Mercurial > repos > iuc > qiime_plot_taxa_summary

annotate plot_taxa_summary.xml @ 6:c6d84b3ad9db draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 19:40:30 -0400
parents d0910542c8f6
children ab12aca3ede9
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78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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1 <tool id="qiime_plot_taxa_summary" name="Make taxonomy summary charts" version="@WRAPPER_VERSION@.0">
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iuc
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2 <description> based on taxonomy assignment (plot_taxa_summary)</description>
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3 <macros>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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4 <import>macros.xml</import>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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5 </macros>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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6 <expand macro="requirements"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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7 <version_command>MPLBACKEND="Agg" plot_taxa_summary.py --version</version_command>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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8 <command detect_errors="aggressive"><![CDATA[
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9 #set $chosen_chart_type = str( $chart_type ).split( "," )
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78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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10
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11 ## set matplotlib backend
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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12 export MPLBACKEND="Agg" &&
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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13 echo "backend:agg" > matplotlibrc &&
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78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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14
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15 plot_taxa_summary.py
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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16 --counts_fname '$counts_fname'
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17 --dir_path taxa_plots
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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18 --labels '$labels'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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19 --num_categories '$num_categories'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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20 #if str($colorby) != ''
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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21 --colorby '$colorby'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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22 #end if
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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23 --background_color '$background_color'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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24 --dpi '$dpi'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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25 --x_width '$x_width'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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26 --y_height '$y_height'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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27 --bar_width '$bar_width'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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28 --type_of_file '$type_of_file'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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29 --chart_type '$chart_type'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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30 --resize_nth_label '$resize_nth_label'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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31 $include_html_legend
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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32 --label_type '$label_type'
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33
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34 #if "area" in $chosen_chart_type:
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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35 && mkdir -p '$area_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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36 && cp -r 'taxa_plots/area_charts.html' '$area_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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37 && cp -r 'taxa_plots/charts' '$area_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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38 && cp -r 'taxa_plots/css' '$area_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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39 && cp -r 'taxa_plots/js' '$area_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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40 && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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41 #end if
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42
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43 #if "bar" in $chosen_chart_type:
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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44 && mkdir -p '$bar_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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45 && cp -r 'taxa_plots/bar_charts.html' '$bar_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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46 && cp -r 'taxa_plots/charts' '$bar_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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47 && cp -r 'taxa_plots/css' '$bar_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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48 && cp -r 'taxa_plots/js' '$bar_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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49 && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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50 #end if
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51
5
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52 #if "pie" in $chosen_chart_type:
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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53 && mkdir -p '$pie_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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54 && cp -r 'taxa_plots/pie_charts.html' '$pie_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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55 && cp -r 'taxa_plots/charts' '$pie_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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56 && cp -r 'taxa_plots/css' '$pie_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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57 && cp -r 'taxa_plots/js' '$pie_charts_html_report.files_path'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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58 && mv '$pie_charts_html_report.files_path/pie_charts.html' '$pie_charts_html_report'
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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59 #end if
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60 ]]></command>
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61 <inputs>
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62 <param argument="--counts_fname" type="data" format="tabular,txt" multiple="true" label="Summarized taxa files"/>
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63 <param argument="--labels" type="text" value="" label="Comma-separated list of taxonomic levels"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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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"/>
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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"/>
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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66 <param argument="--background_color" type="select" label="Background color to use in the plots">
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67 <option value="white" selected="true">White</option>
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68 <option value="black">Black</option>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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69 </param>
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70 <param argument="--dpi" type="integer" value="80" label="Resolution of the plot"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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71 <param argument="--x_width" type="integer" value="12" label="Width of the x-axis to use in the plots"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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72 <param argument="--y_height" type="integer" value="12" label="Height of the y-axis to use in the plots"/>
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73 <param argument="--bar_width" type="float" value="0.75" min="0" max="1" label="Width of the bars in the bar graph"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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74 <param argument="--type_of_file" type="select" label="Type of image to produce">
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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75 <option value="pdf">PDF</option>
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76 <option value="png" selected="true">PNG</option>
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77 <option value="svg">SVG</option>
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78 </param>
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79 <param argument="--chart_type" type="select" multiple="true" label="Type of chart to plot">
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80 <option value="area" selected="true">Area</option>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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81 <option value="bar" selected="true">Bar</option>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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82 <option value="pie">Pie</option>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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diff changeset
83 </param>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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diff changeset
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"/>
5
d0910542c8f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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diff changeset
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"/>
0
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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diff changeset
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">
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
87 <option value="categorical" selected="true">Categorical</option>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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88 <option value="numeric">Numeric</option>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
89 </param>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
90 </inputs>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
91 <outputs>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
92 <data name="bar_charts_html_report" format="html" label="${tool.name} on ${on_string}: Bar charts">
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
93 <filter>'bar' in chart_type</filter>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
94 </data>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
95 <data name="pie_charts_html_report" format="html" label="${tool.name} on ${on_string}: Pie charts">
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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96 <filter>'pie' in chart_type</filter>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
97 </data>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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98 <data name="area_charts_html_report" format="html" label="${tool.name} on ${on_string}: Area charts">
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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99 <filter>'area' in chart_type</filter>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
100 </data>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
101 </outputs>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
102 <tests>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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103 <test>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
104 <param name="counts_fname" value="plot_taxa_summary/phylum.txt"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
105 <param name="labels" value="phylum"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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106 <param name="num_categories" value="20"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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107 <param name="background_color" value="white"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
108 <param name="dpi" value="80"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
109 <param name="x_width" value="12"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
110 <param name="y_height" value="12"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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111 <param name="bar_width" value="0.75"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
112 <param name="type_of_file" value="png"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
113 <param name="chart_type" value="area,bar,pie"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
114 <param name="include_html_legend" value="" />
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
115 <param name="resize_nth_label" value="0"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
116 <param name="label_type" value="categorical" />
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
117 <output name="bar_charts_html_report" value="plot_taxa_summary/phylum/bar_charts.html" compare="sim_size"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
118 <output name="pie_charts_html_report" value="plot_taxa_summary/phylum/pie_charts.html" compare="sim_size"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
119 <output name="area_charts_html_report" value="plot_taxa_summary/phylum/area_charts.html" compare="sim_size"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
120 </test>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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121 <test>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
122 <param name="counts_fname" value="plot_taxa_summary/phylum.txt,plot_taxa_summary/class.txt,plot_taxa_summary/genus.txt"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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123 <param name="labels" value="Phylum,Class,Genus"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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124 <param name="num_categories" value="20"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
125 <param name="background_color" value="white"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
126 <param name="dpi" value="80"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
127 <param name="x_width" value="12"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
128 <param name="y_height" value="12"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
129 <param name="bar_width" value="0.75"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
130 <param name="type_of_file" value="png"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
131 <param name="chart_type" value="area,bar,pie"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
132 <param name="include_html_legend" value="" />
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
133 <param name="resize_nth_label" value="0"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
134 <param name="label_type" value="categorical" />
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
135 <output name="bar_charts_html_report" value="plot_taxa_summary/phylum_class_genus/bar_charts.html" compare="sim_size"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
136 <output name="pie_charts_html_report" value="plot_taxa_summary/phylum_class_genus/pie_charts.html" compare="sim_size"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
137 <output name="area_charts_html_report" value="plot_taxa_summary/phylum_class_genus/area_charts.html" compare="sim_size"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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138 </test>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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139 <test>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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140 <param name="counts_fname" value="plot_taxa_summary/class.txt"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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141 <param name="labels" value="Class"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
142 <param name="num_categories" value="10"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
143 <param name="background_color" value="white"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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144 <param name="dpi" value="80"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
145 <param name="x_width" value="12"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
146 <param name="y_height" value="12"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
147 <param name="bar_width" value="0.75"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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148 <param name="chart_type" value="pie"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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149 <param name="type_of_file" value="svg"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
150 <param name="include_html_legend" value="--include_html_legend" />
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
151 <param name="resize_nth_label" value="0"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
152 <param name="label_type" value="categorical" />
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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153 <output name="pie_charts_html_report" value="plot_taxa_summary/class/pie_charts.html" compare="sim_size"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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154 </test>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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155 <test>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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156 <param name="counts_fname" value="plot_taxa_summary/class.txt"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
157 <param name="labels" value="Class"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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158 <param name="num_categories" value="20"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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159 <param name="colorby" value="PC.636,PC.635"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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160 <param name="background_color" value="white"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
161 <param name="dpi" value="80"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
162 <param name="x_width" value="12"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
163 <param name="y_height" value="12"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
164 <param name="bar_width" value="0.75"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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165 <param name="type_of_file" value="pdf"/>
78b8aba19876 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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166 <param name="chart_type" value="area,bar,pie"/>
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167 <param name="include_html_legend" value="" />
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168 <param name="resize_nth_label" value="0"/>
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169 <param name="label_type" value="categorical" />
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170 <output name="bar_charts_html_report" value="plot_taxa_summary/class_colorby/bar_charts.html" compare="sim_size"/>
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171 <output name="pie_charts_html_report" value="plot_taxa_summary/class_colorby/pie_charts.html" compare="sim_size"/>
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172 <output name="area_charts_html_report" value="plot_taxa_summary/class_colorby/area_charts.html" compare="sim_size"/>
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173 </test>
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174 </tests>
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175 <help><![CDATA[
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176 **What it does**
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177
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178 This script automates the construction of pie, bar and area charts showing the breakdown of taxonomy by given levels.
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179
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180 More information about this tool is available on
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181 `QIIME documentation <http://qiime.org/scripts/plot_taxa_summary.html>`_.
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182 ]]></help>
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183 <citations>
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184 <expand macro="citations"/>
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185 </citations>
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186 </tool>