Mercurial > repos > iuc > phyloseq_plot_richness

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit fa72d860839082a926004d8a97a03a3e27701333
author iuc
date Fri, 04 Apr 2025 10:13:51 +0000
parents b6b41cf9c30a
children
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7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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1 <tool id="phyloseq_plot_richness" name="Phyloseq: plot alpha diverstiy measure" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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2 <description></description>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
1
b6b41cf9c30a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '${__tool_directory__}/phyloseq_plot_richness.R'
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10 --input '$input'
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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11 --output '$output'
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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12 ]]></command>
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13 <inputs>
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14 <expand macro="phyloseq_input"/>
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15 </inputs>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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16 <outputs>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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17 <data name="output" format="pdf"/>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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22 <output name="output" ftype="pdf">
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23 <assert_contents>
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24 <has_text text="%PDF"/>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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25 <has_text text="%%EOF"/>
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26 </assert_contents>
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27 </output>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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28 </test>
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29 </tests>
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30 <help>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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31 **What it does**
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33 Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table,
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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34 estimates a number of alpha-diversity metrics, and generates a colored plot that includes the alpha diverstiy measure
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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35 of each sample.
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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36 </help>
7a27e9711e4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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37 <expand macro="citations"/>
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38 </tool>
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