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annotate plot_barplot.xml @ 1:7e3103db022d draft default tip

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5653f2982dc5aeccd7701970fdfea444e3e53e3c-dirty
author bebatut
date Wed, 18 May 2016 12:26:19 -0400
parents a8e03ffaaedc
children
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a8e03ffaaedc planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 74beefba9d138c892208b103b52e706ab4313a4a-dirty
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1 <tool id="plot_barplot" name="Plot barplot" version="0.1.0">
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2 <description>with R</description>
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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_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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28 --data_column $column_with_data
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29 --names_column $names_column
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30 --xlab "$xlab"
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31 --log $log
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32 --col $col
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33 --bottom_margin $bottom_margin
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34 --left_margin $left_margin
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35 --top_margin $top_margin
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36 --right_margin $right_margin
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37 ]]></command>
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38
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39 <inputs>
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40 <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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42 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
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44 <param name="output_format" label="Format for output image" type="select" help="">
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45 <option value="pdf" selected="True">PDF</option>
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46 <option value="svg">SVG</option>
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47 </param>
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48
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49 <param name="column_with_data" type="data_column" data_ref="input_file" multiple="false" numerical="true" label="Column containing data?" help="(--data_column)" />
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50
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51 <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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52
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53 <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/>
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54
1
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55 <param name="log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log scale?" help="(--log)"/>
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56
0
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57 <param name="col" label="Bar color" type="text" value= "blue" help="R color (--col)"/>
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58
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59 <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
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60 <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/>
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61 <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
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62 <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
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63 </inputs>
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64
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65 <outputs>
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66 <data name="output_pdf_file" format="pdf"
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67 label="${tool.name} on ${on_string}: PDF barplot">
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68 <filter>output_format=="pdf"</filter>
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69 </data>
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70 <data name="output_png_file" format="png"
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71 label="${tool.name} on ${on_string}: PNG barplot">
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72 <filter>output_format=="png"</filter>
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73 </data>
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74 <data name="output_svg_file" format="svg"
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75 label="${tool.name} on ${on_string}: SVG barplot">
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76 <filter>output_format=="svg"</filter>
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77 </data>
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78 </outputs>
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79
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80 <tests>
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81 <test>
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82 <param name="input_file" value="input_file.txt"/>
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83 <param name="header" value="FALSE"/>
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84 <param name="output_format" value="pdf"/>
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85 <param name="column_with_data" value="2"/>
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86 <param name="names_column" value="1"/>
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87 <param name="xlab" value=""/>
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88 <param name="col" value="blue"/>
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89 <param name='log' value="FALSE"/>
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90 <param name="bottom_margin" value="5"/>
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91 <param name="left_margin" value="19"/>
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92 <param name="top_margin" value="1"/>
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93 <param name="right_margin" value="1"/>
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94 <output name="output_pdf_file" file="output_test_col_2.pdf"/>
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95 </test>
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96 <test>
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97 <param name="input_file" value="input_file.txt"/>
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98 <param name="header" value="FALSE"/>
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99 <param name="output_format" value="pdf"/>
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100 <param name="column_with_data" value="3"/>
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101 <param name="names_column" value="1"/>
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102 <param name="xlab" value=""/>
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103 <param name='log' value="FALSE"/>
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104 <param name="col" value="red"/>
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105 <param name="bottom_margin" value="5"/>
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106 <param name="left_margin" value="19"/>
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107 <param name="top_margin" value="1"/>
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108 <param name="right_margin" value="1"/>
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109 <output name="output_pdf_file" file="output_test_col_3.pdf"/>
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110 </test>
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111 </tests>
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112
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113 <help><![CDATA[
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114 **What it does**
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115
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116 This tool plot a barplot.
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117
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118 .. image:: $PATH_TO_IMAGES/output.png
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119 :scale: 50 %
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120
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121 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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122 ]]></help>
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123
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124 <citations>
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125 </citations>
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126 </tool>