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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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1 <tool id="plot_generic_x_y_plot" name="Plot generic X-Y plot" version="0.1.0">
2 <description>with R</description>
3
4 <requirements>
5 <requirement type="package" version="3.2.1">R</requirement>
6 <requirement type="package" version="1.20.0">r-getopt</requirement>
7 </requirements>
8
9 <stdio>
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 </stdio>
13
14 <version_command></version_command>
15
16 <command><![CDATA[
17 Rscript $__tool_directory__/plot_generic_x_y_plot.R
18 --input_file $input_file
19 --header $header
20
21 #if str($output_format)=="pdf"
22 --output_pdf_file $output_pdf_file
23 #else
24 --output_svg_file $output_svg_file
25 #end if
26
27 --x_column_id $x_column_id
28 --y_column_id $y_column_id
29 --xlog $xlog
30 --ylog $ylog
31 --xlab "$xlab"
32 --ylab "$ylab"
33 --col $color
34 --lim $lim
35 --abline $abline
36 --bottom_margin $bottom_margin
37 --left_margin $left_margin
38 --top_margin $top_margin
39 --right_margin $right_margin
40 --pch $pch
41 ]]></command>
42
43 <inputs>
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)"/>
45
46 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
47
48 <param name="output_format" label="Format for output image" type="select" help="">
49 <option value="pdf" selected="True">PDF</option>
50 <option value="svg">SVG</option>
51 </param>
52
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)"/>
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)"/>
55
56 <param name="xlog" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scale with log for X axis?" help="(--xlog)"/>
57 <param name="ylog" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scale with log for Y axis?" help="(--ylog)"/>
58
59 <param name="xlab" type="text" value="" label="Label for X axis" help="(--xlab)"/>
60 <param name="ylab" type="text" value="" label="Label for Y axis" help="(--ylab)"/>
61
62 <param name="color" label="Color for the points" type="text" value= "grey25" help="R color (--col)"/>
63 <param name="pch" type="integer" value="21" label="Point type" help="(--pch)"/>
64
65 <param name="lim" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Use same limits for both axis?" help="(--lim)"/>
66 <param name="abline" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Add a line for x = y?" help="(--abline)"/>
67
68 <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
69 <param name="left_margin" type="integer" value="5" label="Left margin" help="(--left_margin)"/>
70 <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
71 <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
72 </inputs>
73
74 <outputs>
75 <data name="output_pdf_file" format="pdf"
76 label="${tool.name} on ${on_string}: PDF X-Y plot">
77 <filter>output_format=="pdf"</filter>
78 </data>
79 <data name="output_png_file" format="png"
80 label="${tool.name} on ${on_string}: PNG X-Y plot">
81 <filter>output_format=="png"</filter>
82 </data>
83 <data name="output_svg_file" format="svg"
84 label="${tool.name} on ${on_string}: SVG X-Y plot">
85 <filter>output_format=="svg"</filter>
86 </data>
87 </outputs>
88
89 <tests>
90 <test>
91 <param name="input_file" value="input_file.txt" />
92 <param name="header" value="FALSE" />
93 <param name="output_format" value="pdf" />
94 <param name="x_column_id" value="2" />
95 <param name="y_column_id" value="3" />
96 <param name="xlog" value="FALSE" />
97 <param name="ylog" value="FALSE" />
98 <param name="xlab" value="" />
99 <param name="ylab" value="" />
100 <param name="color" value= "grey25" />
101 <param name="pch" value="21" />
102 <param name="lim" value="FALSE" />
103 <param name="abline" value="FALSE" />
104 <param name="bottom_margin" value="5" />
105 <param name="left_margin" value="5" />
106 <param name="top_margin" value="1" />
107 <param name="right_margin" value="1" />
108 <output name="output_pdf_file" file="output_file.pdf" />
109 </test>
110 </tests>
111
112 <help><![CDATA[
113 **What it does**
114
115 This tool plot a generic X-Y plot:
116
117 .. image:: $PATH_TO_IMAGES/output.png
118 :scale: 50 %
119
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.
121 ]]></help>
122
123 <citations>
124 </citations>
125 </tool>