Mercurial > repos > iuc > qiime_plot_taxa_summary

comparison plot_taxa_summary.xml @ 0:f800bc979a42 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:12:21 -0400
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children 486cb1834c3d
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-1:000000000000 0:f800bc979a42
1 <tool id="qiime_plot_taxa_summary" name="Make taxonomy summary charts" version="@WRAPPER_VERSION@.0">
2 <description>based on taxonomy assignment</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>MPLBACKEND="Agg" plot_taxa_summary.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[
9 #set $chosen_chart_type = str( $chart_type ).split( "," )
10
11 ## set matplotlib backend
12 export MPLBACKEND="Agg" &&
13 echo "backend:agg" > matplotlibrc &&
14
15 plot_taxa_summary.py
16 --counts_fname '$counts_fname'
17 --dir_path taxa_plots
18 --labels '$labels'
19 --num_categories '$num_categories'
20 #if str($colorby) != ''
21 --colorby '$colorby'
22 #end if
23 --background_color '$background_color'
24 --dpi '$dpi'
25 --x_width '$x_width'
26 --y_height '$y_height'
27 --bar_width '$bar_width'
28 --type_of_file '$type_of_file'
29 --chart_type '$chart_type'
30 --resize_nth_label '$resize_nth_label'
31 $include_html_legend
32 --label_type '$label_type'
33
34 #if "area" in $chosen_chart_type:
35 && mkdir -p '$area_charts_html_report.files_path'
36 && cp -r 'taxa_plots/area_charts.html' '$area_charts_html_report.files_path'
37 && cp -r 'taxa_plots/charts' '$area_charts_html_report.files_path'
38 && cp -r 'taxa_plots/css' '$area_charts_html_report.files_path'
39 && cp -r 'taxa_plots/js' '$area_charts_html_report.files_path'
40 && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report'
41 #end if
42
43 #if "bar" in $chosen_chart_type:
44 && mkdir -p '$bar_charts_html_report.files_path'
45 && cp -r 'taxa_plots/bar_charts.html' '$bar_charts_html_report.files_path'
46 && cp -r 'taxa_plots/charts' '$bar_charts_html_report.files_path'
47 && cp -r 'taxa_plots/css' '$bar_charts_html_report.files_path'
48 && cp -r 'taxa_plots/js' '$bar_charts_html_report.files_path'
49 && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report'
50 #end if
51
52 #if "pie" in $chosen_chart_type:
53 && mkdir -p '$pie_charts_html_report.files_path'
54 && cp -r 'taxa_plots/pie_charts.html' '$pie_charts_html_report.files_path'
55 && cp -r 'taxa_plots/charts' '$pie_charts_html_report.files_path'
56 && cp -r 'taxa_plots/css' '$pie_charts_html_report.files_path'
57 && cp -r 'taxa_plots/js' '$pie_charts_html_report.files_path'
58 && mv '$pie_charts_html_report.files_path/pie_charts.html' '$pie_charts_html_report'
59 #end if
60 ]]></command>
61 <inputs>
62 <param argument="--counts_fname" type="data" format="tabular,txt" label="Summarized taxa files" multiple="True"/>
63 <param argument="--labels" type="text" value="" label="Comma-separated list of taxonomic levels"/>
64 <param argument="--num_categories" type="integer" value="20" label="Maximum number of taxonomies to show in each pie chart" help="All additional taxonomies are grouped into an 'other' category. This functionality only applies to the pie charts"/>
65 <param argument="--colorby" type="text" value="" label="Categories to color by in the plots from the metadata mapping file" help="The categories must match the name of a column header in the mapping file exactly and multiple categories can be list by comma separating them without spaces" optional="True"/>
66 <param argument="--background_color" type="select" label="Background color to
67 use in the plots">
68 <option value="white" selected="true">White</option>
69 <option value="black">Black</option>
70 </param>
71 <param argument="--dpi" type="integer" value="80" label="Resolution of the plot"/>
72 <param argument="--x_width" type="integer" value="12" label="Width of the x-axis to use in the plots"/>
73 <param argument="--y_height" type="integer" value="12" label="Height of the y-axis to use in the plots"/>
74 <param argument="--bar_width" type="float" value="0.75" min="0" max="1" label="Width of the bars in the bar graph"/>
75 <param argument="--type_of_file" type="select" label="Type of image to produce">
76 <option value="pdf">PDF</option>
77 <option value="png" selected="true">PNG</option>
78 <option value="svg">SVG</option>
79 </param>
80 <param argument="--chart_type" type="select" label="Type of chart to plot" multiple="True">
81 <option value="area" selected="true">Area</option>
82 <option value="bar" selected="true">Bar</option>
83 <option value="pie">Pie</option>
84 </param>
85 <param argument="--resize_nth_label" type="integer" value="0" label="Make every nth label larger than the other lables" help="This is for large area and bar charts where the font on the x-axis is small. This requires an integer value greater than 0"/>
86 <param argument="--include_html_legend" type="boolean" label="Include HTML legend?" truevalue="--include_html_legend" falsevalue="" checked="False" help="If checked, the writing of the legend in the html page is included"/>
87 <param argument="--label_type" type="select" label="Label type" help="If the label type is defined as numeric, the x-axis will be scaled accordingly. Otherwise the x-values will treated categorically and be evenly spaced">
88 <option value="categorical" selected="true">Categorical</option>
89 <option value="numeric">Numeric</option>
90 </param>
91 </inputs>
92 <outputs>
93 <data name="bar_charts_html_report" format="html" label="${tool.name} on ${on_string}: Bar charts">
94 <filter>'bar' in chart_type</filter>
95 </data>
96 <data name="pie_charts_html_report" format="html" label="${tool.name} on ${on_string}: Pie charts">
97 <filter>'pie' in chart_type</filter>
98 </data>
99 <data name="area_charts_html_report" format="html" label="${tool.name} on ${on_string}: Area charts">
100 <filter>'area' in chart_type</filter>
101 </data>
102 </outputs>
103 <tests>
104 <test>
105 <param name="counts_fname" value="plot_taxa_summary/phylum.txt"/>
106 <param name="labels" value="phylum"/>
107 <param name="num_categories" value="20"/>
108 <param name="background_color" value="white"/>
109 <param name="dpi" value="80"/>
110 <param name="x_width" value="12"/>
111 <param name="y_height" value="12"/>
112 <param name="bar_width" value="0.75"/>
113 <param name="type_of_file" value="png"/>
114 <param name="chart_type" value="area,bar,pie"/>
115 <param name="include_html_legend" value="" />
116 <param name="resize_nth_label" value="0"/>
117 <param name="label_type" value="categorical" />
118 <output name="bar_charts_html_report" value="plot_taxa_summary/phylum/bar_charts.html" compare="sim_size"/>
119 <output name="pie_charts_html_report" value="plot_taxa_summary/phylum/pie_charts.html" compare="sim_size"/>
120 <output name="area_charts_html_report" value="plot_taxa_summary/phylum/area_charts.html" compare="sim_size"/>
121 </test>
122 <test>
123 <param name="counts_fname" value="plot_taxa_summary/phylum.txt,plot_taxa_summary/class.txt,plot_taxa_summary/genus.txt"/>
124 <param name="labels" value="Phylum,Class,Genus"/>
125 <param name="num_categories" value="20"/>
126 <param name="background_color" value="white"/>
127 <param name="dpi" value="80"/>
128 <param name="x_width" value="12"/>
129 <param name="y_height" value="12"/>
130 <param name="bar_width" value="0.75"/>
131 <param name="type_of_file" value="png"/>
132 <param name="chart_type" value="area,bar,pie"/>
133 <param name="include_html_legend" value="" />
134 <param name="resize_nth_label" value="0"/>
135 <param name="label_type" value="categorical" />
136 <output name="bar_charts_html_report" value="plot_taxa_summary/phylum_class_genus/bar_charts.html" compare="sim_size"/>
137 <output name="pie_charts_html_report" value="plot_taxa_summary/phylum_class_genus/pie_charts.html" compare="sim_size"/>
138 <output name="area_charts_html_report" value="plot_taxa_summary/phylum_class_genus/area_charts.html" compare="sim_size"/>
139 </test>
140 <test>
141 <param name="counts_fname" value="plot_taxa_summary/class.txt"/>
142 <param name="labels" value="Class"/>
143 <param name="num_categories" value="10"/>
144 <param name="background_color" value="white"/>
145 <param name="dpi" value="80"/>
146 <param name="x_width" value="12"/>
147 <param name="y_height" value="12"/>
148 <param name="bar_width" value="0.75"/>
149 <param name="chart_type" value="pie"/>
150 <param name="type_of_file" value="svg"/>
151 <param name="include_html_legend" value="--include_html_legend" />
152 <param name="resize_nth_label" value="0"/>
153 <param name="label_type" value="categorical" />
154 <output name="pie_charts_html_report" value="plot_taxa_summary/class/pie_charts.html" compare="sim_size"/>
155 </test>
156 <test>
157 <param name="counts_fname" value="plot_taxa_summary/class.txt"/>
158 <param name="labels" value="Class"/>
159 <param name="num_categories" value="20"/>
160 <param name="colorby" value="PC.636,PC.635"/>
161 <param name="background_color" value="white"/>
162 <param name="dpi" value="80"/>
163 <param name="x_width" value="12"/>
164 <param name="y_height" value="12"/>
165 <param name="bar_width" value="0.75"/>
166 <param name="type_of_file" value="pdf"/>
167 <param name="chart_type" value="area,bar,pie"/>
168 <param name="include_html_legend" value="" />
169 <param name="resize_nth_label" value="0"/>
170 <param name="label_type" value="categorical" />
171 <output name="bar_charts_html_report" value="plot_taxa_summary/class_colorby/bar_charts.html" compare="sim_size"/>
172 <output name="pie_charts_html_report" value="plot_taxa_summary/class_colorby/pie_charts.html" compare="sim_size"/>
173 <output name="area_charts_html_report" value="plot_taxa_summary/class_colorby/area_charts.html" compare="sim_size"/>
174 </test>
175 </tests>
176 <help><![CDATA[
177 **What it does**
178
179 This script automates the construction of pie, bar and area charts showing the breakdown of taxonomy by given levels.
180
181 More information about this tool is available on
182 `QIIME documentation <http://qiime.org/scripts/plot_taxa_summary.html>`_.
183 ]]></help>
184 <citations>
185 <expand macro="citations"/>
186 </citations>
187 </tool>