Mercurial > repos > iuc > qiime_plot_taxa_summary

comparison plot_taxa_summary.xml @ 5:d0910542c8f6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:25:17 -0400
parents 78b8aba19876
children ab12aca3ede9
comparison
equal deleted inserted replaced
4:7d1a644d1032 5:d0910542c8f6
1 <tool id="qiime_plot_taxa_summary" name="Make taxonomy summary charts" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_plot_taxa_summary" name="Make taxonomy summary charts" version="@WRAPPER_VERSION@.0">
2 <description>based on taxonomy assignment</description> 2 <description> based on taxonomy assignment (plot_taxa_summary)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>MPLBACKEND="Agg" plot_taxa_summary.py --version</version_command> 7 <version_command>MPLBACKEND="Agg" plot_taxa_summary.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #set $chosen_chart_type = str( $chart_type ).split( "," ) 9 #set $chosen_chart_type = str( $chart_type ).split( "," )
10 10
11 ## set matplotlib backend 11 ## set matplotlib backend
12 export MPLBACKEND="Agg" && 12 export MPLBACKEND="Agg" &&
13 echo "backend:agg" > matplotlibrc && 13 echo "backend:agg" > matplotlibrc &&
14 14
15 plot_taxa_summary.py 15 plot_taxa_summary.py
16 --counts_fname '$counts_fname' 16 --counts_fname '$counts_fname'
17 --dir_path taxa_plots 17 --dir_path taxa_plots
18 --labels '$labels' 18 --labels '$labels'
19 --num_categories '$num_categories' 19 --num_categories '$num_categories'
20 #if str($colorby) != '' 20 #if str($colorby) != ''
21 --colorby '$colorby' 21 --colorby '$colorby'
22 #end if 22 #end if
23 --background_color '$background_color' 23 --background_color '$background_color'
24 --dpi '$dpi' 24 --dpi '$dpi'
25 --x_width '$x_width' 25 --x_width '$x_width'
26 --y_height '$y_height' 26 --y_height '$y_height'
27 --bar_width '$bar_width' 27 --bar_width '$bar_width'
28 --type_of_file '$type_of_file' 28 --type_of_file '$type_of_file'
29 --chart_type '$chart_type' 29 --chart_type '$chart_type'
30 --resize_nth_label '$resize_nth_label' 30 --resize_nth_label '$resize_nth_label'
31 $include_html_legend 31 $include_html_legend
32 --label_type '$label_type' 32 --label_type '$label_type'
33 33
34 #if "area" in $chosen_chart_type: 34 #if "area" in $chosen_chart_type:
35 && mkdir -p '$area_charts_html_report.files_path' 35 && mkdir -p '$area_charts_html_report.files_path'
36 && cp -r 'taxa_plots/area_charts.html' '$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' 37 && cp -r 'taxa_plots/charts' '$area_charts_html_report.files_path'
38 && cp -r 'taxa_plots/css' '$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' 39 && cp -r 'taxa_plots/js' '$area_charts_html_report.files_path'
40 && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report' 40 && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report'
41 #end if 41 #end if
42 42
43 #if "bar" in $chosen_chart_type: 43 #if "bar" in $chosen_chart_type:
44 && mkdir -p '$bar_charts_html_report.files_path' 44 && mkdir -p '$bar_charts_html_report.files_path'
45 && cp -r 'taxa_plots/bar_charts.html' '$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' 46 && cp -r 'taxa_plots/charts' '$bar_charts_html_report.files_path'
47 && cp -r 'taxa_plots/css' '$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' 48 && cp -r 'taxa_plots/js' '$bar_charts_html_report.files_path'
49 && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report' 49 && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report'
50 #end if 50 #end if
51 51
52 #if "pie" in $chosen_chart_type: 52 #if "pie" in $chosen_chart_type:
53 && mkdir -p '$pie_charts_html_report.files_path' 53 && mkdir -p '$pie_charts_html_report.files_path'
54 && cp -r 'taxa_plots/pie_charts.html' '$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' 55 && cp -r 'taxa_plots/charts' '$pie_charts_html_report.files_path'
56 && cp -r 'taxa_plots/css' '$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' 57 && cp -r 'taxa_plots/js' '$pie_charts_html_report.files_path'
58 && mv '$pie_charts_html_report.files_path/pie_charts.html' '$pie_charts_html_report' 58 && mv '$pie_charts_html_report.files_path/pie_charts.html' '$pie_charts_html_report'
59 #end if 59 #end if
60 ]]></command> 60 ]]></command>
61 <inputs> 61 <inputs>
62 <param argument="--counts_fname" type="data" format="tabular,txt" label="Summarized taxa files" multiple="True"/> 62 <param argument="--counts_fname" type="data" format="tabular,txt" multiple="true" label="Summarized taxa files"/>
63 <param argument="--labels" type="text" value="" label="Comma-separated list of taxonomic levels"/> 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"/> 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"/> 65 <param argument="--colorby" type="text" value="" optional="true" 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"/>
66 <param argument="--background_color" type="select" label="Background color to 66 <param argument="--background_color" type="select" label="Background color to use in the plots">
67 use in the plots">
68 <option value="white" selected="true">White</option> 67 <option value="white" selected="true">White</option>
69 <option value="black">Black</option> 68 <option value="black">Black</option>
70 </param> 69 </param>
71 <param argument="--dpi" type="integer" value="80" label="Resolution of the plot"/> 70 <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"/> 71 <param argument="--x_width" type="integer" value="12" label="Width of the x-axis to use in the plots"/>
75 <param argument="--type_of_file" type="select" label="Type of image to produce"> 74 <param argument="--type_of_file" type="select" label="Type of image to produce">
76 <option value="pdf">PDF</option> 75 <option value="pdf">PDF</option>
77 <option value="png" selected="true">PNG</option> 76 <option value="png" selected="true">PNG</option>
78 <option value="svg">SVG</option> 77 <option value="svg">SVG</option>
79 </param> 78 </param>
80 <param argument="--chart_type" type="select" label="Type of chart to plot" multiple="True"> 79 <param argument="--chart_type" type="select" multiple="true" label="Type of chart to plot">
81 <option value="area" selected="true">Area</option> 80 <option value="area" selected="true">Area</option>
82 <option value="bar" selected="true">Bar</option> 81 <option value="bar" selected="true">Bar</option>
83 <option value="pie">Pie</option> 82 <option value="pie">Pie</option>
84 </param> 83 </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"/> 84 <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"/> 85 <param argument="--include_html_legend" type="boolean" truevalue="--include_html_legend" falsevalue="" checked="False" label="Include HTML legend?" 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"> 86 <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> 87 <option value="categorical" selected="true">Categorical</option>
89 <option value="numeric">Numeric</option> 88 <option value="numeric">Numeric</option>
90 </param> 89 </param>
91 </inputs> 90 </inputs>