
54 data_long <- dplyr::left_join(data_long, metadata_input, by = c("samples" = sampleID_column), keep = TRUE)
55
56 #if $grouping_boxplot.facet_x
57 facet_x <- rlang::sym(colnames(metadata_input)[$grouping_boxplot.facet_x])
58 #else
59 facet_x <- NULL
60 #end if
61
62 #if $grouping_boxplot.facet_y
63 facet_y <- rlang::sym(colnames(metadata_input)[$grouping_boxplot.facet_y])
64 #else
65 facet_y <- NULL
66 #end if
67
68 plot_boxplot <- ggplot2::ggplot(data_long, ggplot2::aes(
69 x = !!rlang::sym(plotting_column),
70 y = intensity,
71 #if $grouping_boxplot.colorCol
72 fill = !!rlang::sym(colnames(metadata_input)[$grouping_boxplot.colorCol])
73 #end if
74 )) +
75 ggplot2::geom_boxplot() +
76 ggplot2::theme_bw()+
77 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust=1)) +
78 ggplot2::facet_grid(rows = if(!is.null(facet_y)) dplyr::vars(!!facet_y) else NULL,
79 cols = if(!is.null(facet_x)) dplyr::vars(!!facet_x) else NULL,
80 scales = "free")
81
82
83 #else
84
85 plot_boxplot <- ggplot2::ggplot(data_long, ggplot2::aes(x = samples, y = intensity)) +
86 ggplot2::geom_boxplot() +
87 ggplot2::theme_bw()+
88 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust=1))
89
90 #end if
91
92 #if $xlab
93 plot_boxplot <- plot_boxplot + ggplot2::xlab("$xlab")
94 #end if
95
96 #if $ylab
97 plot_boxplot <- plot_boxplot + ggplot2::ylab("$ylab")
98 #end if
99
100 #if $flip_axes == "true"
101 plot_boxplot <- plot_boxplot + ggplot2::coord_flip()
102 #end if
103
104 ggplot2::ggsave(filename = "boxplot.png", plot_boxplot)
105
106 ]]></configfile>
107 </configfiles>
108
109 <inputs>
110 <expand macro="boxplot_param"/>
111 </inputs>
112
113 <outputs>
114 <data name="boxplot" format="png" label="Boxplot on ${on_string}" from_work_dir="boxplot.png"/>
115 <data name="script" format="txt" label="R script">
116 <filter>export_R_script</filter>
117 </data>
118 </outputs>
119
120 <tests>
121 <test expect_num_outputs="1">
122 <param name="input_data" value="test_data.txt"/>
123 <param name="has_rownames" value="true"/>
124 <output name="boxplot" ftype="png">
125 <assert_contents>
126 <has_size size="1164615" delta="200"/>
127 </assert_contents>
128 </output>
129 </test>
130 <test expect_num_outputs="2">
131 <param name="input_data" value="test_data.txt"/>
132 <param name="has_rownames" value="true"/>
133 <param name="use_grouping" value="yes"/>
134 <param name="input_metadata" value="test_expDesign.txt"/>
135 <param name="sampleID" value="1"/>
136 <param name="groupingCol" value="1"/>
137 <param name="export_R_script" value="TRUE"/>
138 <output name="boxplot" ftype="png">
139 <assert_contents>
140 <has_size size="1164615" delta="200"/>
141 </assert_contents>
142 </output>
143 </test>
144 </tests>
145
146 <help><![CDATA[
147 @GENERAL_HELP@
148 ]]></help>
149
150 <expand macro="citations" />
151 </tool>