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annotate kraken2.xml @ 6:e452fed07fbb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
author iuc
date Sun, 07 Dec 2025 11:30:46 +0000
parents 9c5599b8c9a0
children
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6
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
iuc
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1 <tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 assign taxonomic labels to sequencing reads
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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4 </description>
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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5 <macros>
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6 <import>macros.xml</import>
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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7 </macros>
5
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8 <xrefs>
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9 <xref type="bio.tools">kraken2</xref>
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10 </xrefs>
0
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11 <requirements>
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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12 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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13 </requirements>
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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14 <version_command>kraken2 --version</version_command>
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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15 <command detect_errors="exit_code">
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16 <![CDATA[
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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17 kraken2
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18 --threads \${GALAXY_SLOTS:-1}
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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19 --db '${kraken2_database.fields.path}'
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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20
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21 $quick
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22
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e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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23 #if $single_paired.single_paired_selector == "collection":
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24 --paired
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25 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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26 #else:
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27 '${single_paired.input_sequences}'
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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28 #end if
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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29
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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30 #if $split_reads:
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31 #if $single_paired.single_paired_selector == "no":
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32 --unclassified-out 'un_out'
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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33 --classified-out 'cl_out'
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34 #else:
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e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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35 --unclassified-out 'un_out#'
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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36 --classified-out 'cl_out#'
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37 #end if
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38 #end if
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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39
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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40 --confidence '${confidence}'
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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41 --minimum-base-quality '${min_base_quality}'
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030b90f10e5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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42 --minimum-hit-groups '${minimum_hit_groups}'
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43
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030b90f10e5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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44 $use_names
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45
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46 #if $report.create_report == "true":
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47 --report '${report_output}'
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48 $report.use_mpa_style
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f30addbfcb2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 055a83d01b077101110272c44ef0ff2a04d5d1d4"
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49 $report.report_zero_counts
f30addbfcb2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 055a83d01b077101110272c44ef0ff2a04d5d1d4"
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50 $report.report_minimizer_data
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51 #end if
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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52
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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53 > '${output}'
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54
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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55 #if $split_reads:
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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56 #if $single_paired.single_paired_selector == "no":
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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57 #if $single_paired.input_sequences.ext.endswith(".gz")
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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58 #set command = "gzip -c"
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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59 #elif $single_paired.input_sequences.ext.endswith(".bz2")
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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60 #set command = "bzip2 -c"
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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61 #else
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62 #set command = "cat"
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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63 #end if
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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64 && $command un_out > '$unclassified_out_s'
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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65 && $command cl_out > '$classified_out_s'
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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66 #else:
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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67 #if $single_paired.input_pair.forward.ext.endswith(".gz")
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68 #set command = "gzip -c"
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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69 #elif $single_paired.input_pair.forward.ext.endswith(".bz2")
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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70 #set command = "bzip2 -c"
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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71 #else
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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72 #set command = "cat"
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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73 #end if
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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74 && $command un_out_1 > '$out_unclassified_paired.forward'
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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75 && $command un_out_2 > '$out_unclassified_paired.reverse'
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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76 && $command cl_out_1 > '$out_classified_paired.forward'
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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77 && $command cl_out_1 > '$out_classified_paired.forward'
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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78 #end if
e452fed07fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
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79 #end if
0
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80 ]]></command>
71c9fcf9384b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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81 <inputs>
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82 <conditional name="single_paired">
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83 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
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84 <option value="collection">Paired</option>
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85 <option selected="True" value="no">Single</option>
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86 </param>
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87 <when value="collection">
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88 <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
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89 </when>
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90 <when value="no">
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91 <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
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92 </when>
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93 </conditional>
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94 <param argument="--use-names" type="boolean" truevalue="--use-names" falsevalue="" label="Print scientific names instead of just taxids"/>
030b90f10e5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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95 <param argument="--confidence" type="float" label="Confidence" value="0.0" min="0" max="1" help="Confidence score threshold. Must be in [0, 1]"/>
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96 <param argument="--minimum-base-quality" name="min_base_quality" type="integer" label="Minimum Base Quality" value="0" help="Minimum base quality used in classification (only effective with FASTQ input)"/>
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97 <param argument="--minimum-hit-groups" type="integer" label="Minimum hit groups" value="2" help="Number of overlapping k-mers sharing the same minimizer needed to make a call" />
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98 <param argument="--quick" type="boolean" truevalue="--quick" falsevalue="" label="Enable quick operation" help="Quick operation (use first hit)"/>
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99 <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/>
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100 <conditional name="report">
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101 <param argument="--report" name="create_report" type="select" label="Print a report with aggregrate counts/clade to file" help="Can be used as input for bracken">
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102 <option value="true">Yes</option>
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103 <option value="false" selected="true">No</option>
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104 </param>
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105 <when value="true">
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106 <param argument="--use-mpa-style" type="boolean" truevalue="--use-mpa-style" falsevalue="" label="Format report output like Kraken 1's kraken-mpa-report" />
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107 <param argument="--report-zero-counts" type="boolean" truevalue="--report-zero-counts" falsevalue="" label="Report counts for ALL taxa, even if counts are zero" />
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108 <param argument="--report-minimizer-data" type="boolean" truevalue="--report-minimizer-data" falsevalue="" label="Report minimizer data" help="Report minimizer and distinct minimizer count information in addition to normal Kraken report" />
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109 </when>
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110 <when value="false"/>
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111 </conditional>
1
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112 <expand macro="input_database"/>
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113 </inputs>
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114 <outputs>
1
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115 <data name="classified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads">
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116 <filter>split_reads and single_paired['single_paired_selector'] == "no"</filter>
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117 </data>
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118 <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
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119 <filter>split_reads and single_paired['single_paired_selector'] == "no"</filter>
1
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120 </data>
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121 <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report">
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122 <filter>report['create_report'] == "true"</filter>
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123 </data>
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124 <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs">
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125 <filter>split_reads and single_paired['single_paired_selector'] == "collection"</filter>
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126 </collection>
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127 <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs">
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128 <filter>split_reads and "collection" in single_paired['single_paired_selector'] == "collection"</filter>
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129 </collection>
1
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130
0
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131 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
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132 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
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133 </outputs>
1
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134 <tests>
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135 <test expect_num_outputs="1">
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136 <conditional name="single_paired">
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137 <param name="single_paired_selector" value="no"/>
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138 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
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139 </conditional>
0
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140 <param name="split_reads" value="false"/>
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141 <param name="quick" value="no"/>
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142 <param name="confidence" value=".2"/>
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143 <param name="kraken2_database" value="test_entry"/>
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144 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
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145 </test>
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146
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147 <test expect_num_outputs="3">
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148 <conditional name="single_paired">
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149 <param name="single_paired_selector" value="no"/>
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150 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
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151 </conditional>
1
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152 <param name="split_reads" value="true"/>
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153 <param name="quick" value="no"/>
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154 <param name="confidence" value=".2"/>
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155 <param name="kraken2_database" value="test_entry"/>
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156 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
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157 <output name="classified_out_s" file="kraken_test1_cl.fas" ftype="fasta"/>
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158 <output name="unclassified_out_s" file="kraken_test1_un.fas" ftype="fasta"/>
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159 </test>
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160
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161 <test expect_num_outputs="7">
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162 <conditional name="single_paired">
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163 <param name="single_paired_selector" value="collection"/>
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164 <param name="input_pair">
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165 <collection type="paired">
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166 <element name="forward" value="kraken_test2_R1.fastq.gz" ftype="fastqsanger.gz"/>
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167 <element name="reverse" value="kraken_test2_R2.fastq.gz" ftype="fastqsanger.gz"/>
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168 </collection>
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169 </param>
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170 <param name="single_paired_selector" value="collection"/>
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171 </conditional>
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172 <param name="split_reads" value="true"/>
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173 <param name="quick" value="no"/>
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174 <param name="confidence" value="0"/>
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175 <param name="kraken2_database" value="test_entry"/>
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176 <output_collection name="out_unclassified_paired" type="paired">
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177 <element name="forward" file="un_test2_output_1.fastq" ftype="fastqsanger.gz" decompress="true"/>
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178 <element name="reverse" file="un_test2_output_2.fastq" ftype="fastqsanger.gz" decompress="true"/>
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179 </output_collection>
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180 <output_collection name="out_classified_paired" type="paired">
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181 <element name="forward" file="cl_test2_output_1.fastq" ftype="fastqsanger.gz" decompress="true"/>
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182 <element name="reverse" file="cl_test2_output_2.fastq" ftype="fastqsanger.gz" decompress="true"/>
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183 </output_collection>
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184 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
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185 <assert_command>
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186 <has_text text="gzip -c"/>
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187 </assert_command>
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188 </test>
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189
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190 <test expect_num_outputs="2">
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191 <conditional name="single_paired">
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192 <param name="single_paired_selector" value="collection"/>
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193 <param name="input_pair">
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194 <collection type="paired">
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195 <element name="forward" value="kraken_test2_R1.fastq" ftype="fastqsanger"/>
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196 <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastqsanger"/>
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197 </collection>
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198 </param>
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199 </conditional>
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200 <param name="use_names" value="true"/>
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201 <conditional name="report">
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202 <param name="create_report" value="true"/>
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203 <param name="report_minimizer_data" value="true"/>
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204 </conditional>
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205 <param name="kraken2_database" value="test_entry"/>
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206 <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/>
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207 </test>
0
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208 </tests>
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209 <help>
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210 <![CDATA[
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211 **What it does**
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212
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213 Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise.
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214
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215 -----
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216
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217 **Output Format**
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218
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219 Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are::
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220
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221 1. "C"/"U": a one letter code indicating that the sequence was either classified or unclassified.
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222 2. The sequence ID, obtained from the FASTA/FASTQ header.
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223 3. The taxonomy ID Kraken 2 used to label the sequence; this is 0 if the sequence is unclassified.
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224 4. The length of the sequence in bp.
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225 5. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. For example, "562:13 561:4 A:31 0:1 562:3" would indicate that:
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226 a) the first 13 k-mers mapped to taxonomy ID #562
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227 b) the next 4 k-mers mapped to taxonomy ID #561
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228 c) the next 31 k-mers contained an ambiguous nucleotide
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229 d) the next k-mer was not in the database
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230 e) the last 3 k-mers mapped to taxonomy ID #562
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231 ]]>
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232 </help>
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233 <expand macro="citations" />
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234 </tool>