Mercurial > repos > iuc > kraken_taxonomy_report

annotate kraken_taxonomy_report.xml @ 2:528a1d91b066 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 14:06:54 -0500
parents b97694b21bc3
children 27d65c78863c
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1 <?xml version="1.0"?>
1
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2 <tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="0.0.2">
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3 <description>view report of classification for multiple samples</description>
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4 <requirements>
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5 <requirement type="package" version="1.66">biopython</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 </stdio>
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11 <version_command>python '${__tool_directory__}/kraken_taxonomy_report.py' --version</version_command>
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12 <command><![CDATA[
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13 #for $input_classification in $classification:
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14 ln -s "${input_classification}" "${input_classification.element_identifier}" &&
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15 #end for
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16
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17 export KRAKEN_DB_PATH='${kraken_database.fields.path}' &&
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
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18 python '${__tool_directory__}/kraken_taxonomy_report.py'
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19
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20 --db '${kraken_database.fields.name}'
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21 ${show_zeros}
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22 ${header_line}
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23 ${otu_name}
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24 ${taxonomy}
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25 ${show_rank}
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26 ${intermediate}
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27 ${sanitize_names}
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28 #if str( $cluster.cluster ):
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29 --cluster ${cluster.cluster}
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30 #else:
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31 ${cluster.summation}
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32 #end if
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33
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34 --output '${output_report}'
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36 #if $output_tree:
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37 --output-tree '${output_tree}'
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38 #end if
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39
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40 #for $input_classification in $classification:
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41 '${input_classification.element_identifier}'
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42 #end for
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43 ]]></command>
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44 <inputs>
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45 <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
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46 <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
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47 <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
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48 <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads">
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49 <options from_data_table="kraken_databases">
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50 <validator message="No Kraken databases are available" type="no_options" />
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51 </options>
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52 </param>
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53 <param label="How to name OTUs" name="otu_name" type="select" multiple="False">
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54 <option value="" selected="True">Node name only</option>
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55 <option value="--name-long">Taxonified Name</option>
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56 <option value="--name-id">Node ID</option>
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57 </param>
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58 <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\t| |\||\.;) with underscore (_)" />
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59 <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="show_rank" truevalue="--show-rank" type="boolean" />
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60 <param checked="False" falsevalue="" argument="--taxonomy" label="Output taxonomy in last column" name="taxonomy" truevalue="--taxonomy" type="boolean" />
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61 <param checked="True" falsevalue="" argument="--intermediate" label="Display intermediate ranks" name="intermediate" truevalue="--intermediate" type="boolean" />
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62 <conditional name="cluster">
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63 <param argument="--cluster" help="Combines rows under the selected taxon and reports only selected rank." label="Cluster by taxonomic rank" name="cluster" type="select">
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64 <option value="Superkingdom">Superkingdom</option>
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65 <option value="Kingdom">Kingdom</option>
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66 <option value="Subkingdom">Subkingdom</option>
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67 <option value="Superphylum">Superphylum</option>
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68 <option value="Phylum">Phylum</option>
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69 <option value="Subphylum">Subphylum</option>
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70 <option value="Superclass">Superclass</option>
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71 <option value="Class">Class</option>
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72 <option value="Subclass">Subclass</option>
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73 <option value="Infraclass">Infraclass</option>
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74 <option value="Superorder">Superorder</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
75 <option value="Order">Order</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
76 <option value="Suborder">Suborder</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
77 <option value="Infraorder">infraorder</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
78 <option value="Parvorder">Parvorder</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
79 <option value="Superfamily">Superfamily</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
80 <option value="Family">Family</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
81 <option value="Subfamily">Subfamily</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
82 <option value="Tribe">Tribe</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
83 <option value="Subtribe">Subtribe</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
84 <option value="Genus">Genus</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
85 <option value="Subgenus">Subgenus</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
86 <option value="Species Group">Species Group</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
87 <option value="Species Subgroup">Species Subgroup</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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88 <option value="Species">Species</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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89 <option value="Subspecies">Subspecies</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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90 <option value="Varietas">Varietas</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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91 <option value="Forma">Forma</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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92 <option value="" selected="True">No Clustering</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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93 </param>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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94 <when value="">
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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95 <param checked="False" falsevalue="" argument="--summation" label="Summation of lower ranks into higher ranks" name="summation" truevalue="--summation" type="boolean" />
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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96 </when>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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97 <when value="Superkingdom"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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98 <when value="Kingdom"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
99 <when value="Subkingdom"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
100 <when value="Superphylum"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
101 <when value="Phylum"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
102 <when value="Subphylum"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
103 <when value="Superclass"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
104 <when value="Class"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
105 <when value="Subclass"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
106 <when value="Infraclass"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
107 <when value="Superorder"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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108 <when value="Order"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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109 <when value="Suborder"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
110 <when value="Infraorder"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
111 <when value="Parvorder"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
112 <when value="Superfamily"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
113 <when value="Family"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
114 <when value="Subfamily"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
115 <when value="Tribe"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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116 <when value="Subtribe"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
117 <when value="Genus"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
118 <when value="Subgenus"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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119 <when value="Species Group"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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120 <when value="Species Subgroup"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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121 <when value="Species"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
122 <when value="Subspecies"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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123 <when value="Varietas"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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124 <when value="Forma"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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125 </conditional>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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126 <param checked="False" falsevalue="" label="Output a newick tree" name="tree" truevalue="true" type="boolean" help="Trees are pruned at specified rank when clustering"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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127 </inputs>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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128 <outputs>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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129 <data format="tabular" name="output_report" label="${tool.name} on ${on_string} (Abundances)"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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130 <data format="txt" name="output_tree" label="${tool.name} on ${on_string} (Newick Tree)">
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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131 <filter>tree</filter>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
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132 </data>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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133 </outputs>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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134 <tests>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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135 <test>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
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136 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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137 <param name="show_zeros" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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138 <param name="header_line" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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139 <param name="kraken_database" value="test_db"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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140 <param name="otu_name" value=""/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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141 <param name="sanitize_names" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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142 <param name="show_rank" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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143 <param name="taxonomy" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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144 <param name="intermediate" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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145 <conditional name="cluster">
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
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146 <param name="cluster" value=""/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
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147 <param name="summation" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
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148 </conditional>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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149 <param name="tree" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
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150 <output name="output_report" file="output_abundance_1.tabular" ftype="tabular"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
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151 <output name="output_tree" file="output_tree_1.newick" />
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152 </test>
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153 <test>
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154 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
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155 <param name="show_zeros" value="True"/>
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156 <param name="header_line" value="True"/>
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157 <param name="kraken_database" value="test_db"/>
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158 <param name="otu_name" value=""/>
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159 <param name="sanitize_names" value="True"/>
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160 <param name="show_rank" value="True"/>
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161 <param name="taxonomy" value="True"/>
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162 <param name="intermediate" value="True"/>
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163 <conditional name="cluster">
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164 <param name="cluster" value=""/>
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165 <param name="summation" value="False"/>
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166 </conditional>
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167 <param name="tree" value="True"/>
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168 <output name="output_report" file="output_abundance_2.tabular" ftype="tabular"/>
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169 <output name="output_tree" file="output_tree_1.newick" />
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170 </test>
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171 <test>
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172 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
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173 <param name="show_zeros" value="True"/>
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174 <param name="header_line" value="True"/>
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175 <param name="kraken_database" value="test_db"/>
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176 <param name="otu_name" value=""/>
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177 <param name="sanitize_names" value="True"/>
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178 <param name="show_rank" value="True"/>
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179 <param name="taxonomy" value="True"/>
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180 <param name="intermediate" value="False"/>
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181 <conditional name="cluster">
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182 <param name="cluster" value="Species"/>
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183 </conditional>
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184 <param name="tree" value="True"/>
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185 <output name="output_report" file="output_abundance_3.tabular" ftype="tabular"/>
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186 <output name="output_tree" file="output_tree_3.newick" />
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187 </test>
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188 <test>
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189 <param name="classification" value="input_kraken_1.tabular,input_kraken_2.tabular" ftype="tabular"/>
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190 <param name="show_zeros" value="True"/>
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191 <param name="header_line" value="True"/>
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192 <param name="kraken_database" value="test_db"/>
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193 <param name="otu_name" value=""/>
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194 <param name="sanitize_names" value="True"/>
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195 <param name="show_rank" value="True"/>
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196 <param name="taxonomy" value="True"/>
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197 <param name="intermediate" value="False"/>
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198 <conditional name="cluster">
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199 <param name="cluster" value="Species"/>
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200 </conditional>
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201 <param name="tree" value="True"/>
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202 <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/>
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203 <output name="output_tree" file="output_tree_3.newick" />
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204 </test>
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205 </tests>
2
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206 <help><![CDATA[
0
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207 .. class:: warningmark
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208
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209 **Note**: the database used must be the same as the one used in the original Kraken run
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210
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211 -----
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212
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213 **What is Does**
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214
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215 Summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple experiments, conditions, locations, etc.
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216
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217 -----
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218
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219 **Output**
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220
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221 The output is tab-delimited, with one line per taxon.
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222
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223 Will optionally output a newick tree built from the kraken database taxonomy using the specified options. Tree branch lengths will be set to "1.00000".
2
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224 ]]></help>
0
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225 <citations>
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226 <citation type="bibtex">@unpublished{Kraken-Taxonomy-Report:2016,
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227 title = "Kraken Taxonomy Report",
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228 author = "Daniel Blankenberg",
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229 url = "https://github.com/blankenberg/Kraken-Taxonomy-Report",
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230 year = "2016 (accessed June 1, 2016)"
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231 }</citation>
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232 </citations>
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233 </tool>