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comparison alpha_diversity.xml @ 0:2ceee245d97c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:32:36 -0400
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1 <tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="@WRAPPER_VERSION@.0">
2 <description>on each sample in an otu table</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>alpha_diversity.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[
9 #set $chosen_metrics = str( $metrics ).split( "," )
10 alpha_diversity.py
11 --input_path '$input_path'
12 -o alphadiv
13 --metrics '$metrics'
14 #if "PD_whole_tree" in $chosen_metrics:
15 --tree_path '$tree_path'
16 #end if
17 ]]></command>
18 <inputs>
19 <param argument="--input_path" type="data" format="tabular,txt,tsv,biom" multiple="True" label="OTU table"/>
20 <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Alpha-diversity metric(s) to use">
21 <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option>
22 <option value="berger_parker_d">Berger-Parker dominance</option>
23 <option value="brillouin_d">Brillouin index of alpha diversity</option>
24 <option value="chao1" selected="true">chao1 richness estimator</option>
25 <option value="chao1_ci">chao1 confidence interval</option>
26 <option value="dominance">Dominance</option>
27 <option value="doubles">Number of double occurrences (doubletons)</option>
28 <option value="enspie">ENS_pie alpha diversity measure</option>
29 <option value="equitability">Equitability</option>
30 <option value="esty_ci">Esty’s CI</option>
31 <option value="fisher_alpha">Fisher’s alpha</option>
32 <option value="gini_index">Gini index</option>
33 <option value="goods_coverage">Good’s coverage of counts</option>
34 <option value="heip_e">Heip’s evenness measure</option>
35 <option value="kempton_taylor_q">Kempton-Taylor Q index of alpha diversity</option>
36 <option value="margalef">Margalef’s richness index</option>
37 <option value="mcintosh_d">McIntosh dominance index D</option>
38 <option value="mcintosh_e">McIntosh’s evenness measure E</option>
39 <option value="menhinick">Menhinick’s richness index</option>
40 <option value="michaelis_menten_fit">Michaelis-Menten fit to rarefaction curve of observed OTUs</option>
41 <option value="observed_otus">Number of distinct OTUs</option>
42 <option value="observed_species" selected="true">Number of distinct species</option>
43 <option value="osd">Observed OTUs, singles, and doubles</option>
44 <option value="simpson_reciprocal">simpson_reciprocal</option>
45 <option value="robbins">Robbins’ estimator for the probability of unobserved outcomes</option>
46 <option value="shannon">Shannon entropy of counts</option>
47 <option value="simpson">Simpson’s index</option>
48 <option value="simpson_e">Simpson’s evenness measure E</option>
49 <option value="singles">Number of single occurrencesles</option>
50 <option value="strong"> Strong’s dominance index</option>
51 <option value="PD_whole_tree">Phylogenetic diversity</option>
52 </param>
53 <param argument="--tree_path" type="data" format="nhx" optional="True" label="Newick tree (optional, except for PD_whole_tree metric)"/>
54 </inputs>
55 <outputs>
56 <data name="alpha_diversity" format="tabular" from_work_dir="alphadiv" label="${tool.name} on ${on_string}: Alpha diversity"/>
57 </outputs>
58 <tests>
59 <test><!-- test with defaults -->
60 <param name="input_path" value="alpha_diversity/otu_table.biom"/>
61 <output name="alpha_diversity" file="alpha_diversity/alphadiv"/>
62 </test>
63 <test><!-- test with all metrics and tree file -->
64 <param name="input_path" value="alpha_diversity/otu_table.biom"/>
65 <param name="metrics" value="ace,berger_parker_d,brillouin_d,chao1,chao1_ci,dominance,doubles,enspie,equitability,esty_ci,fisher_alpha,gini_index,goods_coverage,heip_e,kempton_taylor_q,margalef,mcintosh_d,mcintosh_e,menhinick,michaelis_menten_fit,observed_otus,observed_species,osd,simpson_reciprocal,robbins,shannon,simpson,simpson_e,singles,strong,PD_whole_tree"/>
66 <param name="tree_path" value="alpha_diversity/rep_set.tre"/>
67 <output name="alpha_diversity" ftype="tabular">
68 <assert_contents>
69 <has_text text="ace"/>
70 <has_text text="simpson"/>
71 <has_text text="PD_whole_tree"/>
72 </assert_contents>
73 </output>
74 </test>
75 </tests>
76 <help><![CDATA[
77 **What it does**
78
79 This tool calculates alpha diversity, or within-sample diversity, using an
80 OTU table.
81
82 The resulting file(s) is a tab-delimited text file, where the columns correspond
83 to alpha diversity metrics and the rows correspond to samples and their calculated
84 diversity measurements. When a folder is given as input (-i), the script processes
85 every otu table file in the given folder, and creates a corresponding file in the
86 output directory.
87
88 More information about this tool is available on
89 `QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_.
90 ]]></help>
91 <citations>
92 <expand macro="citations"/>
93 </citations>
94 </tool>