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annotate alpha_diversity.xml @ 0:c1bd0c560018 draft default tip

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author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="1.9.1">
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2 <description>on each sample in an otu table</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="requirements" />
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9
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10 <version_command><![CDATA[
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11 alpha_diversity.py --version
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12 ]]>
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13 </version_command>
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15 <command>
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16 <![CDATA[
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17 #set $chosen_metrics = str( $metrics ).split( "," )
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19 alpha_diversity.py
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20 -i $input_table
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21 -o $alpha_diversity
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23 -m $metrics
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25 #if "PD_whole_tree" in $chosen_metrics:
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26 -t $tree_file
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27 #end if
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29 ]]>
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30 </command>
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32 <inputs>
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33 <param name="input_table" type="data" format="tabular,txt,tsv,biom"
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34 label="OTU table" help="(-i/--input_path)"
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35 multiple="True"/>
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36
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37 <param name="metrics" type="select" multiple="True" label="Alpha-diversity
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38 metric(s) to use" help="(-m/--metrics)"
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39 display="checkboxes">
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40 <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option>
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41 <option value="berger_parker_d">Berger-Parker dominance</option>
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42 <option value="brillouin_d">Brillouin index of alpha diversity</option>
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43 <option value="chao1" selected="true">chao1 richness estimator</option>
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44 <option value="chao1_ci">chao1 confidence interval</option>
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45 <option value="dominance">Dominance</option>
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46 <option value="doubles">Number of double occurrences (doubletons)</option>
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47 <option value="enspie">ENS_pie alpha diversity measure</option>
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48 <option value="equitability">Equitability</option>
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49 <option value="esty_ci">Esty’s CI</option>
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50 <option value="fisher_alpha">Fisher’s alpha</option>
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51 <option value="gini_index">Gini index</option>
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52 <option value="goods_coverage">Good’s coverage of counts</option>
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53 <option value="heip_e">Heip’s evenness measure</option>
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54 <option value="kempton_taylor_q">Kempton-Taylor Q index of alpha diversity</option>
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55 <option value="margalef">Margalef’s richness index</option>
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56 <option value="mcintosh_d">McIntosh dominance index D</option>
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57 <option value="mcintosh_e">McIntosh’s evenness measure E</option>
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58 <option value="menhinick">Menhinick’s richness index</option>
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59 <option value="michaelis_menten_fit">Michaelis-Menten fit to rarefaction curve of observed OTUs</option>
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60 <option value="observed_otus">Number of distinct OTUs</option>
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61 <option value="observed_species" selected="true">Number of distinct species</option>
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62 <option value="osd">Observed OTUs, singles, and doubles</option>
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63 <option value="simpson_reciprocal">simpson_reciprocal</option>
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64 <option value="robbins">Robbins’ estimator for the probability of unobserved outcomes</option>
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65 <option value="shannon">Shannon entropy of counts</option>
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66 <option value="simpson">Simpson’s index</option>
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67 <option value="simpson_e">Simpson’s evenness measure E</option>
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68 <option value="singles">Number of single occurrencesles</option>
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69 <option value="strong"> Strong’s dominance index</option>
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70 <option value="PD_whole_tree">Phylogenetic diversity</option>
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71 </param>
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72
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73 <param name="tree_file" type="data" label="Newick tree (optional, except
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74 for PD_whole_tree metric" help="(-t/--tree_path)" optional="True"/>
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75 </inputs>
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76
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77 <outputs>
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78 <data name="alpha_diversity" format="tabular"
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79 from_work_dir="alpha_diversity/alpha_div.txt"
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80 label="${tool.name} on ${on_string}: Alpha diversity" />
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81 </outputs>
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82
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83 <tests>
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84 <test>
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85 <param name="input_table" value="pick_open_reference_otus_otu_table.txt"/>
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86 <param name="metrics" value="chao1,observed_species" />
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87 <output name="alpha_diversity" value="" />
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88 </test>
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89 </tests>
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90
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91 <help><![CDATA[
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92
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93 **What it does?**
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94
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95 This tool calculates alpha diversity, or within-sample diversity, using an
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96 OTU table.
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97
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98 The resulting file(s) is a tab-delimited text file, where the columns correspond
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99 to alpha diversity metrics and the rows correspond to samples and their calculated
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100 diversity measurements. When a folder is given as input (-i), the script processes
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101 every otu table file in the given folder, and creates a corresponding file in the
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102 output directory.
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103
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104 More information about this tool is available on
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105 `QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_.
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106 ]]>
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107 </help>
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108
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109 <citations>
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110 <expand macro="citations" />
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111 </citations>
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112 </tool>