Mercurial > repos > iuc > phyloseq_plot_richness
diff phyloseq_plot_richness.xml @ 0:92b82deaaed1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
author | iuc |
---|---|
date | Thu, 03 Mar 2022 13:28:55 +0000 |
parents | |
children | 1ff178d1757e |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_plot_richness.xml Thu Mar 03 13:28:55 2022 +0000 @@ -0,0 +1,38 @@ +<tool id="phyloseq_plot_richness" name="Phyloseq: plot alpha diverstiy measure" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +Rscript '${__tool_directory__}/phyloseq_plot_richness.R' +--input '$input' +--output '$output' + ]]></command> + <inputs> + <expand macro="phyloseq_input"/> + </inputs> + <outputs> + <data name="output" format="pdf"/> + </outputs> + <tests> + <test> + <param name="input" value="output.phyloseq" ftype="phyloseq"/> + <output name="output" ftype="pdf"> + <assert_contents> + <has_text text="%PDF"/> + <has_text text="%%EOF"/> + </assert_contents> + </output> + </test> + </tests> + <help> +**What it does** + +Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table, +estimates a number of alpha-diversity metrics, and generates a colored plot that includes the alpha diverstiy measure +of each sample. + </help> + <expand macro="citations"/> +</tool> +