Mercurial > repos > iuc > qiime_plot_taxa_summary
diff 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 |
|---|---|
| date | Sat, 05 Aug 2017 07:25:17 -0400 |
| parents | 78b8aba19876 |
| children | ab12aca3ede9 |
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--- a/plot_taxa_summary.xml Mon Jul 10 16:40:35 2017 -0400 +++ b/plot_taxa_summary.xml Sat Aug 05 07:25:17 2017 -0400 @@ -1,70 +1,69 @@ <tool id="qiime_plot_taxa_summary" name="Make taxonomy summary charts" version="@WRAPPER_VERSION@.0"> - <description>based on taxonomy assignment</description> + <description> based on taxonomy assignment (plot_taxa_summary)</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>MPLBACKEND="Agg" plot_taxa_summary.py --version</version_command> <command detect_errors="aggressive"><![CDATA[ - #set $chosen_chart_type = str( $chart_type ).split( "," ) +#set $chosen_chart_type = str( $chart_type ).split( "," ) - ## set matplotlib backend - export MPLBACKEND="Agg" && - echo "backend:agg" > matplotlibrc && +## set matplotlib backend +export MPLBACKEND="Agg" && +echo "backend:agg" > matplotlibrc && - plot_taxa_summary.py - --counts_fname '$counts_fname' - --dir_path taxa_plots - --labels '$labels' - --num_categories '$num_categories' - #if str($colorby) != '' - --colorby '$colorby' - #end if - --background_color '$background_color' - --dpi '$dpi' - --x_width '$x_width' - --y_height '$y_height' - --bar_width '$bar_width' - --type_of_file '$type_of_file' - --chart_type '$chart_type' - --resize_nth_label '$resize_nth_label' - $include_html_legend - --label_type '$label_type' +plot_taxa_summary.py + --counts_fname '$counts_fname' + --dir_path taxa_plots + --labels '$labels' + --num_categories '$num_categories' + #if str($colorby) != '' + --colorby '$colorby' + #end if + --background_color '$background_color' + --dpi '$dpi' + --x_width '$x_width' + --y_height '$y_height' + --bar_width '$bar_width' + --type_of_file '$type_of_file' + --chart_type '$chart_type' + --resize_nth_label '$resize_nth_label' + $include_html_legend + --label_type '$label_type' - #if "area" in $chosen_chart_type: - && mkdir -p '$area_charts_html_report.files_path' - && cp -r 'taxa_plots/area_charts.html' '$area_charts_html_report.files_path' - && cp -r 'taxa_plots/charts' '$area_charts_html_report.files_path' - && cp -r 'taxa_plots/css' '$area_charts_html_report.files_path' - && cp -r 'taxa_plots/js' '$area_charts_html_report.files_path' - && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report' - #end if +#if "area" in $chosen_chart_type: + && mkdir -p '$area_charts_html_report.files_path' + && cp -r 'taxa_plots/area_charts.html' '$area_charts_html_report.files_path' + && cp -r 'taxa_plots/charts' '$area_charts_html_report.files_path' + && cp -r 'taxa_plots/css' '$area_charts_html_report.files_path' + && cp -r 'taxa_plots/js' '$area_charts_html_report.files_path' + && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report' +#end if - #if "bar" in $chosen_chart_type: - && mkdir -p '$bar_charts_html_report.files_path' - && cp -r 'taxa_plots/bar_charts.html' '$bar_charts_html_report.files_path' - && cp -r 'taxa_plots/charts' '$bar_charts_html_report.files_path' - && cp -r 'taxa_plots/css' '$bar_charts_html_report.files_path' - && cp -r 'taxa_plots/js' '$bar_charts_html_report.files_path' - && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report' - #end if +#if "bar" in $chosen_chart_type: + && mkdir -p '$bar_charts_html_report.files_path' + && cp -r 'taxa_plots/bar_charts.html' '$bar_charts_html_report.files_path' + && cp -r 'taxa_plots/charts' '$bar_charts_html_report.files_path' + && cp -r 'taxa_plots/css' '$bar_charts_html_report.files_path' + && cp -r 'taxa_plots/js' '$bar_charts_html_report.files_path' + && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report' +#end if - #if "pie" in $chosen_chart_type: - && mkdir -p '$pie_charts_html_report.files_path' - && cp -r 'taxa_plots/pie_charts.html' '$pie_charts_html_report.files_path' - && cp -r 'taxa_plots/charts' '$pie_charts_html_report.files_path' - && cp -r 'taxa_plots/css' '$pie_charts_html_report.files_path' - && cp -r 'taxa_plots/js' '$pie_charts_html_report.files_path' - && mv '$pie_charts_html_report.files_path/pie_charts.html' '$pie_charts_html_report' - #end if +#if "pie" in $chosen_chart_type: + && mkdir -p '$pie_charts_html_report.files_path' + && cp -r 'taxa_plots/pie_charts.html' '$pie_charts_html_report.files_path' + && cp -r 'taxa_plots/charts' '$pie_charts_html_report.files_path' + && cp -r 'taxa_plots/css' '$pie_charts_html_report.files_path' + && cp -r 'taxa_plots/js' '$pie_charts_html_report.files_path' + && mv '$pie_charts_html_report.files_path/pie_charts.html' '$pie_charts_html_report' +#end if ]]></command> <inputs> - <param argument="--counts_fname" type="data" format="tabular,txt" label="Summarized taxa files" multiple="True"/> + <param argument="--counts_fname" type="data" format="tabular,txt" multiple="true" label="Summarized taxa files"/> <param argument="--labels" type="text" value="" label="Comma-separated list of taxonomic levels"/> <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"/> - <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"/> - <param argument="--background_color" type="select" label="Background color to - use in the plots"> + <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"/> + <param argument="--background_color" type="select" label="Background color to use in the plots"> <option value="white" selected="true">White</option> <option value="black">Black</option> </param> @@ -77,13 +76,13 @@ <option value="png" selected="true">PNG</option> <option value="svg">SVG</option> </param> - <param argument="--chart_type" type="select" label="Type of chart to plot" multiple="True"> + <param argument="--chart_type" type="select" multiple="true" label="Type of chart to plot"> <option value="area" selected="true">Area</option> <option value="bar" selected="true">Bar</option> <option value="pie">Pie</option> </param> <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"/> - <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"/> + <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"/> <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"> <option value="categorical" selected="true">Categorical</option> <option value="numeric">Numeric</option>