Mercurial > repos > bebatut > plot_grouped_barplot

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_grouped_barplot commit c6ba903395dc6d41cb318c7d95a2d9cf3ca65313-dirty
author bebatut
date Mon, 18 Apr 2016 10:08:25 -0400
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6c9aac0d6ca2 planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_grouped_barplot commit c6ba903395dc6d41cb318c7d95a2d9cf3ca65313-dirty
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1 <tool id="plot_grouped_barplot" name="Plot grouped barplot" version="0.1.0">
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2 <description>with R</description>
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3
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4 <requirements>
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5 <requirement type="package" version="3.2.1">R</requirement>
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6 <requirement type="package" version="1.20.0">r-getopt</requirement>
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7 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 </stdio>
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14 <version_command></version_command>
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16 <command><![CDATA[
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17 Rscript $__tool_directory__/plot_grouped_barplot.R
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18 --input_file $input_file
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19 --header $header
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21 #if str($output_format)=="pdf"
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22 --output_pdf_file $output_pdf_file
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23 #else
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24 --output_svg_file $output_svg_file
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25 #end if
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26
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27 #set $column_with_data=""
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28 #set $colors=""
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29 #set $names=""
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30 #set $sep=""
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31 #for sample in $samples:
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32 #set $column_with_data = $column_with_data + $sep + str($sample.column_id)
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33 #set $colors = $colors + $sep + str($sample.color)
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34 #set $names = $names + $sep +str($sample.name)
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35 #set $sep=","
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36 #end for
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37 #set $column_with_data = $column_with_data
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38 #set $colors = $colors
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39 #set $names = $names
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40
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41 --data_column $column_with_data
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42 --col "$colors"
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43 --names "$names"
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44 --replace_null $replace_null
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45 --order $order
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46 --names_column $names_column
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47 --xlab "$xlab"
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48 --log $log
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49 --bottom_margin $bottom_margin
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50 --left_margin $left_margin
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51 --top_margin $top_margin
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52 --right_margin $right_margin
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53 --legend_pos $legend_pos
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54 ]]></command>
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55
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56 <inputs>
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57 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
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58
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59 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
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60
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61 <param name="output_format" label="Format for output image" type="select" help="">
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62 <option value="pdf" selected="True">PDF</option>
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63 <option value="svg">SVG</option>
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64 </param>
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65
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66 <repeat name="samples" title="Add sample information (column id, name, color)" >
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67 <param name="name" type="text" label="Name of the data" help="(--sample_name)"/>
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68 <param name="column_id" type="data_column" data_ref="input_file" label="Column containing corresponding data" multiple="false" numerical="true" help="(after normalization, --charact_input_file)"/>
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69 <param name="color" label="Bar color" type="text" value= "blue" help="R color (--col)"/>
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70 </repeat>
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71 <param name="replace_null" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Replace null values by NA?" help="(--replace_null)"/>
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72 <param name="order" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Order given the first chosen data?" help="(--order)"/>
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73
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74 <param name="names_column" type="data_column" data_ref="input_file" multiple="false" numerical="false" label="Column containing data names?" help="(--names_column)" />
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75
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76 <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/>
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78 <param name="log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log scale?" help="(--log)"/>
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80 <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
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81 <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/>
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82 <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
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83 <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
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84 <param name="legend_pos" label="Position of the legend" type="select" help="">
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85 <option value="topright" selected="True">Top right</option>
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86 <option value="topleft">Top left</option>
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87 <option value="bottomright">Bottom right</option>
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88 <option value="bottomleft">Bottom left</option>
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89 </param>
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90 </inputs>
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91
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92 <outputs>
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93 <data name="output_pdf_file" format="pdf"
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94 label="${tool.name} on ${on_string}: PDF barplot">
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95 <filter>output_format=="pdf"</filter>
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96 </data>
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97 <data name="output_png_file" format="png"
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98 label="${tool.name} on ${on_string}: PNG barplot">
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99 <filter>output_format=="png"</filter>
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100 </data>
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101 <data name="output_svg_file" format="svg"
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102 label="${tool.name} on ${on_string}: SVG barplot">
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103 <filter>output_format=="svg"</filter>
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104 </data>
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105 </outputs>
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106
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107 <tests>
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108 <test>
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109 <param name="input_file" value="input_file.txt"/>
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110 <param name='header' value="FALSE"/>
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111 <param name="output_format" value="pdf"/>
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112 <param name="samples_0|name" value="A"/>
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113 <param name="samples_0|column_id" value="2"/>
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114 <param name="samples_0|color" value="blue"/>
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115 <param name="samples_1|name" value="B"/>
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116 <param name="samples_1|column_id" value="3"/>
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117 <param name="samples_1|color" value="red"/>
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118 <param name="replace_null" value="FALSE"/>
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119 <param name="order" value="FALSE"/>
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120 <param name="names_column" value="1"/>
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121 <param name='xlab' value=""/>
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122 <param name='log' value="FALSE"/>
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123 <param name='bottom_margin' value="5"/>
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124 <param name="left_margin" value="19"/>
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125 <param name='top_margin' value="1"/>
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126 <param name='right_margin' value="1"/>
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127 <param name="legend_pos" value="topright"/>
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128 <output name="output_pdf_file" file="output_file.pdf"/>
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129 </test>
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130 </tests>
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131
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132 <help><![CDATA[
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133 **What it does**
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134
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135 This tool plot a grouped barplot with multiple data:
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136
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137 .. image:: $PATH_TO_IMAGES/output.png
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138 :scale: 50 %
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139
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140 This tool relies on R's barplot function. The input file must be a tabular file with multiple columns: a column with row names (for bar names) and a least a column with data. The output image is customizable (margin, legend positions, ...) and can be export in different format.
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141 ]]></help>
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142
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143 <citations>
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144 </citations>
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145 </tool>