Mercurial > repos > bebatut > plot_generic_x_y_plot

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
author bebatut
date Mon, 18 Apr 2016 11:11:02 -0400
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5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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1 <tool id="plot_generic_x_y_plot" name="Plot generic X-Y plot" 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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5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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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_generic_x_y_plot.R
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18 --input_file $input_file
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19 --header $header
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20
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21 #if str($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 --x_column_id $x_column_id
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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28 --y_column_id $y_column_id
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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29 --xlog $xlog
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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30 --ylog $ylog
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31 --xlab "$xlab"
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32 --ylab "$ylab"
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33 --col $color
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34 --lim $lim
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35 --abline $abline
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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36 --bottom_margin $bottom_margin
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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37 --left_margin $left_margin
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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38 --top_margin $top_margin
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39 --right_margin $right_margin
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40 --pch $pch
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41 ]]></command>
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42
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43 <inputs>
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44 <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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45
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46 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
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47
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48 <param name="output_format" label="Format for output image" type="select" help="">
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49 <option value="pdf" selected="True">PDF</option>
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50 <option value="svg">SVG</option>
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51 </param>
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52
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53 <param name="x_column_id" type="data_column" data_ref="input_file" label="Column containing data for X axis" multiple="false" numerical="true" help="--x_column_id)"/>
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54 <param name="y_column_id" type="data_column" data_ref="input_file" label="Column containing data for Y axis" multiple="false" numerical="true" help="--y_column_id)"/>
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55
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56 <param name="xlog" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scale with log for X axis?" help="(--xlog)"/>
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57 <param name="ylog" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scale with log for Y axis?" help="(--ylog)"/>
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58
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59 <param name="xlab" type="text" value="" label="Label for X axis" help="(--xlab)"/>
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60 <param name="ylab" type="text" value="" label="Label for Y axis" help="(--ylab)"/>
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61
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62 <param name="color" label="Color for the points" type="text" value= "grey25" help="R color (--col)"/>
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63 <param name="pch" type="integer" value="21" label="Point type" help="(--pch)"/>
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64
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65 <param name="lim" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Use same limits for both axis?" help="(--lim)"/>
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66 <param name="abline" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Add a line for x = y?" help="(--abline)"/>
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67
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68 <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
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69 <param name="left_margin" type="integer" value="5" label="Left margin" help="(--left_margin)"/>
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70 <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
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71 <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
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72 </inputs>
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73
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74 <outputs>
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75 <data name="output_pdf_file" format="pdf"
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76 label="${tool.name} on ${on_string}: PDF X-Y plot">
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77 <filter>output_format=="pdf"</filter>
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78 </data>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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79 <data name="output_png_file" format="png"
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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80 label="${tool.name} on ${on_string}: PNG X-Y plot">
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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81 <filter>output_format=="png"</filter>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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82 </data>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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83 <data name="output_svg_file" format="svg"
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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84 label="${tool.name} on ${on_string}: SVG X-Y plot">
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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85 <filter>output_format=="svg"</filter>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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86 </data>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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87 </outputs>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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88
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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89 <tests>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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90 <test>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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91 <param name="input_file" value="input_file.txt" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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92 <param name="header" value="FALSE" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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93 <param name="output_format" value="pdf" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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94 <param name="x_column_id" value="2" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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95 <param name="y_column_id" value="3" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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96 <param name="xlog" value="FALSE" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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97 <param name="ylog" value="FALSE" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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98 <param name="xlab" value="" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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99 <param name="ylab" value="" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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100 <param name="color" value= "grey25" />
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101 <param name="pch" value="21" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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102 <param name="lim" value="FALSE" />
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103 <param name="abline" value="FALSE" />
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104 <param name="bottom_margin" value="5" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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105 <param name="left_margin" value="5" />
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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106 <param name="top_margin" value="1" />
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107 <param name="right_margin" value="1" />
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108 <output name="output_pdf_file" file="output_file.pdf" />
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109 </test>
5118d839acae planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty
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110 </tests>
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111
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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 This tool plot a generic X-Y plot:
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116
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117 .. image:: $PATH_TO_IMAGES/output.png
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118 :scale: 50 %
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119
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120 This tool relies on R's plot function. The input file must be a tabular file with at least two data columns. The output image is customizable (margin, legend positions, ...) and can be export in different format.
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121 ]]></help>
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122
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123 <citations>
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124 </citations>
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125 </tool>