Mercurial > repos > iuc > qiime_summarize_taxa_through_plots
annotate summarize_taxa_through_plots.xml @ 7:834ef917138f draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2019 07:54:07 -0500 |
| parents | 62eb36dff24d |
| children |
| rev | line source |
|---|---|
|
7
834ef917138f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
iuc
parents:
5
diff
changeset
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1 <tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy summaries and plots" version="@WRAPPER_VERSION@.0" profile="@PROFILE@"> |
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5
62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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2 <description>(summarize_taxa_through_plots)</description> |
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0
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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3 <macros> |
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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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4 <import>macros.xml</import> |
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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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5 </macros> |
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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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6 <expand macro="requirements"/> |
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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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7 <version_command>summarize_taxa_through_plots.py --version</version_command> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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8 <command detect_errors="aggressive"><![CDATA[ |
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7
834ef917138f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
iuc
parents:
5
diff
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9 @MPLBACKEND@ |
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5
62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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10 summarize_taxa_through_plots.py |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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11 --otu_table_fp '$otu_table_fp' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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12 --output_dir output |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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13 #if $parameter_fp |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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14 --parameter_fp '$parameter_fp' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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15 #end if |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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16 #if $mapping.use_mapping == "yes" |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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17 --mapping_fp '$mapping.mapping_fp' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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18 #if str($mapping.mapping_category) != '' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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19 --mapping_category '$mapping.mapping_category' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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20 #end if |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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21 #end if |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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22 $sort |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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23 && mkdir -p '$area_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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24 && cp -r 'output/taxa_summary_plots/area_charts.html' '$area_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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25 && cp -r 'output/taxa_summary_plots/charts' '$area_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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26 && cp -r 'output/taxa_summary_plots/css' '$area_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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27 && cp -r 'output/taxa_summary_plots/js' '$area_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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28 && cp -r 'output/taxa_summary_plots/raw_data' '$area_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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29 && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report' |
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0
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
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30 |
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5
62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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31 && mkdir -p '$bar_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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32 && cp -r 'output/taxa_summary_plots/bar_charts.html' '$bar_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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33 && cp -r 'output/taxa_summary_plots/charts' '$bar_charts_html_report.files_path' |
|
62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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34 && cp -r 'output/taxa_summary_plots/css' '$bar_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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35 && cp -r 'output/taxa_summary_plots/js' '$bar_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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36 && cp -r 'output/taxa_summary_plots/raw_data' '$bar_charts_html_report.files_path' |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
diff
changeset
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37 && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report' |
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0
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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38 ]]></command> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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39 <inputs> |
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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 <param argument="--otu_table_fp" type="data" format="biom1,tabular,txt" label="Input OTU table"/> |
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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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41 <conditional name="mapping"> |
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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 <param name="use_mapping" type="select" label="Use a metadata mapping file?"> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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43 <option value="yes">Yes</option> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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44 <option value="no">No</option> |
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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> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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46 <when value="yes"> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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47 <param argument="--mapping_fp" type="data" format="tabular,csv" label="Input metadata mapping"/> |
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5
62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
0
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48 <param argument="--mapping_category" type="text" value="" optional="true" label="Category to use to summarize OTU table"/> |
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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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49 </when> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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50 <when value="no"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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51 </conditional> |
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5
62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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52 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends"/> |
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62eb36dff24d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
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53 <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="" checked="false" label="Sort OTU table?"/> |
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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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54 </inputs> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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55 <outputs> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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56 <collection name="otu_table" type="list" label="${tool.name} on ${on_string}: OTU tables for the different taxonomic levels"> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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57 <discover_datasets pattern=".*_L(?P<designation>.+)\.txt" directory="output/" /> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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58 </collection> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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59 <collection name="biom_otu_table" type="list" label="${tool.name} on ${on_string}: BIOM OTU tables for the different taxonomic levels"> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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60 <discover_datasets pattern=".*_L(?P<designation>.+)\.biom" format="biom1" directory="output/" /> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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61 </collection> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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62 <data name="bar_charts_html_report" format="html" label="${tool.name} on ${on_string}: Bar charts"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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63 <data name="area_charts_html_report" format="html" label="${tool.name} on ${on_string}: Area charts"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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64 </outputs> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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65 <tests> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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66 <test> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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67 <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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68 <conditional name="mapping"> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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69 <param name="use_mapping" value="yes"/> |
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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="mapping_fp" value="summarize_taxa_through_plots/Fasting_Map.txt"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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71 </conditional> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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72 <output_collection name="otu_table" type="list"> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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73 <element name="2" file="summarize_taxa_through_plots/mapping/otu_table_L2.txt"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
74 <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
|
75 <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
|
76 <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
|
77 <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
|
78 </output_collection> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
79 <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
|
80 <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
|
81 <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
|
82 <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
|
83 <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
|
84 <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
|
85 </output_collection> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
86 <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping/bar_charts.html" compare="sim_size" /> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
87 <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
|
88 </test> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
89 <test> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
90 <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
|
91 <conditional name="mapping"> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
92 <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
|
93 <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
|
94 <param name="mapping_category" value="Treatment"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
95 </conditional> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
96 <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
|
97 <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
|
98 <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
|
99 <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
|
100 <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
|
101 <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
|
102 </output_collection> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
103 <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
|
104 <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
parents:
diff
changeset
|
105 <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
|
106 <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
|
107 <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
|
108 <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
|
109 </output_collection> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
110 <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping_categories/bar_charts.html" compare="sim_size" /> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
111 <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
|
112 </test> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
113 <test> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
114 <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
115 <conditional name="mapping"> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
116 <param name="use_mapping" value="yes"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
117 <param name="mapping_fp" value="summarize_taxa_through_plots/Fasting_Map.txt"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
118 </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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119 <param name="sort" value="--sort"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
120 <output_collection name="otu_table" type="list"> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
121 <element name="2" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2.txt"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
122 <element name="3" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3.txt"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
123 <element name="4" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4.txt"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
124 <element name="5" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5.txt"/> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
125 <element name="6" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6.txt"/> |
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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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126 </output_collection> |
|
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 <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
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128 <element name="2" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2_json.biom" compare="sim_size" /> |
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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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129 <element name="3" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3_json.biom" compare="sim_size" /> |
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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 <element name="4" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4_json.biom" compare="sim_size" /> |
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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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131 <element name="5" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5_json.biom" compare="sim_size" /> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
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132 <element name="6" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6_json.biom" compare="sim_size" /> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
133 </output_collection> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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134 <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping_sort/bar_charts.html" compare="sim_size" /> |
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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 <output name="area_charts_html_report" file="summarize_taxa_through_plots/mapping_sort/area_charts.html" compare="sim_size" /> |
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72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
136 </test> |
|
72b02cea4123
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff
changeset
|
137 <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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138 <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> |
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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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139 <conditional name="mapping"> |
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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 <param name="use_mapping" value="no"/> |
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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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141 </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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142 <output_collection name="otu_table" type="list"> |
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143 <element name="2" file="summarize_taxa_through_plots/without_mapping/otu_table_L2.txt"/> |
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144 <element name="3" file="summarize_taxa_through_plots/without_mapping/otu_table_L3.txt"/> |
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145 <element name="4" file="summarize_taxa_through_plots/without_mapping/otu_table_L4.txt"/> |
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146 <element name="5" file="summarize_taxa_through_plots/without_mapping/otu_table_L5.txt"/> |
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147 <element name="6" file="summarize_taxa_through_plots/without_mapping/otu_table_L6.txt"/> |
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148 </output_collection> |
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149 <output_collection name="biom_otu_table" type="list"> |
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150 <element name="2" file="summarize_taxa_through_plots/without_mapping/otu_table_L2_json.biom" compare="sim_size" /> |
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151 <element name="3" file="summarize_taxa_through_plots/without_mapping/otu_table_L3_json.biom" compare="sim_size" /> |
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152 <element name="4" file="summarize_taxa_through_plots/without_mapping/otu_table_L4_json.biom" compare="sim_size" /> |
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153 <element name="5" file="summarize_taxa_through_plots/without_mapping/otu_table_L5_json.biom" compare="sim_size" /> |
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154 <element name="6" file="summarize_taxa_through_plots/without_mapping/otu_table_L6_json.biom" compare="sim_size" /> |
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155 </output_collection> |
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156 <output name="bar_charts_html_report" file="summarize_taxa_through_plots/without_mapping/bar_charts.html" compare="sim_size" /> |
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157 <output name="area_charts_html_report" file="summarize_taxa_through_plots/without_mapping/area_charts.html" compare="sim_size" /> |
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158 </test> |
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159 </tests> |
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160 <help><![CDATA[ |
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161 **What it does** |
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162 |
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163 This tool summarizes OTU by Category (optional), summarizes taxonomy and plots |
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164 taxonomy summary. |
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165 |
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166 More information about this tool is available on |
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167 `QIIME documentation <http://qiime.org/scripts/summarize_taxa_through_plots.html>`_. |
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168 ]]></help> |
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169 <citations> |
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170 <expand macro="citations"/> |
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171 </citations> |
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172 </tool> |