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comparison alpha_diversity.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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1 <tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="1.9.1">
2 <description>on each sample in an otu table</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements" />
9
10 <version_command><![CDATA[
11 alpha_diversity.py --version
12 ]]>
13 </version_command>
14
15 <command>
16 <![CDATA[
17 #set $chosen_metrics = str( $metrics ).split( "," )
18
19 alpha_diversity.py
20 -i $input_table
21 -o $alpha_diversity
22
23 -m $metrics
24
25 #if "PD_whole_tree" in $chosen_metrics:
26 -t $tree_file
27 #end if
28
29 ]]>
30 </command>
31
32 <inputs>
33 <param name="input_table" type="data" format="tabular,txt,tsv,biom"
34 label="OTU table" help="(-i/--input_path)"
35 multiple="True"/>
36
37 <param name="metrics" type="select" multiple="True" label="Alpha-diversity
38 metric(s) to use" help="(-m/--metrics)"
39 display="checkboxes">
40 <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option>
41 <option value="berger_parker_d">Berger-Parker dominance</option>
42 <option value="brillouin_d">Brillouin index of alpha diversity</option>
43 <option value="chao1" selected="true">chao1 richness estimator</option>
44 <option value="chao1_ci">chao1 confidence interval</option>
45 <option value="dominance">Dominance</option>
46 <option value="doubles">Number of double occurrences (doubletons)</option>
47 <option value="enspie">ENS_pie alpha diversity measure</option>
48 <option value="equitability">Equitability</option>
49 <option value="esty_ci">Esty’s CI</option>
50 <option value="fisher_alpha">Fisher’s alpha</option>
51 <option value="gini_index">Gini index</option>
52 <option value="goods_coverage">Good’s coverage of counts</option>
53 <option value="heip_e">Heip’s evenness measure</option>
54 <option value="kempton_taylor_q">Kempton-Taylor Q index of alpha diversity</option>
55 <option value="margalef">Margalef’s richness index</option>
56 <option value="mcintosh_d">McIntosh dominance index D</option>
57 <option value="mcintosh_e">McIntosh’s evenness measure E</option>
58 <option value="menhinick">Menhinick’s richness index</option>
59 <option value="michaelis_menten_fit">Michaelis-Menten fit to rarefaction curve of observed OTUs</option>
60 <option value="observed_otus">Number of distinct OTUs</option>
61 <option value="observed_species" selected="true">Number of distinct species</option>
62 <option value="osd">Observed OTUs, singles, and doubles</option>
63 <option value="simpson_reciprocal">simpson_reciprocal</option>
64 <option value="robbins">Robbins’ estimator for the probability of unobserved outcomes</option>
65 <option value="shannon">Shannon entropy of counts</option>
66 <option value="simpson">Simpson’s index</option>
67 <option value="simpson_e">Simpson’s evenness measure E</option>
68 <option value="singles">Number of single occurrencesles</option>
69 <option value="strong"> Strong’s dominance index</option>
70 <option value="PD_whole_tree">Phylogenetic diversity</option>
71 </param>
72
73 <param name="tree_file" type="data" label="Newick tree (optional, except
74 for PD_whole_tree metric" help="(-t/--tree_path)" optional="True"/>
75 </inputs>
76
77 <outputs>
78 <data name="alpha_diversity" format="tabular"
79 from_work_dir="alpha_diversity/alpha_div.txt"
80 label="${tool.name} on ${on_string}: Alpha diversity" />
81 </outputs>
82
83 <tests>
84 <test>
85 <param name="input_table" value="pick_open_reference_otus_otu_table.txt"/>
86 <param name="metrics" value="chao1,observed_species" />
87 <output name="alpha_diversity" value="" />
88 </test>
89 </tests>
90
91 <help><![CDATA[
92
93 **What it does?**
94
95 This tool calculates alpha diversity, or within-sample diversity, using an
96 OTU table.
97
98 The resulting file(s) is a tab-delimited text file, where the columns correspond
99 to alpha diversity metrics and the rows correspond to samples and their calculated
100 diversity measurements. When a folder is given as input (-i), the script processes
101 every otu table file in the given folder, and creates a corresponding file in the
102 output directory.
103
104 More information about this tool is available on
105 `QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_.
106 ]]>
107 </help>
108
109 <citations>
110 <expand macro="citations" />
111 </citations>
112 </tool>