Mercurial > repos > iuc > phyloseq_plot_richness
comparison phyloseq_plot_richness.xml @ 0:7a27e9711e4e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
| author | iuc |
|---|---|
| date | Thu, 03 Mar 2022 13:26:59 +0000 |
| parents | |
| children | b6b41cf9c30a |
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| -1:000000000000 | 0:7a27e9711e4e |
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| 1 <tool id="phyloseq_plot_richness" name="Phyloseq: plot alpha diverstiy measure" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 Rscript '${__tool_directory__}/phyloseq_plot_richness.R' | |
| 9 --input '$input' | |
| 10 --output '$output' | |
| 11 ]]></command> | |
| 12 <inputs> | |
| 13 <expand macro="phyloseq_input"/> | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data name="output" format="pdf"/> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="input" value="output.phyloseq" ftype="phyloseq"/> | |
| 21 <output name="output" ftype="pdf"> | |
| 22 <assert_contents> | |
| 23 <has_text text="%PDF"/> | |
| 24 <has_text text="%%EOF"/> | |
| 25 </assert_contents> | |
| 26 </output> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help> | |
| 30 **What it does** | |
| 31 | |
| 32 Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table, | |
| 33 estimates a number of alpha-diversity metrics, and generates a colored plot that includes the alpha diverstiy measure | |
| 34 of each sample. | |
| 35 </help> | |
| 36 <expand macro="citations"/> | |
| 37 </tool> | |
| 38 |