Mercurial > repos > iuc > qiime_alpha_diversity

annotate 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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2ceee245d97c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="@WRAPPER_VERSION@.0">
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2 <description>on each sample in an otu table</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>alpha_diversity.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #set $chosen_metrics = str( $metrics ).split( "," )
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10 alpha_diversity.py
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11 --input_path '$input_path'
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12 -o alphadiv
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13 --metrics '$metrics'
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14 #if "PD_whole_tree" in $chosen_metrics:
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15 --tree_path '$tree_path'
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <param argument="--input_path" type="data" format="tabular,txt,tsv,biom" multiple="True" label="OTU table"/>
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20 <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Alpha-diversity metric(s) to use">
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21 <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option>
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22 <option value="berger_parker_d">Berger-Parker dominance</option>
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23 <option value="brillouin_d">Brillouin index of alpha diversity</option>
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24 <option value="chao1" selected="true">chao1 richness estimator</option>
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25 <option value="chao1_ci">chao1 confidence interval</option>
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26 <option value="dominance">Dominance</option>
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27 <option value="doubles">Number of double occurrences (doubletons)</option>
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28 <option value="enspie">ENS_pie alpha diversity measure</option>
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29 <option value="equitability">Equitability</option>
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30 <option value="esty_ci">Esty’s CI</option>
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31 <option value="fisher_alpha">Fisher’s alpha</option>
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32 <option value="gini_index">Gini index</option>
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33 <option value="goods_coverage">Good’s coverage of counts</option>
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34 <option value="heip_e">Heip’s evenness measure</option>
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35 <option value="kempton_taylor_q">Kempton-Taylor Q index of alpha diversity</option>
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36 <option value="margalef">Margalef’s richness index</option>
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37 <option value="mcintosh_d">McIntosh dominance index D</option>
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38 <option value="mcintosh_e">McIntosh’s evenness measure E</option>
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39 <option value="menhinick">Menhinick’s richness index</option>
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40 <option value="michaelis_menten_fit">Michaelis-Menten fit to rarefaction curve of observed OTUs</option>
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41 <option value="observed_otus">Number of distinct OTUs</option>
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42 <option value="observed_species" selected="true">Number of distinct species</option>
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43 <option value="osd">Observed OTUs, singles, and doubles</option>
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44 <option value="simpson_reciprocal">simpson_reciprocal</option>
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45 <option value="robbins">Robbins’ estimator for the probability of unobserved outcomes</option>
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46 <option value="shannon">Shannon entropy of counts</option>
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47 <option value="simpson">Simpson’s index</option>
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48 <option value="simpson_e">Simpson’s evenness measure E</option>
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49 <option value="singles">Number of single occurrencesles</option>
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50 <option value="strong"> Strong’s dominance index</option>
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51 <option value="PD_whole_tree">Phylogenetic diversity</option>
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52 </param>
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53 <param argument="--tree_path" type="data" format="nhx" optional="True" label="Newick tree (optional, except for PD_whole_tree metric)"/>
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54 </inputs>
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55 <outputs>
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56 <data name="alpha_diversity" format="tabular" from_work_dir="alphadiv" label="${tool.name} on ${on_string}: Alpha diversity"/>
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57 </outputs>
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58 <tests>
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59 <test><!-- test with defaults -->
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60 <param name="input_path" value="alpha_diversity/otu_table.biom"/>
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61 <output name="alpha_diversity" file="alpha_diversity/alphadiv"/>
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62 </test>
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63 <test><!-- test with all metrics and tree file -->
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64 <param name="input_path" value="alpha_diversity/otu_table.biom"/>
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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"/>
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66 <param name="tree_path" value="alpha_diversity/rep_set.tre"/>
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67 <output name="alpha_diversity" ftype="tabular">
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68 <assert_contents>
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69 <has_text text="ace"/>
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70 <has_text text="simpson"/>
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71 <has_text text="PD_whole_tree"/>
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72 </assert_contents>
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73 </output>
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 **What it does**
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78
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79 This tool calculates alpha diversity, or within-sample diversity, using an
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80 OTU table.
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81
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82 The resulting file(s) is a tab-delimited text file, where the columns correspond
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83 to alpha diversity metrics and the rows correspond to samples and their calculated
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84 diversity measurements. When a folder is given as input (-i), the script processes
2ceee245d97c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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85 every otu table file in the given folder, and creates a corresponding file in the
2ceee245d97c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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86 output directory.
2ceee245d97c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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87
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88 More information about this tool is available on
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89 `QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_.
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90 ]]></help>
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91 <citations>
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92 <expand macro="citations"/>
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93 </citations>
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94 </tool>