Mercurial > repos > iuc > qiime_plot_taxa_summary
comparison plot_taxa_summary.xml @ 5:d0910542c8f6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
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date | Sat, 05 Aug 2017 07:25:17 -0400 |
parents | 78b8aba19876 |
children | ab12aca3ede9 |
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4:7d1a644d1032 | 5:d0910542c8f6 |
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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> |