annotate alpha_diversity.xml @ 1:8ac5d5c9a5e4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 28a15bb06175426ba161f346dff983f3cdd0fc10
author iuc
date Mon, 13 Feb 2023 10:22:57 +0000
parents e400e5ef0e7c
children 78b69342c280
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1 <tool id="krakentools_alpha_diversity" name="Krakentools: Calculates alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from the Bracken abundance estimation file</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="biotools"/>
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7 <expand macro="requirements">
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8 <requirement type="package" version="1.9.3">scipy</requirement>
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9 </expand>
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10 <expand macro="version"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 alpha_diversity.py
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13 --filename '$filename'
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14 --alpha '$alpha'
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15 > '$output'
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16 ]]></command>
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17 <inputs>
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18 <param argument="--filename" type="data" format="tabular" label="Abundance file" help="The file can be created by Bracken"/>
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19 <param argument="--alpha" type="select" label="Specify alpha diversity type">
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20 <option value="Sh" selected="true">Shannon's alpha diversity</option>
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21 <option value="BP">Berger-Parker's alpha</option>
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22 <option value="Si">Simpson's diversity</option>
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23 <option value="ISi">Inverse Simpson's diversity</option>
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24 <option value="F">Fisher's index</option>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data name="output" format="txt" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="filename" value="bracken_abundance.tabular"/>
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33 <param name="alpha" value="Sh"/>
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34 <output name="output" ftype="txt">
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35 <assert_contents>
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36 <has_text text="Shannon's diversity: 4.194127607417342"/>
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37 </assert_contents>
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38 </output>
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39 </test>
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40 <test>
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41 <param name="filename" value="bracken_abundance.tabular"/>
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42 <param name="alpha" value="BP"/>
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43 <output name="output" ftype="txt">
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44 <assert_contents>
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45 <has_text text="Berger-parker's diversity: 0.05525121757950085"/>
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46 </assert_contents>
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47 </output>
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48 </test>
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49 <test>
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50 <param name="filename" value="bracken_abundance.tabular"/>
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51 <param name="alpha" value="Si"/>
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52 <output name="output" ftype="txt">
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53 <assert_contents>
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54 <has_text text="Simpson's diversity: 0.9805668888241948"/>
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55 </assert_contents>
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56 </output>
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57 </test>
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58 <test>
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59 <param name="filename" value="bracken_abundance.tabular"/>
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60 <param name="alpha" value="ISi"/>
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61 <output name="output" ftype="txt">
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62 <assert_contents>
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63 <has_text text="Simpson's Reciprocal Index: 51.45856424909617"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <test>
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68 <param name="filename" value="bracken_abundance.tabular"/>
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69 <param name="alpha" value="F"/>
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70 <output name="output" ftype="txt">
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71 <assert_contents>
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72 <has_text text="Fisher's index: 1688.9352909860668"/>
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73 </assert_contents>
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74 </output>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78
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79 KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results. This program calculates alpha diversity, from the Bracken abundance estimation file. User must specify Bracken output file, and type of alpha diversity to be calculated. Specific options are specified below.
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80
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81 Input
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82 ------
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83 Bracken abundance estimation file.
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84
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85 Input Bracken file must be in standard Bracken output file format and must be run specifically for Abundance Estimation. Example format:
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86 name tax_id tax_lvl kraken... added... new... fraction...
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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87 Homo sapiens 9606 S ... .... 999000 0.999000
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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88 Streptococcus pyogenes 1314 S ... .... 10 0.000001
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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89 Streptococcus agalactiae 1311 S ... .... 5 0.000000
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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90 Streptococcus pneumoniae 1313 S ... .... 3 0.000000
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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91 Bordetella pertussis 520 S ... .... 20 0.000002
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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92
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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93 Output
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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94 ---------
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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95 Alpha diversity with the specified type.
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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96
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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97 ]]></help>
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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98 <expand macro="citations"/>
e400e5ef0e7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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99 </tool>