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annotate ez_histograms.xml @ 0:bdf40b0924cb draft

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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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bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
artbio
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1 <tool id="ez_histograms" name="ez_histograms" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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2 <macros>
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3 <token name="@TOOL_VERSION@">3.4.4</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">23.0</token>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="3.4.4">r-ggplot2</requirement>
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9 <requirement type="package" version="1.4.4">r-reshape2</requirement>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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10 <requirement type="package" version="1.1.4">r-dplyr</requirement>
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11 <requirement type="package" version="1.3.0">r-scales</requirement>
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12 <requirement type="package" version="1.4.6">r-vtable</requirement>
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13 <requirement type="package" version="1.7.4">r-optparse</requirement>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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14 </requirements>
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15
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16 <stdio>
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17 <exit_code range="1:" level="fatal" />
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18 </stdio>
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19
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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20 <command detect_errors="exit_code"><![CDATA[
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21 Rscript $__tool_directory__/ez_histograms.R
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22 --file '$file'
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23 --profile '$plot_options.plot_options_selector'
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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24 --xscale '$plot_options.xscale'
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25 #if str($plot_options.plot_options_selector) == "count":
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26 --yscale '$plot_options.yscale'
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27 #end if
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28 --pdf '$pdf'
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29 --summary '$summary'
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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30 ]]></command>
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31
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32 <inputs>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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33 <param name="file" type="data" format="tabular" label="Input tabular dataset"
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34 help="Only numeric columns will be plotted"/>
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35 <conditional name="plot_options">
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36 <param name="plot_options_selector" type="select" label="Set plot types">
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37 <option value="count" selected="true">Count Histograms</option>
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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38 <option value="density">Density Plots</option>
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39 </param>
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40 <when value="density">
bdf40b0924cb planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846
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41 <param name="xscale" type="select" label="Set x-axis scale">
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42 <option value="cartesian" selected="true">Cartesian</option>
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43 <option value="log2">log2</option>
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44 <option value="log10">log10</option>
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45 </param>
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46 </when>
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47 <when value="count">
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48 <param name="xscale" type="select" label="Set x-axis scale">
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49 <option value="cartesian" selected="true">Cartesian</option>
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50 <option value="log2">log2</option>
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51 <option value="log10">log10</option>
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52 </param>
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53 <param name="yscale" type="select" label="Set y-axis scale">
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54 <option value="cartesian" selected="true">Cartesian</option>
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55 <option value="log2">log2</option>
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56 <option value="log10">log10</option>
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57 </param>
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58 </when>
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59 </conditional>
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60 </inputs>
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61 <outputs>
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62 <data name="pdf" format="pdf" label="${tool.name} plots from ${on_string}"/>
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63 <data name="summary" format="tabular" label="Statistics Summary from ${on_string}"/>
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64 </outputs>
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65 <tests>
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66 <test expect_num_outputs="2">
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67 <param name="file" value="classic.tsv"/>
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68 <param name="plot_options_selector" value="count"/>
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69 <param name="xscale" value="cartesian"/>
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70 <param name="yscale" value="cartesian"/>
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71 <output name="pdf" file="classic.pdf"/>
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72 <output name="summary" file="summary_1.tsv"/>
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73 </test>
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74 <test expect_num_outputs="2">
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75 <param name="file" value="counts.tsv"/>
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76 <param name="plot_options_selector" value="count"/>
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77 <param name="xscale" value="log2"/>
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78 <param name="yscale" value="cartesian"/>
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79 <output name="pdf" file="count.pdf"/>
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80 <output name="summary" file="summary_2.tsv"/>
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81 </test>
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82 <test expect_num_outputs="2">
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83 <param name="file" value="headless.tsv"/>
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84 <param name="plot_options_selector" value="count"/>
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85 <param name="xscale" value="log10"/>
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86 <param name="yscale" value="log2"/>
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87 <output name="pdf" file="headless.pdf"/>
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88 <output name="summary" file="summary_3.tsv"/>
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89 </test>
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90 <test expect_num_outputs="2">
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91 <param name="file" value="large.tsv"/>
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92 <param name="plot_options_selector" value="density"/>
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93 <param name="xscale" value="log2"/>
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94 <output name="pdf" file="large.pdf"/>
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95 <output name="summary" file="summary_4.tsv"/>
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96 </test>
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97 <test expect_num_outputs="2">
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98 <param name="file" value="rowheadless.tsv"/>
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99 <param name="plot_options_selector" value="density"/>
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100 <param name="xscale" value="cartesian"/>
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101 <output name="pdf" file="rowheadless.pdf"/>
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102 <output name="summary" file="summary_5.tsv"/>
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103 </test>
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104 <test expect_num_outputs="2">
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105 <param name="file" value="single_headed_col.tsv"/>
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106 <param name="plot_options_selector" value="density"/>
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107 <param name="xscale" value="log10"/>
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108 <output name="pdf" file="single_headed_col.pdf"/>
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109 <output name="summary" file="summary_6.tsv"/>
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110 </test>
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111 </tests>
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112 <help><![CDATA[
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113 **What it does**
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114
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115 The tool generates faceted histograms or density plots using the ggplot2 functions
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116 geom_histogram() or geom_density(), respectively.
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117
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118 **Inputs**
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119
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120 Any regular tabular data, provided that the number of columns (tabulations) is unchanged
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121 for any row.
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122
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123 Except for the first one, any column will be considered as one variable with n_rows
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124 observations. However, non-numeric columns will be filtered and will not be considered
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125 variables.
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126
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127 If the first column is not numeric, it will be taken as row names (ie observation identifiers),
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128 otherwise, it will be considered as the first numerical variable of the table.
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129
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130 If the first row is not numerical, it will be considered as a header, ie as describing the
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131 variable names.
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132
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133 If you provide a table without header, variable names will be assigned to each column
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134 following the R default rule: (V1), V2, ..., Vn
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135
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136 **Parameters**
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137
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138 For Count Histograms, both x- and y-axis can have linear (cartesian), log2 or log10 scales.
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139
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140 For Density Plots, only x-axis can be customized with linear (cartesian), log2, or log10
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141 scales
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142
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143 **Outputs**
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144
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145 The ez_histograms Galaxy tool returns
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146
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147 - A pdf file with plots faceted on three columns
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148 - A tsv file with statistics summary of the variables generated by the R package vtables
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149
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150 ]]></help>
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151 <citations>
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152 <citation type="bibtex">
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153 @BOOK{Wickham2016-ic,
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154 title = "Ggplot2: Elegant graphics for data analysis",
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155 author = "Wickham, Hadley",
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156 publisher = "Springer International Publishing",
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157 series = "Use R!",
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158 edition = 2,
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159 month = jun,
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160 year = 2016,
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161 address = "Cham, Switzerland",
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162 language = "en",
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163 isbn = "9783319242774"
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164 } </citation>
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165 </citations>
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166 </tool>