Mercurial > repos > iuc > qiime_summarize_taxa_through_plots
diff summarize_taxa_through_plots.xml @ 0:72b02cea4123 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:33:01 -0400 |
| parents | |
| children | 62eb36dff24d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/summarize_taxa_through_plots.xml Thu May 18 09:33:01 2017 -0400 @@ -0,0 +1,175 @@ +<tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="@WRAPPER_VERSION@.0"> + <description>summaries and plots</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>summarize_taxa_through_plots.py --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + ## set matplotlib backend + export MPLBACKEND="Agg" && + echo "backend:agg" > matplotlibrc && + + summarize_taxa_through_plots.py + --otu_table_fp '$otu_table_fp' + --output_dir output + #if $parameter_fp + --parameter_fp '$parameter_fp' + #end if + #if $mapping.use_mapping == "yes" + --mapping_fp '$mapping.mapping_fp' + #if str($mapping.mapping_category) != '' + --mapping_category '$mapping.mapping_category' + #end if + #end if + $sort + && mkdir -p '$area_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/area_charts.html' '$area_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/charts' '$area_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/css' '$area_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/js' '$area_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/raw_data' '$area_charts_html_report.files_path' + && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report' + + && mkdir -p '$bar_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/bar_charts.html' '$bar_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/charts' '$bar_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/css' '$bar_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/js' '$bar_charts_html_report.files_path' + && cp -r 'output/taxa_summary_plots/raw_data' '$bar_charts_html_report.files_path' + && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report' + ]]></command> + <inputs> + <param argument="--otu_table_fp" type="data" format="biom1,tabular,txt" label="Input OTU table"/> + <conditional name="mapping"> + <param name="use_mapping" type="select" label="Use a metadata mapping file?"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param argument="--mapping_fp" type="data" format="tabular,csv" label="Input metadata mapping"/> + <param argument="--mapping_category" type="text" value="" label="Category to use to summarize OTU table" optional="True"/> + </when> + <when value="no"/> + </conditional> + <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends.py" optional="true"/> + <param argument="--sort" type="boolean" label="Sort OTU table?" truevalue="--sort" falsevalue="" checked="False"/> + </inputs> + <outputs> + <collection name="otu_table" type="list" label="${tool.name} on ${on_string}: OTU tables for the different taxonomic levels"> + <discover_datasets pattern=".*_L(?P<designation>.+)\.txt" directory="output/" /> + </collection> + <collection name="biom_otu_table" type="list" label="${tool.name} on ${on_string}: BIOM OTU tables for the different taxonomic levels"> + <discover_datasets pattern=".*_L(?P<designation>.+)\.biom" format="biom1" directory="output/" /> + </collection> + <data name="bar_charts_html_report" format="html" label="${tool.name} on ${on_string}: Bar charts"/> + <data name="area_charts_html_report" format="html" label="${tool.name} on ${on_string}: Area charts"/> + </outputs> + <tests> + <test> + <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> + <conditional name="mapping"> + <param name="use_mapping" value="yes"/> + <param name="mapping_fp" value="summarize_taxa_through_plots/Fasting_Map.txt"/> + </conditional> + <output_collection name="otu_table" type="list"> + <element name="2" file="summarize_taxa_through_plots/mapping/otu_table_L2.txt"/> + <element name="3" file="summarize_taxa_through_plots/mapping/otu_table_L3.txt"/> + <element name="4" file="summarize_taxa_through_plots/mapping/otu_table_L4.txt"/> + <element name="5" file="summarize_taxa_through_plots/mapping/otu_table_L5.txt"/> + <element name="6" file="summarize_taxa_through_plots/mapping/otu_table_L6.txt"/> + </output_collection> + <output_collection name="biom_otu_table" type="list"> + <element name="2" file="summarize_taxa_through_plots/mapping/otu_table_L2_json.biom" compare="sim_size" /> + <element name="3" file="summarize_taxa_through_plots/mapping/otu_table_L3_json.biom" compare="sim_size" /> + <element name="4" file="summarize_taxa_through_plots/mapping/otu_table_L4_json.biom" compare="sim_size" /> + <element name="5" file="summarize_taxa_through_plots/mapping/otu_table_L5_json.biom" compare="sim_size" /> + <element name="6" file="summarize_taxa_through_plots/mapping/otu_table_L6_json.biom" compare="sim_size" /> + </output_collection> + <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping/bar_charts.html" compare="sim_size" /> + <output name="area_charts_html_report" file="summarize_taxa_through_plots/mapping/area_charts.html" compare="sim_size" /> + </test> + <test> + <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> + <conditional name="mapping"> + <param name="use_mapping" value="yes"/> + <param name="mapping_fp" value="summarize_taxa_through_plots/Fasting_Map.txt"/> + <param name="mapping_category" value="Treatment"/> + </conditional> + <output_collection name="otu_table" type="list"> + <element name="2" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L2.txt"/> + <element name="3" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L3.txt"/> + <element name="4" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L4.txt"/> + <element name="5" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L5.txt"/> + <element name="6" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L6.txt"/> + </output_collection> + <output_collection name="biom_otu_table" type="list"> + <element name="2" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L2_json.biom" compare="sim_size" /> + <element name="3" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L3_json.biom" compare="sim_size" /> + <element name="4" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L4_json.biom" compare="sim_size" /> + <element name="5" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L5_json.biom" compare="sim_size" /> + <element name="6" file="summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L6_json.biom" compare="sim_size" /> + </output_collection> + <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping_categories/bar_charts.html" compare="sim_size" /> + <output name="area_charts_html_report" file="summarize_taxa_through_plots/mapping_categories/area_charts.html" compare="sim_size" /> + </test> + <test> + <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> + <conditional name="mapping"> + <param name="use_mapping" value="yes"/> + <param name="mapping_fp" value="summarize_taxa_through_plots/Fasting_Map.txt"/> + </conditional> + <param name="sort" value="--sort"/> + <output_collection name="otu_table" type="list"> + <element name="2" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2.txt"/> + <element name="3" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3.txt"/> + <element name="4" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4.txt"/> + <element name="5" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5.txt"/> + <element name="6" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6.txt"/> + </output_collection> + <output_collection name="biom_otu_table" type="list"> + <element name="2" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2_json.biom" compare="sim_size" /> + <element name="3" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3_json.biom" compare="sim_size" /> + <element name="4" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4_json.biom" compare="sim_size" /> + <element name="5" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5_json.biom" compare="sim_size" /> + <element name="6" file="summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6_json.biom" compare="sim_size" /> + </output_collection> + <output name="bar_charts_html_report" file="summarize_taxa_through_plots/mapping_sort/bar_charts.html" compare="sim_size" /> + <output name="area_charts_html_report" file="summarize_taxa_through_plots/mapping_sort/area_charts.html" compare="sim_size" /> + </test> + <test> + <param name="otu_table_fp" value="summarize_taxa_through_plots/otu_table.biom"/> + <conditional name="mapping"> + <param name="use_mapping" value="no"/> + </conditional> + <output_collection name="otu_table" type="list"> + <element name="2" file="summarize_taxa_through_plots/without_mapping/otu_table_L2.txt"/> + <element name="3" file="summarize_taxa_through_plots/without_mapping/otu_table_L3.txt"/> + <element name="4" file="summarize_taxa_through_plots/without_mapping/otu_table_L4.txt"/> + <element name="5" file="summarize_taxa_through_plots/without_mapping/otu_table_L5.txt"/> + <element name="6" file="summarize_taxa_through_plots/without_mapping/otu_table_L6.txt"/> + </output_collection> + <output_collection name="biom_otu_table" type="list"> + <element name="2" file="summarize_taxa_through_plots/without_mapping/otu_table_L2_json.biom" compare="sim_size" /> + <element name="3" file="summarize_taxa_through_plots/without_mapping/otu_table_L3_json.biom" compare="sim_size" /> + <element name="4" file="summarize_taxa_through_plots/without_mapping/otu_table_L4_json.biom" compare="sim_size" /> + <element name="5" file="summarize_taxa_through_plots/without_mapping/otu_table_L5_json.biom" compare="sim_size" /> + <element name="6" file="summarize_taxa_through_plots/without_mapping/otu_table_L6_json.biom" compare="sim_size" /> + </output_collection> + <output name="bar_charts_html_report" file="summarize_taxa_through_plots/without_mapping/bar_charts.html" compare="sim_size" /> + <output name="area_charts_html_report" file="summarize_taxa_through_plots/without_mapping/area_charts.html" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool summarizes OTU by Category (optional), summarizes taxonomy and plots +taxonomy summary. + +More information about this tool is available on +`QIIME documentation <http://qiime.org/scripts/summarize_taxa_through_plots.html>`_. + ]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool>