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comparison plot_grouped_barplot.xml @ 0:217f96dbd973 draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_grouped_barplot commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author bebatut
date Tue, 12 Apr 2016 03:11:25 -0400
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-1:000000000000 0:217f96dbd973
1 <tool id="plot_grouped_barplot" name="Plot grouped 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_grouped_barplot.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 #set $column_with_data=""
28 #set $colors=""
29 #set $names=""
30 #set $sep=""
31 #for sample in $samples:
32 #set $column_with_data = $column_with_data + $sep + str($sample.column_id)
33 #set $colors = $colors + $sep + str($sample.color)
34 #set $names = $names + $sep +str($sample.name)
35 #set $sep=","
36 #end for
37 #set $column_with_data = $column_with_data
38 #set $colors = $colors
39 #set $names = $names
40
41 --data_column $column_with_data
42 --col "$colors"
43 --names "$names"
44 --replace_null $replace_null
45 --order $order
46 --names_column $names_column
47 --xlab "$xlab"
48 --log $log
49 --bottom_margin $bottom_margin
50 --left_margin $left_margin
51 --top_margin $top_margin
52 --right_margin $right_margin
53 --legend_pos $legend_pos
54 ]]></command>
55
56 <inputs>
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)"/>
58
59 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
60
61 <param name="output_format" label="Format for output image" type="select" help="">
62 <option value="pdf" selected="True">PDF</option>
63 <option value="svg">SVG</option>
64 </param>
65
66 <repeat name="samples" title="Add sample information (column id, name, color)" >
67 <param name="name" type="text" label="Name of the data" help="(--sample_name)"/>
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)"/>
69 <param name="color" label="Bar color" type="text" value= "blue" help="R color (--col)"/>
70 </repeat>
71 <param name="replace_null" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Replace null values by NA?" help="(--replace_null)"/>
72 <param name="order" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Order given the first chosen data?" help="(--order)"/>
73
74 <param name="names_column" type="data_column" data_ref="input_file" multiple="false" numerical="false" label="Column containing data names?" help="(--names_column)" />
75
76 <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/>
77
78 <param name="log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log scale?" help="(--log)"/>
79
80 <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
81 <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/>
82 <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
83 <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
84 <param name="legend_pos" label="Position of the legend" type="select" help="">
85 <option value="topright" selected="True">Top right</option>
86 <option value="topleft">Top left</option>
87 <option value="bottomright">Bottom right</option>
88 <option value="bottomleft">Bottom left</option>
89 </param>
90 </inputs>
91
92 <outputs>
93 <data name="output_pdf_file" format="pdf"
94 label="${tool.name} on ${on_string}: PDF barplot">
95 <filter>output_format=="pdf"</filter>
96 </data>
97 <data name="output_png_file" format="png"
98 label="${tool.name} on ${on_string}: PNG barplot">
99 <filter>output_format=="png"</filter>
100 </data>
101 <data name="output_svg_file" format="svg"
102 label="${tool.name} on ${on_string}: SVG barplot">
103 <filter>output_format=="svg"</filter>
104 </data>
105 </outputs>
106
107 <tests>
108 </tests>
109
110 <help><![CDATA[
111 **What it does**
112
113 This tool plot a grouped barplot from a tabular file into different format files given different customizable parameters:
114
115 .. image:: $PATH_TO_IMAGES/output.png
116 :scale: 50 %
117
118 This tool relies on R's barplot function.
119
120 ]]></help>
121
122 <citations>
123 </citations>
124 </tool>