Mercurial > repos > bebatut > qiime

comparison plot_taxa_summary.xml @ 0:c1bd0c560018 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:c1bd0c560018
1 <tool id="qiime_plot_taxa_summary" name="Make taxonomy summary charts" version="1.9.1">
2 <description>based on taxonomy assignment</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements" />
9
10 <version_command><![CDATA[
11 plot_taxa_summary.py --version
12 ]]>
13 </version_command>
14
15 <command>
16 <![CDATA[
17 #set $chosen_chart_type = str( $chart_type ).split( "," )
18
19 plot_taxa_summary.py
20 -i $counts_fname
21
22 -o taxa_plots
23
24 #if str($labels):
25 -l $labels
26 #end if
27
28 -n $num_categories
29
30 #if str( $colorby)
31 -b $colorby
32 #end if
33
34 -k $background_color
35 -d $dpi
36 -x $x_width
37 -y $y_height
38 -w $bar_width
39
40 -c $chart_type
41 $include_html_legend
42 -a $label_type
43
44 #if "area" in $chosen_chart_type:
45 &&
46 mkdir -p $area_charts_html_report.files_path
47 &&
48 cp -r taxa_plots/area_charts.html $area_charts_html_report.files_path
49 &&
50 cp -r taxa_plots/charts $area_charts_html_report.files_path
51 &&
52 cp -r taxa_plots/css $area_charts_html_report.files_path
53 &&
54 cp -r taxa_plots/js $area_charts_html_report.files_path
55 &&
56 mv $area_charts_html_report.files_path/area_charts.html $area_charts_html_report
57 #end if
58
59 #if "bar" in $chosen_chart_type:
60 &&
61 mkdir -p $bar_charts_html_report.files_path
62 &&
63 cp -r taxa_plots/bar_charts.html $bar_charts_html_report.files_path
64 &&
65 cp -r taxa_plots/charts $bar_charts_html_report.files_path
66 &&
67 cp -r taxa_plots/css $bar_charts_html_report.files_path
68 &&
69 cp -r taxa_plots/js $bar_charts_html_report.files_path
70 &&
71 mv $bar_charts_html_report.files_path/bar_charts.html $bar_charts_html_report
72 #end if
73
74 #if "pie" in $chosen_chart_type:
75 &&
76 mkdir -p $pie_charts_html_report.files_path
77 &&
78 cp -r taxa_plots/pie_charts.html $pie_charts_html_report.files_path
79 &&
80 cp -r taxa_plots/charts $pie_charts_html_report.files_path
81 &&
82 cp -r taxa_plots/css $pie_charts_html_report.files_path
83 &&
84 cp -r taxa_plots/js $pie_charts_html_report.files_path
85 &&
86 mv $pie_charts_html_report.files_path/pie_charts.html $pie_charts_html_report
87 #end if
88 ]]>
89 </command>
90
91 <inputs>
92 <param name="counts_fname" type="data" format="tabular,txt,tsv"
93 label="Summarized taxa files" multiple="True"
94 help="(-i/--counts_fname)"/>
95
96 <param name="labels" type="text" value="" label="Comma-separated list of
97 taxonomic levels (optional)" help="(-l/--labels)" optional="True"/>
98
99 <param name="num_categories" type="integer" value="20" label="Maximum
100 number of taxonomies to show in each pie chart" help="All additional
101 taxonomies are grouped into an 'other' category. This functionality
102 only applies to the pie charts(-n/--num_categories)"/>
103
104 <param name="colorby" type="text" value="" label="Categories to color
105 by in the plots from the metadata mapping file (optional)"
106 help="The categories must match the name of a column header in the
107 mapping file exactly and multiple categories can be list by comma
108 separating them without spaces(-b/--colorby)" optional="True"/>
109
110 <param name="background_color" type="select" label="Background color to
111 use in the plots" help="(-k/--background_color)">
112 <option value="white">White</option>
113 <option value="black">Black</option>
114 </param>
115
116 <param name="dpi" type="integer" value="80" label="Resolution of the plot"
117 help="(-d/--dpi)"/>
118
119 <param name="x_width" type="integer" value="12" label="Width of the
120 x-axis to use in the plots" help="(-x/--x_width)"/>
121
122 <param name="y_height" type="integer" value="12" label="Height of the
123 y-axis to use in the plots" help="(-y/--y_height)"/>
124
125 <param name="bar_width" type="float" value="0.75" min="0" maw="1"
126 label="Width of the bars in the bar graph" help="(-w/--bar_width)"/>
127
128 <param name="chart_type" type="select" label="Type of chart to plot"
129 help="(-c/--chart_type)" multiple="True" display="checkboxes">
130 <option value="area" selected="true">Area</option>
131 <option value="bar" selected="true">Bar</option>
132 <option value="pie">Pie</option>
133 </param>
134
135 <param name="include_html_legend" type="boolean" label="Include HTML
136 legend?" truevalue="--include_html_legend" falsevalue="" checked="False"
137 help="If checked, the writing of the legend in the html page is
138 included (-s/--include_html_legend)" />
139
140 <param name="label_type" type="select" label="Label type"
141 help="If the label type is defined as numeric, the x-axis will be
142 scaled accordingly. Otherwise the x-values will treated categorically
143 and be evenly spaced(-a/--label_type)">
144 <option value="categorical" selected="true">Categorical</option>
145 <option value="numeric">Numeric</option>
146 </param>
147 </inputs>
148
149 <outputs>
150 <data name="bar_charts_html_report" format="html"
151 label="${tool.name} on ${on_string}: Bar charts">
152 <filter>'bar' in chart_type</filter>
153 </data>
154 <data name="pie_charts_html_report" format="html"
155 label="${tool.name} on ${on_string}: Pie charts">
156 <filter>'pie' in chart_type</filter>
157 </data>
158 <data name="area_charts_html_report" format="html"
159 label="${tool.name} on ${on_string}: Area charts">
160 <filter>'area' in chart_type</filter>
161 </data>
162 </outputs>
163
164 <tests>
165 <test>
166 <param name="counts_fname"
167 value="summarize_taxa_L2.tab"/>
168 <param name="num_categories" value="20"/>
169 <param name="background_color" value="white"/>
170 <param name="dpi" value="80" />
171 <param name="x_width" value="12" />
172 <param name="y_height" value="12" />
173 <param name="bar_width" value="0.75" />
174 <param name="chart_type" value="area,bar"/>
175 <param name="include_html_legend" value="" />
176 <param name="label_type" value="categorical"/>
177 </test>
178 </tests>
179
180 <help><![CDATA[
181
182 **What it does**
183
184 This script automates the construction of pie, bar and area charts showing the breakdown of taxonomy by given levels.
185
186 More information about this tool is available on
187 `QIIME documentation <http://qiime.org/scripts/plot_taxa_summary.html>`_.
188 ]]>
189 </help>
190
191 <citations>
192 <expand macro="citations" />
193 </citations>
194 </tool>