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comparison alpha_diversity.xml @ 0:b54f72135f58 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
author iuc
date Mon, 04 Apr 2022 10:26:31 +0000
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1 <tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="header"/>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$rscript'
9 ]]></command>
10 <configfiles>
11 <configfile name="rscript"><![CDATA[
12 #set m='"' + '", "'.join(str($measure).split(",")) + '"'
13 library(ampvis2, quietly = TRUE)
14 d <- readRDS("$data")
15 a <- amp_alphadiv(d,
16 measure = c($m),
17 richness = $richness
18 @RAREFY_TOKEN@
19 )
20 write.table(a, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE)
21 ]]></configfile>
22 </configfiles>
23 <inputs>
24 <expand macro="rds_input_macro"/>
25 <param argument="measure" type="select" multiple="true" optional="false" label="Alpha-diversity measure(s) to be included">
26 <option value="observed" selected="true">observed</option>
27 <option value="shannon" selected="true">shannon</option>
28 <option value="simpson" selected="true">simpson</option>
29 <option value="invsimpson" selected="true">invsimpson</option>
30 </param>
31 <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/>
32 <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/>
33 </inputs>
34 <outputs>
35 <data name="alphadiv" format="tabular"/>
36 </outputs>
37 <tests>
38 <test>
39 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
40 <output name="alphadiv">
41 <assert_contents>
42 <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;Reads&#9;ObservedOTUs&#9;Shannon&#9;Simpson&#9;invSimpson"/>
43 <has_text text="16SAMP-536&#9;"/>
44 <has_text text="&#9;Aalborg West&#9;"/>
45 <has_n_lines n="68"/>
46 <has_n_columns n="10"/>
47 </assert_contents>
48 </output>
49 </test>
50 <test>
51 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
52 <param name="measure" value="observed,shannon"/>
53 <param name="richness" value="true"/>
54 <param name="rarefy" value="500"/>
55 <output name="alphadiv">
56 <assert_contents>
57 <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;RawReads&#9;Reads&#9;ObservedOTUs&#9;Shannon&#9;Chao1&#9;ACE"/>
58 <has_text text="16SAMP-536&#9;"/>
59 <has_text text="&#9;Aalborg West&#9;"/>
60 <has_n_lines n="68"/>
61 <has_n_columns n="11"/>
62 <has_text text="&#9;500&#9;"/>
63 </assert_contents>
64 </output>
65 </test>
66 </tests>
67 <help><![CDATA[
68
69 What it does
70 ============
71
72 Calculate alpha-diversity indices for each sample and combines with the metadata.
73
74 The Galaxy tool calls the `amp_alpha_diversity
75 <https://madsalbertsen.github.io/ampvis2/reference/amp_alphadiv.html>`_ function
76 of the ampvis2 package.
77
78 Usage
79 =====
80
81 The alpha-diversity indices are calculated per sample using the vegan function `diversity <https://rdrr.io/pkg/vegan/man/diversity.html>`_,
82 where the read abundances are first rarefied using `rrarefy <https://rdrr.io/pkg/vegan/man/rarefy.html>`_ by the size of the rarefy argument.
83 Refer to the vegan documentation for details about the different indices and how they are
84 calculated.
85
86
87 Input
88 =====
89
90 @HELP_RDS_INPUT@
91
92 Output
93 ======
94
95 A tabular dataset containing the chosen alpha-diversity measures per sample.
96
97 ]]></help>
98 <expand macro="citations">
99 <citation type="doi">10.1371/journal.pcbi.1003531</citation>
100 </expand>
101 </tool>