annotate kraken2.xml @ 3:4a9da2b6c2e3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
author iuc
date Mon, 23 Nov 2020 20:50:12 +0000
parents d4bb87ca916d
children e674066930b2
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0968856c687c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231
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1 <?xml version="1.0"?>
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2 <tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy0">
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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 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
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11 </requirements>
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12 <version_command>kraken2 --version</version_command>
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13 <command detect_errors="exit_code">
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14 <![CDATA[
1
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15
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16 #def get_type($data)
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17 #if $data.is_of_type('fastq'):
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18 #return 'fastq'
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19 #elif $data.is_of_type('fasta'):
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20 #return 'fasta'
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21 #elif $data.is_of_type('fastqsanger'):
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22 #return 'fastqsanger'
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23 #elif $data.is_of_type('fasta.gz'):
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24 #return 'fasta.gz'
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25 #elif $data.is_of_type('fasta.bz2'):
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26 #return 'fasta.bz2'
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27 #elif $data.is_of_type('fastq.gz'):
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28 #return 'fastq.gz'
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29 #elif $data.is_of_type('fastq.bz2'):
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30 #return 'fastq.bz2'
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31 #end if
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32 #end def
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33
0
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34 kraken2
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35 --threads \${GALAXY_SLOTS:-1}
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36 --db '${kraken2_database.fields.path}'
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37
3
4a9da2b6c2e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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38 $quick
0
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39
1
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40 #if $single_paired.single_paired_selector == "yes"
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41 --paired
0
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42 '${single_paired.forward_input}' '${single_paired.reverse_input}'
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43 #elif $single_paired.single_paired_selector == "collection":
1
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44 --paired
0
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45 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
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46 #else:
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47 '${single_paired.input_sequences}'
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48 #end if
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49
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50 #if $split_reads:
1
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51 #if $single_paired.single_paired_selector == "no":
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52 --classified-out '${classified_out_s}' --unclassified-out '${unclassified_out_s}'
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53 #elif $single_paired.single_paired_selector == "yes":
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54 #set $result = $get_type($single_paired.forward_input)
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55 --unclassified-out 'un_out#.${result}' --classified-out 'cl_out#.${result}'
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56 #else:
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57 #set $result = $get_type($single_paired.input_pair.forward)
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58 --unclassified-out 'un_out#.${result}' --classified-out 'cl_out#.${result}'
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59 #end if
0
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60 #end if
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61
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62 --confidence '${confidence}'
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63 --minimum-base-quality '${min_base_quality}'
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64 --minimum-hit-groups '${minimum_hit_groups}'
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65
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66 $use_names
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67
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68 #if $report.create_report:
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69 --report '${report_output}'
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70 $report.use_mpa_style
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71 $report.report_zero_counts:
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72 $report.report_minimizer_data:
0
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73 #end if
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74
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75 > '${output}'
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76 ]]></command>
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77 <inputs>
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78 <conditional name="single_paired">
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79 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
1
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80 <option value="collection">Paired Collection</option>
0
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81 <option value="yes">Paired</option>
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82 <option selected="True" value="no">Single</option>
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83 </param>
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84 <when value="collection">
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85 <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
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86 </when>
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87 <when value="yes">
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88 <param format="@INTYPES@" name="forward_input" type="data" label="Forward strand"/>
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89 <param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand"/>
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90 </when>
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91 <when value="no">
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92 <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
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93 </when>
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94 </conditional>
3
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95 <param argument="--use-names" type="boolean" truevalue="--use-names" falsevalue="" label="Print scientific names instead of just taxids"/>
4a9da2b6c2e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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96 <param argument="--confidence" type="float" label="Confidence" value="0.0" min="0" max="1" help="Confidence score threshold. Must be in [0, 1]"/>
4a9da2b6c2e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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97 <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)"/>
4a9da2b6c2e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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98 <param argument="--minimum-hit-groups" type="integer" label="Minimum hit goups" value="2" help="Number of overlapping k-mers sharing the same minimizer needed to make a call" />
4a9da2b6c2e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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99 <param argument="--quick" type="boolean" truevalue="--quick" falsevalue="" label="Enable quick operation" help="Quick operation (use first hit)"/>
1
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100 <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/>
0
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101
1
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102 <section name="report" title="Create Report" expanded="false">
3
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103 <param name="create_report" type="boolean" label="Print a report with aggregrate counts/clade to file" help="--report" />
4a9da2b6c2e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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104 <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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105 <param argument="--report-zero-counts" type="boolean" truevalue="--report-zero-counts" falsevalue="" label="Report counts for ALL taxa, even if counts are zero" />
4a9da2b6c2e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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106 <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" />
1
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107 </section>
0
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108
1
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109 <expand macro="input_database"/>
0
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110 </inputs>
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111 <outputs>
1
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112 <data name="classified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads">
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113 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter>
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114 </data>
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115 <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
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116 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter>
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117 </data>
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118 <data name="report_output" format="tabular" label="Report: ${tool.name} on ${on_string}">
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119 <filter>(report['create_report'])</filter>
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120 </data>
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121
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122 <data name="out1" format_source="forward_input" label="Unclassified forward" from_work_dir="un_out_1.*">
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123 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
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124 </data>
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125 <data name="out2" format_source="forward_input" label="Unclassified reverse" from_work_dir="un_out_2.*">
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126 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
0
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127 </data>
1
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128 <data name="out3" format_source="forward_input" label="Classified forward" from_work_dir="cl_out_1.*">
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129 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
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130 </data>
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131 <data name="out4" format_source="forward_input" label="Classified reverse" from_work_dir="cl_out_2.*">
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132 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
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133 </data>
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134
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135 <data name="out1.1" format_source="input_pair['forward']" label="Unclassified forward" from_work_dir="un_out_1.*">
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136 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
0
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137 </data>
1
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138 <data name="out2.1" format_source="input_pair['forward']" label="Unclassified reverse" from_work_dir="un_out_2.*">
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139 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
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140 </data>
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141 <data name="out3.1" format_source="input_pair['forward']" label="Classified forward" from_work_dir="cl_out_1.*">
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142 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
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143 </data>
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144 <data name="out4.1" format_source="input_pair['forward']" label="Classified reverse" from_work_dir="cl_out_2.*">
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145 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
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146 </data>
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147
0
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148 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
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149 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
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150 </outputs>
1
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151 <tests>
0
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152 <test>
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153 <param name="single_paired_selector" value="no"/>
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154 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
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155 <param name="split_reads" value="false"/>
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156 <param name="quick" value="no"/>
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157 <param name="confidence" value=".2"/>
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158 <param name="only-classified-output" value="false"/>
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159 <param name="kraken2_database" value="test_entry"/>
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160 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
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161 </test>
1
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162 <test>
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163 <param name="single_paired_selector" value="yes"/>
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164 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
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165 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>
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166 <param name="split_reads" value="true"/>
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167 <param name="quick" value="no"/>
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168 <param name="confidence" value="0"/>
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169 <param name="only-classified-output" value="false"/>
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170 <param name="kraken2_database" value="test_entry"/>
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171 <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/>
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172 <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/>
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173 <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/>
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174 <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/>
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175 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
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176 </test>
0
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177 </tests>
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178 <help>
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179 <![CDATA[
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180 **What it does**
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181
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182 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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183
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184 -----
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185
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186 **Output Format**
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187
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188 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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189
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190 1. "C"/"U": a one letter code indicating that the sequence was either classified or unclassified.
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191 2. The sequence ID, obtained from the FASTA/FASTQ header.
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192 3. The taxonomy ID Kraken 2 used to label the sequence; this is 0 if the sequence is unclassified.
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193 4. The length of the sequence in bp.
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194 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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195 a) the first 13 k-mers mapped to taxonomy ID #562
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196 b) the next 4 k-mers mapped to taxonomy ID #561
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197 c) the next 31 k-mers contained an ambiguous nucleotide
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198 d) the next k-mer was not in the database
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199 e) the last 3 k-mers mapped to taxonomy ID #562
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200 ]]>
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201 </help>
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202 <expand macro="citations" />
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203 </tool>