Mercurial > repos > iuc > qiime_beta_diversity_through_plots
diff beta_diversity_through_plots.xml @ 0:e5b102db53fd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:34:39 -0400 |
| parents | |
| children | 2140c12755d0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/beta_diversity_through_plots.xml Thu May 18 09:34:39 2017 -0400 @@ -0,0 +1,99 @@ +<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices" version="@WRAPPER_VERSION@.0"> + <description>and generate PCoA plots</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <stdio> + <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/> + </stdio> + <version_command>beta_diversity_through_plots.py --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + beta_diversity_through_plots.py + --otu_table_fp '$otu_table_fp' + --mapping_fp '$mapping_fp' + --output_dir beta_diversity_through_plots + #if $tree_fp + --tree_fp '$tree_fp' + #end if + #if $parameter_fp + --parameter_fp '$parameter_fp' + #end if + $color_by_all_fields + $parallel + -O "\${GALAXY_SLOTS:-4}" + #if $seqs_per_sample + --seqs_per_sample '$seqs_per_sample' + #end if + $suppress_emperor_plots + + && python $__tool_directory__/beta_diversity_through_plots_html_generation.py + --data_directory beta_diversity_through_plots + --html_file '$beta_diversity_pcoa' + --html_dir '$beta_diversity_pcoa.files_path' + ]]></command> + <inputs> + <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="True" label="OTU table"/> + <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="True" label="Mapping file" help=""/> + <param argument="--tree_fp" type="data" format="txt" optional="True" label="Tree file (Optional)" help=""/> + <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/> + <param argument="--color_by_all_fields" type="text" optional="True" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/> + <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?" help=""/> + <param argument="--seqs_per_sample" type="integer" optional="True" label="Depth of coverage for even sampling (Optional)" help=""/> + <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="True" label="Generate emperor plots?" help=""/> + </inputs> + <outputs> + <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics"> + <discover_datasets pattern="(?P<designation>.+)_dm\.txt" ext="txt" directory="beta_diversity_through_plots"/> + </collection> + <collection name="beta_diversity_pc" type="list" label="${tool.name} on ${on_string}: Principal coordinates for each metrics"> + <discover_datasets pattern="(?P<designation>.+)_pc\.txt" ext="txt" directory="beta_diversity_through_plots"/> + </collection> + <data format="html" name="beta_diversity_pcoa" label="${tool.name} on ${on_string}: Emperor PCoA plots"/> + </outputs> + <tests> + <test> + <param name="otu_table_fp" value="beta_diversity_through_plots/otu_table.biom"/> + <param name="mapping_fp" value="beta_diversity_through_plots/map.txt"/> + <param name="tree_fp" value="beta_diversity_through_plots/rep_set.tre"/> + <param name="parallel" value="--parallel"/> + <param name="suppress_emperor_plots" value=""/> + <output_collection name="beta_diversity_matrix" type="list" count="2"> + <element name="unweighted_unifrac" file="beta_diversity_through_plots/unweighted_unifrac_dm.txt" ftype="txt"/> + <element name="weighted_unifrac" file="beta_diversity_through_plots/weighted_unifrac_dm.txt" ftype="txt"/> + </output_collection> + <output_collection name="beta_diversity_pc" type="list" count="2"> + <element name="unweighted_unifrac" ftype="txt"> + <assert_contents> + <has_text text="PC.355"/> + <has_text text="Species"/> + <has_text text="Site"/> + </assert_contents> + </element> + <element name="weighted_unifrac" file="beta_diversity_through_plots/weighted_unifrac_pc.txt" ftype="txt"/> + </output_collection> + <output name="beta_diversity_pcoa"> + <assert_contents> + <has_text text="unweighted_unifrac" /> + <has_text text="weighted_unifrac" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool computes beta diversity distance matrices and generates PCoA plots in +several steps + + - Performs beta diversity analysis + - Performs principal coordinate analysis + - Generates 3D PCoA Plots + +More information about this tool is available on +`QIIME documentation <http://qiime.org/scripts/beta_diversity_through_plots.html>`_. + ]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool>