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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools"
author jdv
date Thu, 30 Sep 2021 17:35:38 +0000
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1 <tool id="krakentools_kreport2krona" name="Kraken To Krona" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="17.09">
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2 <description>Convert a Kraken/Kraken2 report to a Krona-compatible text 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="requirements" />
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7 <expand macro="stdio" />
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8 <version_command>echo -n @TOOL_VERSION@</version_command>
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11
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12 kreport2krona.py
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13 --report '$report'
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14 -o '$output'
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15 $intermediate_ranks
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16
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17 ]]></command>
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18
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19 <inputs>
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20 <param name="report" argument="--report" format="tabular" type="data" label="Report" help="Report (classification) file from Kraken/Kraken2" />
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21 <param name="intermediate_ranks" argument="--intermediate-ranks" type="boolean" value="False" truevalue="--intermediate-ranks" falsevalue="--no-intermediate-ranks" label="Intermediate ranks" help="Include non-standard taxonomic levels" />
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22
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23 </inputs>
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24
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25 <outputs>
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26 <data name="output" format="tabular" label="${tool.name} on ${on_string}: table" />
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27 </outputs>
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28
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29 <tests>
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30
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31 <!-- test Kraken2 input, no intermediate ranks -->
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32 <test>
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33 <param name="report" value="kraken2.report" ftype="tabular"/>
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34 <param name="intermediate_ranks" value="False"/>
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35 <output name="output" file="krona.k2.noint.tsv"/>
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36 </test>
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37 <!-- test KrakenUniq input, intermediate ranks -->
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38 <test>
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39 <param name="report" value="kraken2.report" ftype="tabular"/>
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40 <param name="intermediate_ranks" value="True"/>
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41 <output name="output" file="krona.k2.int.tsv"/>
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42 </test>
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43
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44 </tests>
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45
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46 <help><![CDATA[
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47
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48 .. class:: infomark
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49
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50 **What it does**
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51
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52 -------------------
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53
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54 After running Kraken, Kraken2, or KrakenUniq, users may use the
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55 `kreport2krona.py` program to convert the report file to a tabular format
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56 suitable for input into Krona.
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57
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58 **Example usage**
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59
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60 -------------------
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61
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62 .. code-block:: bash
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63
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64 kraken2 --db KRAKEN2DB --threads THREADNUM --report MYSAMPLE.KREPORT \
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65 --paired SAMPLE_1.FASTA SAMPLE_2.FASTA > MYSAMPLE.KRAKEN2
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66 kreport2krona.py --report MYSAMPLE.KREPORT --output MYSAMPLE.krona
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67 ktImportText MYSAMPLE.krona -o MYSAMPLE.krona.html
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68
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69 -------------------
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70
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71 **Command-line arguments**
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72
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73 -------------------
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74
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75 The following command-line usage corresponds with the Galaxy wrapper
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76 parameters::
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77
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78 usage: kreport2krona.py [-h] -r R_FILE -o O_FILE [--intermediate-ranks] [--no-intermediate-ranks]
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79
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80 optional arguments:
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81 -h, --help show this help message and exit
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82 -r R_FILE, --report-file R_FILE, --report R_FILE
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83 Input kraken report file for converting
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84 -o O_FILE, --output O_FILE
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85 Output krona-report file name
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86 --intermediate-ranks Include non-traditional taxonomic ranks in output
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87 --no-intermediate-ranks
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88 Do not include non-traditional taxonomic ranks in output [default: no intermediate ranks]
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89
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90 --------------------
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91
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92 **More Information**
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93
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94 --------------------
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95
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96 Author: Jennifer Lu
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97
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98 See the `online documentation`_
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99
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100 .. _`online documentation`: https://github.com/jenniferlu717/KrakenTools#kreport2kronapy
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101
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102 --------------------
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103
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104 **Galaxy Wrapper Development**
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105
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106 --------------------
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107
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108 Author: Jeremy Volkening
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109
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110 ]]></help>
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111
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112 <expand macro="citations" />
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113
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114 </tool>