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annotate kraken.xml @ 5:bc918f32d4be draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 4782f9ad9bfe2479685ccaf51b66b0d32f83f193
author devteam
date Thu, 05 Nov 2015 10:09:40 -0500
parents 55d42997c0b5
children 1496744bd2ad
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1 <?xml version="1.0"?>
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2 <tool id="kraken" name="Kraken" version="1.1.2">
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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 ${only_classified_output}
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16 #if str( $quick_operation.quick ) == "yes":
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17 --quick
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18 --min-hits ${quick_operation.min_hits}
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20 #end if
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21
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22 #if $single_paired.single_paired_selector == "yes":
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23 #if $forward_input.is_of_type( 'fastq' ):
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24 --fastq-input
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25 #else:
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26 --fasta-input
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27 #end if
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28 "$forward_input" "$reverse_input"
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29 ${single_paired.check_names}
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30 #elif $single_paired.single_paired_selector == "collection":
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31 #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
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32 --fastq-input
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33 #else:
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34 --fasta-input
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35 #end if
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36 "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}"
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37 ${single_paired.check_names}
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38 #else:
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39 #if $input_sequences.is_of_type( 'fastq' ):
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40 --fastq-input
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41 #else:
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42 --fasta-input
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43 #end if
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44 "$input_sequences"
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45 #end if
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46
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47 #if $split_reads:
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48 --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
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49 #end if
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50 --output "${output}"
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51 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
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52 ]]>
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53 </command>
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54 <inputs>
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55 <conditional name="single_paired">
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56 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
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57 <option value="collection">Collection</option>
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58 <option value="yes">Yes</option>
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59 <option selected="True" value="no">No</option>
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60 </param>
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61 <when value="collection">
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62 <param format="fasta,fastq" label="Collection of paired reads" name="input_pair" type="data_collection1" collection_type="paired" help="FASTA or FASTQ datasets" />
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63 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
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64 </when>
4
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65 <when value="yes">
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66 <param format="fasta,fastq" label="Forward strand" name="forward_input" type="data" help="FASTA or FASTQ dataset"/>
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67 <param format="fasta,fastq" label="Reverse strand" name="reverse_input" type="data" help="FASTA or FASTQ dataset"/>
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68 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
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69 </when>
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70 <when value="no">
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71 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
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72 </when>
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73
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74 </conditional>
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75 <param label="Output classified and unclassified reads?" name="split_reads" type="boolean" help="Sets --unclassified-out and --classified-out"/>
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76
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77 <conditional name="quick_operation">
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78 <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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79 <option value="yes">Yes</option>
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80 <option selected="True" value="no">No</option>
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81 </param>
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82 <when value="yes">
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83 <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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84 </when>
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85 <when value="no">
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86 <!-- Do absolutely nothing -->
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87 </when>
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88 </conditional>
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89
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90 <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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91
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92 <expand macro="input_database" />
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93 </inputs>
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94 <outputs>
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95 <data format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads" name="classified_out">
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96 <filter>(split_reads)</filter>
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97 </data>
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98 <data format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out">
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99 <filter>(split_reads)</filter>
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100 </data>
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101 <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />
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102 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
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103 </outputs>
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104 <help>
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105 <![CDATA[
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106 **What it does**
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107
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108 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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109
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110 -----
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111
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112 **Kraken options**
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113
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114 The Galaxy version of Kraken implements the following options::
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115
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116
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117 --fasta-input Input is FASTA format
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118 --fastq-input Input is FASTQ format
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119 --quick Quick operation (use first hit or hits)
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120 --min-hits NUM In quick op., number of hits req'd for classification
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121 NOTE: this is ignored if --quick is not specified
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122 --unclassified-out Print unclassified sequences to filename
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123 --classified-out Print classified sequences to filename
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124
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125 --only-classified-output Print no Kraken output for unclassified sequences
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126
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127 ------
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128
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129 **Output Format**
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130
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131 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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132
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133 1. "C"/"U": one letter code indicating that the sequence was either classified or unclassified.
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134 2. The sequence ID, obtained from the FASTA/FASTQ header.
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135 3. The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified.
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136 4. The length of the sequence in bp.
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137 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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138 a) the first 13 k-mers mapped to taxonomy ID #562
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139 b) the next 4 k-mers mapped to taxonomy ID #561
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140 c) the next 31 k-mers contained an ambiguous nucleotide
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141 d) the next k-mer was not in the database
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142 e) the last 3 k-mers mapped to taxonomy ID #562
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143 ]]>
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144 </help>
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145 <expand macro="requirements" />
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146 <expand macro="stdio" />
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147 <expand macro="version_command" />
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148 <expand macro="citations" />
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149 </tool>