Mercurial > repos > iuc > qiime_alpha_diversity
diff alpha_diversity.xml @ 5:ffe438e1fc67 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
---|---|
date | Sat, 05 Aug 2017 07:26:40 -0400 |
parents | 2ceee245d97c |
children | 1fa3942bec04 |
line wrap: on
line diff
--- a/alpha_diversity.xml Mon Jul 10 16:42:35 2017 -0400 +++ b/alpha_diversity.xml Sat Aug 05 07:26:40 2017 -0400 @@ -1,23 +1,23 @@ <tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="@WRAPPER_VERSION@.0"> - <description>on each sample in an otu table</description> + <description> on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity)</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>alpha_diversity.py --version</version_command> <command detect_errors="aggressive"><![CDATA[ - #set $chosen_metrics = str( $metrics ).split( "," ) - alpha_diversity.py - --input_path '$input_path' - -o alphadiv - --metrics '$metrics' - #if "PD_whole_tree" in $chosen_metrics: - --tree_path '$tree_path' - #end if +#set $chosen_metrics = str( $metrics ).split( "," ) +alpha_diversity.py + --input_path '$input_path' + -o alphadiv + --metrics '$metrics' + #if "PD_whole_tree" in $chosen_metrics: + --tree_path '$tree_path' + #end if ]]></command> <inputs> <param argument="--input_path" type="data" format="tabular,txt,tsv,biom" multiple="True" label="OTU table"/> - <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Alpha-diversity metric(s) to use"> + <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Alpha-diversity metric(s) to use"> <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option> <option value="berger_parker_d">Berger-Parker dominance</option> <option value="brillouin_d">Brillouin index of alpha diversity</option> @@ -50,7 +50,7 @@ <option value="strong"> Strong’s dominance index</option> <option value="PD_whole_tree">Phylogenetic diversity</option> </param> - <param argument="--tree_path" type="data" format="nhx" optional="True" label="Newick tree (optional, except for PD_whole_tree metric)"/> + <param argument="--tree_path" type="data" format="nhx" optional="true" label="Newick tree (optional, except for PD_whole_tree metric)"/> </inputs> <outputs> <data name="alpha_diversity" format="tabular" from_work_dir="alphadiv" label="${tool.name} on ${on_string}: Alpha diversity"/>