Mercurial > repos > iuc > qiime_summarize_taxa_through_plots
annotate summarize_taxa_through_plots.xml @ 4:edd4e009d866 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
author | iuc |
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date | Mon, 10 Jul 2017 16:42:50 -0400 |
parents | 72b02cea4123 |
children | 62eb36dff24d |
rev | line source |
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0
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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1 <tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="@WRAPPER_VERSION@.0"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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2 <description>summaries and plots</description> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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3 <macros> |
72b02cea4123
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> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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5 </macros> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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6 <expand macro="requirements"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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7 <version_command>summarize_taxa_through_plots.py --version</version_command> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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8 <command detect_errors="aggressive"><![CDATA[ |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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9 ## set matplotlib backend |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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10 export MPLBACKEND="Agg" && |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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11 echo "backend:agg" > matplotlibrc && |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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12 |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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13 summarize_taxa_through_plots.py |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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14 --otu_table_fp '$otu_table_fp' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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15 --output_dir output |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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16 #if $parameter_fp |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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17 --parameter_fp '$parameter_fp' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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18 #end if |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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19 #if $mapping.use_mapping == "yes" |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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20 --mapping_fp '$mapping.mapping_fp' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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21 #if str($mapping.mapping_category) != '' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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22 --mapping_category '$mapping.mapping_category' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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23 #end if |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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24 #end if |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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25 $sort |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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26 && mkdir -p '$area_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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27 && cp -r 'output/taxa_summary_plots/area_charts.html' '$area_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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28 && cp -r 'output/taxa_summary_plots/charts' '$area_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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29 && cp -r 'output/taxa_summary_plots/css' '$area_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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30 && cp -r 'output/taxa_summary_plots/js' '$area_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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31 && cp -r 'output/taxa_summary_plots/raw_data' '$area_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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32 && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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33 |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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34 && mkdir -p '$bar_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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35 && cp -r 'output/taxa_summary_plots/bar_charts.html' '$bar_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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36 && cp -r 'output/taxa_summary_plots/charts' '$bar_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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37 && cp -r 'output/taxa_summary_plots/css' '$bar_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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38 && cp -r 'output/taxa_summary_plots/js' '$bar_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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39 && cp -r 'output/taxa_summary_plots/raw_data' '$bar_charts_html_report.files_path' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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40 && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report' |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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41 ]]></command> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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42 <inputs> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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43 <param argument="--otu_table_fp" type="data" format="biom1,tabular,txt" label="Input OTU table"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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44 <conditional name="mapping"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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45 <param name="use_mapping" type="select" label="Use a metadata mapping file?"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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46 <option value="yes">Yes</option> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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47 <option value="no">No</option> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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48 </param> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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49 <when value="yes"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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50 <param argument="--mapping_fp" type="data" format="tabular,csv" label="Input metadata mapping"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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51 <param argument="--mapping_category" type="text" value="" label="Category to use to summarize OTU table" optional="True"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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52 </when> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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53 <when value="no"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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54 </conditional> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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55 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends.py" optional="true"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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56 <param argument="--sort" type="boolean" label="Sort OTU table?" truevalue="--sort" falsevalue="" checked="False"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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57 </inputs> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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58 <outputs> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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59 <collection name="otu_table" type="list" label="${tool.name} on ${on_string}: OTU tables for the different taxonomic levels"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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60 <discover_datasets pattern=".*_L(?P<designation>.+)\.txt" directory="output/" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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61 </collection> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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62 <collection name="biom_otu_table" type="list" label="${tool.name} on ${on_string}: BIOM OTU tables for the different taxonomic levels"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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63 <discover_datasets pattern=".*_L(?P<designation>.+)\.biom" format="biom1" directory="output/" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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64 </collection> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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65 <data name="bar_charts_html_report" format="html" label="${tool.name} on ${on_string}: Bar charts"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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66 <data name="area_charts_html_report" format="html" label="${tool.name} on ${on_string}: Area charts"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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67 </outputs> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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68 <tests> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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69 <test> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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70 <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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71 <conditional name="mapping"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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72 <param name="use_mapping" value="yes"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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73 <param name="mapping_fp" value="summarize_taxa_through_plots/Fasting_Map.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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74 </conditional> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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75 <output_collection name="otu_table" type="list"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
76 <element name="2" file="summarize_taxa_through_plots/mapping/otu_table_L2.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
77 <element name="3" file="summarize_taxa_through_plots/mapping/otu_table_L3.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
78 <element name="4" file="summarize_taxa_through_plots/mapping/otu_table_L4.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
79 <element name="5" file="summarize_taxa_through_plots/mapping/otu_table_L5.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
80 <element name="6" file="summarize_taxa_through_plots/mapping/otu_table_L6.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
81 </output_collection> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
82 <output_collection name="biom_otu_table" type="list"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
83 <element name="2" file="summarize_taxa_through_plots/mapping/otu_table_L2_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
84 <element name="3" file="summarize_taxa_through_plots/mapping/otu_table_L3_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
85 <element name="4" file="summarize_taxa_through_plots/mapping/otu_table_L4_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
86 <element name="5" file="summarize_taxa_through_plots/mapping/otu_table_L5_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
87 <element name="6" file="summarize_taxa_through_plots/mapping/otu_table_L6_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
88 </output_collection> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
89 <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping/bar_charts.html" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
90 <output name="area_charts_html_report" file="summarize_taxa_through_plots/mapping/area_charts.html" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
91 </test> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
92 <test> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
93 <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
94 <conditional name="mapping"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
95 <param name="use_mapping" value="yes"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
96 <param name="mapping_fp" value="summarize_taxa_through_plots/Fasting_Map.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
97 <param name="mapping_category" value="Treatment"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
98 </conditional> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
99 <output_collection name="otu_table" type="list"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
100 <element name="2" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L2.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
101 <element name="3" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L3.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
102 <element name="4" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L4.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
103 <element name="5" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L5.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
104 <element name="6" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L6.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
105 </output_collection> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
106 <output_collection name="biom_otu_table" type="list"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
107 <element name="2" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L2_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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changeset
|
108 <element name="3" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L3_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
109 <element name="4" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L4_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
110 <element name="5" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L5_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
111 <element name="6" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L6_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
112 </output_collection> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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|
113 <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping_categories/bar_charts.html" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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|
114 <output name="area_charts_html_report" file="summarize_taxa_through_plots/mapping_categories/area_charts.html" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
115 </test> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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116 <test> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
117 <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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118 <conditional name="mapping"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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changeset
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119 <param name="use_mapping" value="yes"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
120 <param name="mapping_fp" value="summarize_taxa_through_plots/Fasting_Map.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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121 </conditional> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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122 <param name="sort" value="--sort"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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123 <output_collection name="otu_table" type="list"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
124 <element name="2" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
125 <element name="3" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
126 <element name="4" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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127 <element name="5" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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128 <element name="6" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6.txt"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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129 </output_collection> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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130 <output_collection name="biom_otu_table" type="list"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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|
131 <element name="2" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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132 <element name="3" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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|
133 <element name="4" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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|
134 <element name="5" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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135 <element name="6" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6_json.biom" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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136 </output_collection> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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137 <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping_sort/bar_charts.html" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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138 <output name="area_charts_html_report" file="summarize_taxa_through_plots/mapping_sort/area_charts.html" compare="sim_size" /> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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139 </test> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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140 <test> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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141 <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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142 <conditional name="mapping"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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143 <param name="use_mapping" value="no"/> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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144 </conditional> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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145 <output_collection name="otu_table" type="list"> |
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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146 <element name="2" file="summarize_taxa_through_plots/without_mapping/otu_table_L2.txt"/> |
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147 <element name="3" file="summarize_taxa_through_plots/without_mapping/otu_table_L3.txt"/> |
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148 <element name="4" file="summarize_taxa_through_plots/without_mapping/otu_table_L4.txt"/> |
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149 <element name="5" file="summarize_taxa_through_plots/without_mapping/otu_table_L5.txt"/> |
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150 <element name="6" file="summarize_taxa_through_plots/without_mapping/otu_table_L6.txt"/> |
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151 </output_collection> |
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152 <output_collection name="biom_otu_table" type="list"> |
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153 <element name="2" file="summarize_taxa_through_plots/without_mapping/otu_table_L2_json.biom" compare="sim_size" /> |
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154 <element name="3" file="summarize_taxa_through_plots/without_mapping/otu_table_L3_json.biom" compare="sim_size" /> |
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155 <element name="4" file="summarize_taxa_through_plots/without_mapping/otu_table_L4_json.biom" compare="sim_size" /> |
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156 <element name="5" file="summarize_taxa_through_plots/without_mapping/otu_table_L5_json.biom" compare="sim_size" /> |
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157 <element name="6" file="summarize_taxa_through_plots/without_mapping/otu_table_L6_json.biom" compare="sim_size" /> |
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158 </output_collection> |
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159 <output name="bar_charts_html_report" file="summarize_taxa_through_plots/without_mapping/bar_charts.html" compare="sim_size" /> |
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160 <output name="area_charts_html_report" file="summarize_taxa_through_plots/without_mapping/area_charts.html" compare="sim_size" /> |
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161 </test> |
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162 </tests> |
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163 <help><![CDATA[ |
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164 **What it does** |
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165 |
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166 This tool summarizes OTU by Category (optional), summarizes taxonomy and plots |
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167 taxonomy summary. |
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168 |
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169 More information about this tool is available on |
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170 `QIIME documentation <http://qiime.org/scripts/summarize_taxa_through_plots.html>`_. |
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171 ]]></help> |
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172 <citations> |
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173 <expand macro="citations"/> |
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174 </citations> |
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175 </tool> |