Mercurial > repos > iuc > qiime_beta_diversity_through_plots
diff beta_diversity_through_plots.xml @ 5:2140c12755d0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
---|---|
date | Sat, 05 Aug 2017 07:17:55 -0400 |
parents | e5b102db53fd |
children | 70c4237c3a00 |
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--- a/beta_diversity_through_plots.xml Mon Jul 10 16:43:51 2017 -0400 +++ b/beta_diversity_through_plots.xml Sat Aug 05 07:17:55 2017 -0400 @@ -1,5 +1,5 @@ -<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices" version="@WRAPPER_VERSION@.0"> - <description>and generate PCoA plots</description> +<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices and generate PCoA plots" version="@WRAPPER_VERSION@.0"> + <description>(beta_diversity_through_plots)</description> <macros> <import>macros.xml</import> </macros> @@ -9,38 +9,38 @@ </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 - $suppress_emperor_plots +beta_diversity_through_plots.py + --otu_table_fp '$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' +&& 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="--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"/> + <param argument="--tree_fp" type="data" format="txt" optional="true" label="Tree file (Optional)"/> <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=""/> + <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?"/> + <param argument="--seqs_per_sample" type="integer" optional="true" label="Depth of coverage for even sampling (Optional)"/> + <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">