Mercurial > repos > iuc > kaiju_kaiju2table

annotate kaiju2table.xml @ 1:eedcb4cc9e5a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju commit ace4e37c66a95ee5f648b95a92911e1fdf212967
author iuc
date Wed, 07 May 2025 08:51:58 +0000
parents e7d2c4ed18a5
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1 <tool id="kaiju_kaiju2table" name="kaiju2table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description></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="xrefs"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10
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11 #for $kaiju_table in $kaiju_tables
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12 ln -s '$kaiju_table' #echo re.sub('[^\w\-_]', '_', str($kaiju_table.element_identifier))
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13 &&
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14 #end for
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15
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16 kaiju2table
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17 -t '$reference.fields.path'/nodes.dmp
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18 -n '$reference.fields.path'/names.dmp
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19 -r $rank
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20 -o '$kaiju_summary'
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21 #for $kaiju_table in $kaiju_tables
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22 #echo re.sub('[^\w\-_]', '_', str($kaiju_table.element_identifier))
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23 #end for
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24 #if str($optional.m)
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25 -m $optional.m
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26 #end if
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27 #if str($optional.c)
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28 -m $optional.c
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29 #end if
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30 $optional.e
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31 $optional.u
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32 #if $optional.l
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33 -l #echo ",".join($optional.l)
0
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34 #end if
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35 ]]></command>
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36 <inputs>
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37 <param name="kaiju_tables" type="data" format="tabular" multiple="true" optional="false" label="kaiju output tables"/>
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38 <expand macro="reference"/>
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39 <param argument="-r" name="rank" type="select" label="rank">
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40 <option value="phylum">phylum</option>
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41 <option value="class">class</option>
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42 <option value="order">order</option>
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43 <option value="family">family</option>
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44 <option value="genus">genus</option>
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45 <option value="species">species</option>
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46 </param>
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47 <section name="optional" title="Optional arguments" expanded="false">
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48 <param argument="-m" type="float" min="0" max="100" optional="true" value="" label="Minimum reporting percentage" help="Can not be combined with -c" />
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49 <param argument="-c" type="integer" min="1" optional="true" value="" label="Minimum required number of reads" help="Can not be combined with -m" />
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50 <param argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Expand viruses" help="which are always hown as full taxon path and read counts are not summarized in higher taxonomic levels" />
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51 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Do not count unclassified reads" help="Disables counting unclassified reads towards the total number of reads when calculating percentages."/>
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52 <expand macro="l"/>
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53 </section>
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54 </inputs>
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55 <outputs>
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56 <data name="kaiju_summary" format="tabular"/>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="kaiju_tables" value="kaiju.out"/>
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61 <param name="reference" value="test"/>
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62 <param name="rank" value="phylum"/>
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63 <output name="kaiju_summary" value="kaiju2table.out"/>
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64 </test>
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65 <test>
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66 <param name="kaiju_tables" value="kaiju.out"/>
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67 <param name="reference" value="test"/>
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68 <param name="rank" value="order"/>
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69 <section name="optional">
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70 <param name="e" value="true"/>
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71 </section>
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72 <output name="kaiju_summary" value="kaiju2table.out" lines_diff="4">
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73 <assert_contents>
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74 <has_text text="Severe acute respiratory syndrome coronavirus 2"/>
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75 <has_text text="cannot be assigned to a (non-viral) order"/>
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76 </assert_contents>
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77 </output>
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78 </test>
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79 </tests>
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80 <help><![CDATA[
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81
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82 .. class:: infomark
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83
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84 **What it does**
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85
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86 The program kaiju2table converts Kaiju's output file(s) into a summary table for a given taxonomic rank, e.g., genus.
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87 It uses the taxonomic information of the reference data for mapping the taxon identifiers from the third column in the
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88 Kaiju output to the corresponding taxon names.
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89
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90 The program can also filter out taxa with low abundances, e.g. for only showing genera that comprise at least 1 percent of the total reads
e7d2c4ed18a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju commit 59064c06143fdc7d7b17178e46911ba1009cd32e
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91 Similarly, a threshold on the absolute read count can be given.
e7d2c4ed18a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju commit 59064c06143fdc7d7b17178e46911ba1009cd32e
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92
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93 ]]></help>
e7d2c4ed18a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju commit 59064c06143fdc7d7b17178e46911ba1009cd32e
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94 <expand macro="citations"/>
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95 </tool>