Mercurial > repos > iuc > krakentools_beta_diversity

annotate beta_diversity.xml @ 5:e1172268cc6b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 60eb96ad3ff782075ca1f29e26ffe5487bbb93ed
author iuc
date Fri, 22 Nov 2024 09:27:08 +0000
parents 56bf015afbd1
children
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56bf015afbd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
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1 <tool id="krakentools_beta_diversity" name="Krakentools: calculates beta diversity (Bray-Curtis dissimilarity)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from Kraken, Krona and Bracken files</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 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #import re
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11 #set input_names=[]
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12
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13 #for $input in $inputs
e1172268cc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 60eb96ad3ff782075ca1f29e26ffe5487bbb93ed
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14 #set identifier = re.sub('[^\s\w\-.]', '_', str($input.element_identifier))
e1172268cc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 60eb96ad3ff782075ca1f29e26ffe5487bbb93ed
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15 #silent $input_names.append($identifier)
e1172268cc6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 60eb96ad3ff782075ca1f29e26ffe5487bbb93ed
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16 ln -s '$input' '${identifier}' &&
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17 #end for
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18
0
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19 beta_diversity.py
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20 --inputs
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21 #for $input_name in $input_names
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22 '${input_name}'
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23 #end for
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24 --type '$sample.type'
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25 #if $sample.type == 'kreport'
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26 --level '$sample.level'
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27 #else if $sample.type == 'krona'
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28 --level '$sample.level'
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29 #end if
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30 > '$output'
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31 ]]></command>
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32 <inputs>
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33 <param argument="--inputs" type="data" multiple="true" format="tabular" label="Taxonomy file(s)" help="The files can be generated by Kraken, Bracken or Krona"/>
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34 <conditional name="sample">
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35 <param argument="--type" type="select" label="Specify type of input file(s)">
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36 <option value="single" selected="true">Single tabular data file</option>
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37 <option value="simple">Tabular data files</option>
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38 <option value="bracken">Braken species abundance file</option>
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39 <option value="kreport">Kraken report file</option>
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40 <option value="krona">Krona file</option>
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41 </param>
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42 <when value="single"/>
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43 <when value="simple"/>
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44 <when value="bracken"/>
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45 <when value="kreport">
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46 <expand macro="param_level"/>
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47 </when>
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48 <when value="krona">
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49 <expand macro="param_level"/>
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50 </when>
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51 </conditional>
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52
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53 </inputs>
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54 <outputs>
5
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55 <data name="output" format="tabular" />
0
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="inputs" value="beta_bracken_1.tabular,beta_bracken_2.tabular,beta_bracken_3.tabular"/>
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60 <param name="type" value="bracken"/>
5
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61 <output name="output" ftype="tabular">
0
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62 <assert_contents>
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63 <has_text_matching expression="#[012]&#9;beta_[a-z]+_[123].tabular \([0-9]+ reads\)" n="3"/>
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64 <has_n_columns n="4" comment="#"/>
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65 <has_n_lines n="7"/>
0
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66 <has_text text="0.629"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 <test>
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71 <param name="inputs" value="beta_kreport_1.tabular,beta_kreport_2.tabular,beta_kreport_3.tabular"/>
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72 <param name="type" value="kreport"/>
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73 <output name="output" ftype="tabular">
0
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74 <assert_contents>
5
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75 <has_text text="beta_kreport_1.tabular"/>
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76 <has_text_matching expression="#[012]&#9;beta_[a-z]+_[123].tabular \([0-9]+ reads\)" n="3"/>
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77 <has_n_columns n="4" comment="#"/>
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78 <has_n_lines n="7"/>
0
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79 <has_text text="0.584"/>
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80 </assert_contents>
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81 </output>
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82 </test>
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83 <test>
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84 <param name="inputs" value="beta_krona_1.tabular,beta_krona_2.tabular"/>
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85 <param name="type" value="krona"/>
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86 <param name="level" value="G"/>
5
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87 <output name="output" ftype="tabular">
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88 <assert_contents>
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89 <has_text_matching expression="#[01]&#9;beta_[a-z]+_[12].tabular \([0-9]+ reads\)" n="2"/>
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90 <has_n_columns n="3" comment="#"/>
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91 <has_n_lines n="5"/>
0
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92 <has_text text="0.993"/>
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93 </assert_contents>
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94 </output>
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98 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 the beta diversity (Bray-Curtis dissimilarity) from kraken, krona and bracken files.
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99
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100 Input
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101 ------
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102 Bracken files, Kraken and Kracken2 report files and Krona files. Additionally, you can pass any tab-separated file and specify the columns with the taxonomical information and read counts (--cols).
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103
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104 Output
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105 ------
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106 Beta diversity of the input files
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107
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108 ]]></help>
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109 <expand macro="citations"/>
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110 </tool>