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1 <tool id="alpha_diversity" name="alpha_diversity" version="1.2.0">
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2 <description>Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics</description>
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3 <requirements>
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4 <requirement type="binary">alpha_diversity.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 #if $run_type.input_type.__str__ == "multi":
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9 --galaxy_logfile=$output_path
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10 --galaxy_outputdir=$output_path.extra_files_path
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11 #end if
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12 alpha_diversity.py
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13 #if $run_type.input_type.__str__ == "multi":
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14 --input_path=$input_path.extra_files_path
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15 --output_path=$output_path.extra_files_path
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16 #else:
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17 --output_path=$output_path
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18 --input_path=$input_path
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19 #end if
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20 --metrics=$metrics
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21 #if $metrics.__str__ == 'PD_whole_tree':
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22 --tree_path=$tree_path
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23 #end if
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24
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25 </command>
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26 <inputs>
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27 <conditional name="run_type">
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28 <param name="input_type" type="select" label="Input Type" help="Select the type/number of input file(s). If multiple rarefactions have been run, select Multiple File Alpha Diversity.">
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29 <option value="single">Single File Alpha Diversity</option>
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30 <option value="multi" selected="true">Multiple File (batch) Alpha Diversity</option>
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31 </param>
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32 <when value="single">
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33 <param name="input_path" type="data" format="txt" label="OTU table" help="Rarefied table for single file operation [REQUIRED]"/>
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34 </when>
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35 <when value="multi">
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36 <param name="input_path" type="data" format="txt" label="Multiple Rarefactions Log File" help="multiple_rarefactions log file for multiple file operation. [REQUIRED]"/>
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37 </when>
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38 </conditional>
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39 <param name="metrics" type="select" multiple="true" label="metrics"
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40 help="metrics to use">
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41 <option value="ACE">ACE</option>
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42 <option value="berger_parker_d">berger_parker_d</option>
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43 <option value="brillouin_d">brillouin_d</option>
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44 <option value="chao1">chao1</option>
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45 <option value="chao1_confidence">chao1_confidence</option>
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46 <option value="dominance">dominance</option>
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47 <option value="doubles">doubles</option>
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48 <option value="equitability">equitability</option>
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49 <option value="fisher_alpha">fisher_alpha</option>
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50 <option value="heip_e">heip_e</option>
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51 <option value="kempton_taylor_q">kempton_taylor_q</option>
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52 <option value="margalef">margalef</option>
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53 <option value="mcintosh_d">mcintosh_d</option>
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54 <option value="mcintosh_e">mcintosh_e</option>
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55 <option value="menhinick">menhinick</option>
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56 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
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57 <option value="observed_species">observed_species</option>
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58 <option value="osd">osd</option>
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59 <option value="reciprocal_simpson">reciprocal_simpson</option>
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60 <option value="robbins">robbins</option>
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61 <option value="shannon">shannon</option>
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62 <option value="simpson">simpson</option>
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63 <option value="simpson_e">simpson_e</option>
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64 <option value="singles">singles</option>
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65 <option value="strong">strong</option>
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66 <option value="PD_whole_tree">PD_whole_tree</option>
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67 </param>
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68 <param name="tree_path" type="data" format="tre" label="tree_path" optional="true"
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69 help="path to newick tree file, REQUIRED for phylogenetic metrics: PD_whole_tree"/>
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70 </inputs>
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71 <outputs>
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72 <data format="txt" name="output_path" label="${tool.name} on ${on_string}: alpha_diversity log file"/>
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73 </outputs>
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74 <tests>
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75 </tests>
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76 <help>This tool calculates alpha diversity, or within-sample diversity, using an otu table. Metrics may be selected in any combination. Input can be the log file from multiple_rarefactions (batch alpha diversity), or a single rarefied OTU table (single_rarefaction/single file alpha diversity). When the phylogenetic metric PD_whole_tree is selected, a .tre file must be supplied for the tool to run. The output file is a log file listing all the alpha rarefaction files produced.
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77
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78 For more information, see alpha_diversity_ in the Qiime documentation.
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79
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80 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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81
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82 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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83
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84 .. _alpha_diversity: http://qiime.org/scripts/alpha_diversity.html</help>
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85 </tool>
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86
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