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comparison plot_barplot.xml @ 0:de039abf9641 draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit ec57288980629acd7768b28d1fbc94fc12f23561-dirty
author bebatut
date Tue, 23 Feb 2016 05:17:12 -0500
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-1:000000000000 0:de039abf9641
1 <tool id="plot_barplot" name="Plot barplot" 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">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_barplot.R
18 --input_file $input_file
19
20 #if str($output_format)=="pdf"
21 --output_pdf_file $output_pdf_file
22 #else
23 --output_svg_file $output_svg_file
24 #end if
25
26
27 --data_column $column_with_data
28 --names_column $names_column
29 --xlab $xlab
30 --col $col
31 --bottom_margin $bottom_margin
32 --left_margin $left_margin
33 --top_margin $top_margin
34 --right_margin $right_margin
35 ]]></command>
36
37 <inputs>
38 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
39
40 <param name="output_format" label="Format for output image" type="select" help="">
41 <option value="pdf" selected="True">PDF</option>
42 <option value="svg">SVG</option>
43 </param>
44
45 <param name="column_with_data" type="data_column" data_ref="input_file" multiple="false" numerical="true" label="Column containing data?" help="(--data_column)" />
46
47 <param name="names_column" type="data_column" data_ref="input_file" multiple="false" numerical="false" label="Column containing data names?" help="(--names_column)" />
48
49 <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/>
50
51 <param name="col" label="Bar color" type="text" value= "blue" help="R color (--col)"/>
52
53 <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
54 <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/>
55 <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
56 <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
57 </inputs>
58
59 <outputs>
60 <data name="output_pdf_file" format="pdf"
61 label="${tool.name} on ${on_string}: PDF barplot">
62 <filter>output_format=="pdf"</filter>
63 </data>
64 <data name="output_png_file" format="png"
65 label="${tool.name} on ${on_string}: PNG barplot">
66 <filter>output_format=="png"</filter>
67 </data>
68 <data name="output_svg_file" format="svg"
69 label="${tool.name} on ${on_string}: SVG barplot">
70 <filter>output_format=="svg"</filter>
71 </data>
72 </outputs>
73
74 <tests>
75 </tests>
76
77 <help><![CDATA[
78 **What it does**
79
80 This tool plot a barplot from a tabular file into different format files given different customizable parameters.
81
82 This tool relies on R's barplot function.
83
84 ]]></help>
85
86 <citations>
87 </citations>
88 </tool>