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annotate kraken.xml @ 0:0f17a8816b28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 23 Jul 2015 10:55:44 -0400
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children 7b3ef9b4af80
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0f17a8816b28 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <?xml version="1.0"?>
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2 <tool id="kraken" name="Kraken" version="1.1.0">
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3 <description>
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4 assign taxonomic labels to sequencing reads
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5 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 @SET_DATABASE_PATH@ &&
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12 kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@
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13
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14 #if $input_sequences.is_of_type( 'fastq' ):
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15 --fastq-input
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16 #else:
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17 --fasta-input
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18 #end if
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20 ${only_classified_output}
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21
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22 #if str( $quick_operation.quick ) == "yes":
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23 --quick
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24 --min-hits ${quick_operation.min_hits}
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26 #end if
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27
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28 "$input_sequences"
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29
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30 #if $split_reads:
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31 --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
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32 #end if
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33 --output "${output}"
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34 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
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35 ]]>
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36 </command>
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37 <inputs>
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38 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
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39 <param label="Output classified and unclassified reads?" name="split_reads" type="boolean" help="Sets --unclassified-out and --classified-out"/>
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40
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41 <conditional name="quick_operation">
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42 <param name="quick" type="select" label="Enable quick operation?" help="--quick; Rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
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43 <option value="yes">Yes</option>
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44 <option selected="True" value="no">No</option>
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45 </param>
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46 <when value="yes">
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47 <param name="min_hits" type="integer" value="1" label="Number of hits required for classification" help="--min-hits; min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
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48 </when>
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49 <when value="no">
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50 <!-- Do absolutely nothing -->
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51 </when>
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52 </conditional>
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53
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54 <param name="only_classified_output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" label="Print no Kraken output for unclassified sequences" help="--only-classified-output"/>
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55
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56 <expand macro="input_database" />
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57 </inputs>
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58 <outputs>
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59 <data format="tabular" label="${tool.name} on ${on_string}: Classified reads" name="classified_out">
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60 <filter>(split_reads)</filter>
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61 </data>
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62 <data format="tabular" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out">
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63 <filter>(split_reads)</filter>
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64 </data>
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65 <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />
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66 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
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67 </outputs>
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68 <help>
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69 <![CDATA[
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70 **What it does**
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71
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72 Kraken 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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73
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74 -----
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75
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76 **Kraken options**
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77
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78 The Galaxy version of Kraken implements the following options::
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79
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80
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81 --fasta-input Input is FASTA format
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82 --fastq-input Input is FASTQ format
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83 --quick Quick operation (use first hit or hits)
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84 --min-hits NUM In quick op., number of hits req'd for classification
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85 NOTE: this is ignored if --quick is not specified
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86 --unclassified-out Print unclassified sequences to filename
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87 --classified-out Print classified sequences to filename
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88
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89 --only-classified-output Print no Kraken output for unclassified sequences
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90
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91 ------
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92
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93 **Output Format**
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94
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95 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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96
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97 1. "C"/"U": one letter code indicating that the sequence was either classified or unclassified.
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98 2. The sequence ID, obtained from the FASTA/FASTQ header.
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99 3. The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified.
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100 4. The length of the sequence in bp.
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101 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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102 a) the first 13 k-mers mapped to taxonomy ID #562
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103 b) the next 4 k-mers mapped to taxonomy ID #561
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104 c) the next 31 k-mers contained an ambiguous nucleotide
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105 d) the next k-mer was not in the database
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106 e) the last 3 k-mers mapped to taxonomy ID #562
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107 ]]>
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108 </help>
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109 <expand macro="requirements" />
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110 <expand macro="stdio" />
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111 <expand macro="version_command" />
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112 <expand macro="citations" />
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113 </tool>