Mercurial > repos > iuc > bracken

annotate est-abundance.xml @ 9:0c7b6eb7e752 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 9af8730b86781bcbbe1cb62402967fa316cfec80
author iuc
date Mon, 29 Jul 2024 07:25:12 +0000
parents 1d4bd12f01cf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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1 <tool id="est_abundance" name="Bracken" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>to re-estimate abundance at a taxonomic level from kraken output</description>
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3 <macros>
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4 <import>macros.xml</import>
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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5 </macros>
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6 <expand macro="edam"/>
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7 <expand macro="xref"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ## Prevent logfile pipe below from quenching the raised error.
978ae4147c29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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11 set -o pipefail &&
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12
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13 est_abundance.py
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14 -i '$input'
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15 -k '$kmer_distr.fields.path'
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16 -l $level
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17 -t $threshold
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18 -o '$report'
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19
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20 ## --out-report needs to be set always, since it is written next to the input file
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
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21 --out-report bracken.report
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22
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23 #if $logfile_output == "True"
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
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24 | tee '$logfile'
79450f7fd718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649
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25 #end if
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26 ]]>
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27 </command>
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28 <inputs>
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29 <param name="input" type="data" format="tabular" label="Kraken report file"/>
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30 <param label="Select a Kmer distribution" name="kmer_distr" type="select">
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31 <options from_data_table="bracken_databases">
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32 <validator message="No database is available" type="no_options"/>
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33 </options>
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34 </param>
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35 <param name="level" type="select" label="Level" help="Level to push all reads to">
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36 <option value="S2">Subspecies 2</option>
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37 <option value="S1">Subspecies 1</option>
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38 <option value="S" selected="true">Species</option>
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39 <option value="G">Genus</option>
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40 <option value="F">Family</option>
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41 <option value="O">Order</option>
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42 <option value="C">Class</option>
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43 <option value="P">Phylum</option>
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44 <option value="D">Domain</option>
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45 </param>
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46 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
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47 help="Threshold for the minimum number of reads kraken must assign to a classification for that
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48 classification to be considered in the final abundance estimation."/>
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49 <param argument="--out-report" type="boolean" checked="false" label="Produce Kraken-Style Bracken report"/>
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50 <param name="logfile_output" type="boolean" truevalue="True" falsevalue="False" label="Add log file output"/>
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51 </inputs>
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52 <outputs>
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53 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report"/>
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54 <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${tool.name} on ${on_string}: Kraken style report">
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55 <filter>out_report</filter>
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56 </data>
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57 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
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58 <filter> logfile_output == True </filter>
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59 </data>
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60 </outputs>
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61 <tests>
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62 <test expect_num_outputs="1">
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63 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
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64 <param name="level" value="S"/>
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65 <param name="kmer_distr" value="test_entry"/>
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66 <param name="logfile_output" value="False"/>
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67 <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
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68 </test>
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69 <test expect_num_outputs="3">
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70 <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
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71 <param name="level" value="S"/>
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72 <param name="kmer_distr" value="test_entry"/>
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73 <param name="out_report" value="true"/>
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74 <param name="logfile_output" value="True"/>
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75 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
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76 <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/>
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77 <output name="logfile" file="test2.log" lines_diff="8"/>
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78 </test>
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79 <test expect_num_outputs="1">
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80 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
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81 <param name="level" value="S1"/>
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82 <param name="kmer_distr" value="test_entry"/>
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83 <param name="logfile_output" value="False"/>
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84 <output name="report" file="NC_003198.1_simulated_bracken_report_S1.txt" ftype="tabular"/>
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85 </test>
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86 <test expect_num_outputs="1">
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87 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
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88 <param name="level" value="S2"/>
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89 <param name="kmer_distr" value="test_entry"/>
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90 <param name="logfile_output" value="False"/>
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91 <output name="report" file="NC_003198.1_simulated_bracken_report_S2.txt" ftype="tabular"/>
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92 </test>
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93 </tests>
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94 <help>
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95 <![CDATA[
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96 Bracken relies on Bayesian probabilities that derive from the knowledge about the Kraken classification of each read-length kmer from all genomes within the provided Kraken database. It takes the tabular report output of kraken/kraken2 representing abundance of all detected taxa and provides as output a table representing the re-estimated abundances of different taxa at the taxonomy level pre-determined by the user. For more information about the operation behind the scene, visit http://ccb.jhu.edu/software/bracken/index.shtml?t=manual.
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97
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98 Prior to abundance estimation with bracken, we must divide each genome in the Kraken database into read-length kmers, classify each of those kmers and store as a data structure. This indexing step has already been performed for you and it suffices to select the name of the correct kraken DB that you used for read classification.
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99
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100 Bracken output file format (tabular):
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101 * Taxon name
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102 * Taxonomy ID
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103 * Level ID (S=Species, G=Genus, O=Order, F=Family, P=Phylum, K=Kingdom)
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104 * Kraken assigned reads
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105 * Added reads with abundance re-estimation
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106 * Total reads after abundance re-estimation
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107 * Fraction of total reads
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108 ]]></help>
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109 <expand macro="citations"/>
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110 </tool>