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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
author iuc
date Sun, 07 Dec 2025 11:30:46 +0000
parents 9c5599b8c9a0
children
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5:9c5599b8c9a0 6:e452fed07fbb
1 <?xml version="1.0"?> 1 <tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy1">
3 <description> 2 <description>
4 assign taxonomic labels to sequencing reads 3 assign taxonomic labels to sequencing reads
5 </description> 4 </description>
6 <macros> 5 <macros>
7 <import>macros.xml</import> 6 <import>macros.xml</import>
13 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
14 </requirements> 13 </requirements>
15 <version_command>kraken2 --version</version_command> 14 <version_command>kraken2 --version</version_command>
16 <command detect_errors="exit_code"> 15 <command detect_errors="exit_code">
17 <![CDATA[ 16 <![CDATA[
18
19 #def get_type($data)
20 #if $data.is_of_type('fastq'):
21 #return 'fastq'
22 #elif $data.is_of_type('fasta'):
23 #return 'fasta'
24 #elif $data.is_of_type('fastqsanger'):
25 #return 'fastqsanger'
26 #elif $data.is_of_type('fasta.gz'):
27 #return 'fasta.gz'
28 #elif $data.is_of_type('fasta.bz2'):
29 #return 'fasta.bz2'
30 #elif $data.is_of_type('fastq.gz'):
31 #return 'fastq.gz'
32 #elif $data.is_of_type('fastq.bz2'):
33 #return 'fastq.bz2'
34 #end if
35 #end def
36
37 kraken2 17 kraken2
38 --threads \${GALAXY_SLOTS:-1} 18 --threads \${GALAXY_SLOTS:-1}
39 --db '${kraken2_database.fields.path}' 19 --db '${kraken2_database.fields.path}'
40 20
41 $quick 21 $quick
42 22
43 #if $single_paired.single_paired_selector == "yes" 23 #if $single_paired.single_paired_selector == "collection":
44 --paired
45 '${single_paired.forward_input}' '${single_paired.reverse_input}'
46 #elif $single_paired.single_paired_selector == "collection":
47 --paired 24 --paired
48 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}' 25 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
49 #else: 26 #else:
50 '${single_paired.input_sequences}' 27 '${single_paired.input_sequences}'
51 #end if 28 #end if
52 29
53 #if $split_reads: 30 #if $split_reads:
54 #if $single_paired.single_paired_selector == "no": 31 #if $single_paired.single_paired_selector == "no":
55 --classified-out '${classified_out_s}' --unclassified-out '${unclassified_out_s}' 32 --unclassified-out 'un_out'
56 #elif $single_paired.single_paired_selector == "yes": 33 --classified-out 'cl_out'
57 #set $result = $get_type($single_paired.forward_input)
58 --unclassified-out 'un_out#.${result}' --classified-out 'cl_out#.${result}'
59 #else: 34 #else:
60 #set $result = $get_type($single_paired.input_pair.forward) 35 --unclassified-out 'un_out#'
61 --unclassified-out 'un_out#.${result}' --classified-out 'cl_out#.${result}' 36 --classified-out 'cl_out#'
62 #end if 37 #end if
63 #end if 38 #end if
64 39
65 --confidence '${confidence}' 40 --confidence '${confidence}'
66 --minimum-base-quality '${min_base_quality}' 41 --minimum-base-quality '${min_base_quality}'
67 --minimum-hit-groups '${minimum_hit_groups}' 42 --minimum-hit-groups '${minimum_hit_groups}'
68 43
69 $use_names 44 $use_names
70 45
71 #if $report.create_report: 46 #if $report.create_report == "true":
72 --report '${report_output}' 47 --report '${report_output}'
73 $report.use_mpa_style 48 $report.use_mpa_style
74 $report.report_zero_counts 49 $report.report_zero_counts
75 $report.report_minimizer_data 50 $report.report_minimizer_data
76 #end if 51 #end if
77 52
78 > '${output}' 53 > '${output}'
54
55 #if $split_reads:
56 #if $single_paired.single_paired_selector == "no":
57 #if $single_paired.input_sequences.ext.endswith(".gz")
58 #set command = "gzip -c"
59 #elif $single_paired.input_sequences.ext.endswith(".bz2")
60 #set command = "bzip2 -c"
61 #else
62 #set command = "cat"
63 #end if
64 && $command un_out > '$unclassified_out_s'
65 && $command cl_out > '$classified_out_s'
66 #else:
67 #if $single_paired.input_pair.forward.ext.endswith(".gz")
68 #set command = "gzip -c"
69 #elif $single_paired.input_pair.forward.ext.endswith(".bz2")
70 #set command = "bzip2 -c"
71 #else
72 #set command = "cat"
73 #end if
74 && $command un_out_1 > '$out_unclassified_paired.forward'
75 && $command un_out_2 > '$out_unclassified_paired.reverse'
76 && $command cl_out_1 > '$out_classified_paired.forward'
77 && $command cl_out_1 > '$out_classified_paired.forward'
78 #end if
79 #end if
79 ]]></command> 80 ]]></command>
80 <inputs> 81 <inputs>
81 <conditional name="single_paired"> 82 <conditional name="single_paired">
82 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> 83 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
83 <option value="collection">Paired Collection</option> 84 <option value="collection">Paired</option>
84 <option value="yes">Paired</option>
85 <option selected="True" value="no">Single</option> 85 <option selected="True" value="no">Single</option>
86 </param> 86 </param>
87 <when value="collection"> 87 <when value="collection">
88 <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/> 88 <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
89 </when>
90 <when value="yes">
91 <param format="@INTYPES@" name="forward_input" type="data" label="Forward strand"/>
92 <param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand"/>
93 </when> 89 </when>
94 <when value="no"> 90 <when value="no">
95 <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/> 91 <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
96 </when> 92 </when>
97 </conditional> 93 </conditional>
99 <param argument="--confidence" type="float" label="Confidence" value="0.0" min="0" max="1" help="Confidence score threshold. Must be in [0, 1]"/> 95 <param argument="--confidence" type="float" label="Confidence" value="0.0" min="0" max="1" help="Confidence score threshold. Must be in [0, 1]"/>
100 <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)"/> 96 <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)"/>
101 <param argument="--minimum-hit-groups" type="integer" label="Minimum hit groups" value="2" help="Number of overlapping k-mers sharing the same minimizer needed to make a call" /> 97 <param argument="--minimum-hit-groups" type="integer" label="Minimum hit groups" value="2" help="Number of overlapping k-mers sharing the same minimizer needed to make a call" />
102 <param argument="--quick" type="boolean" truevalue="--quick" falsevalue="" label="Enable quick operation" help="Quick operation (use first hit)"/> 98 <param argument="--quick" type="boolean" truevalue="--quick" falsevalue="" label="Enable quick operation" help="Quick operation (use first hit)"/>
103 <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/> 99 <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/>
104 100 <conditional name="report">
105 <section name="report" title="Create Report" expanded="false"> 101 <param argument="--report" name="create_report" type="select" label="Print a report with aggregrate counts/clade to file" help="Can be used as input for bracken">
106 <param name="create_report" type="boolean" label="Print a report with aggregrate counts/clade to file" help="--report" /> 102 <option value="true">Yes</option>
107 <param argument="--use-mpa-style" type="boolean" truevalue="--use-mpa-style" falsevalue="" label="Format report output like Kraken 1's kraken-mpa-report" /> 103 <option value="false" selected="true">No</option>
108 <param argument="--report-zero-counts" type="boolean" truevalue="--report-zero-counts" falsevalue="" label="Report counts for ALL taxa, even if counts are zero" /> 104 </param>
109 <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" /> 105 <when value="true">
110 </section> 106 <param argument="--use-mpa-style" type="boolean" truevalue="--use-mpa-style" falsevalue="" label="Format report output like Kraken 1's kraken-mpa-report" />
111 107 <param argument="--report-zero-counts" type="boolean" truevalue="--report-zero-counts" falsevalue="" label="Report counts for ALL taxa, even if counts are zero" />
108 <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" />
109 </when>
110 <when value="false"/>
111 </conditional>
112 <expand macro="input_database"/> 112 <expand macro="input_database"/>
113 </inputs> 113 </inputs>
114 <outputs> 114 <outputs>
115 <data name="classified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads"> 115 <data name="classified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads">
116 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> 116 <filter>split_reads and single_paired['single_paired_selector'] == "no"</filter>
117 </data> 117 </data>
118 <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads"> 118 <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
119 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> 119 <filter>split_reads and single_paired['single_paired_selector'] == "no"</filter>
120 </data> 120 </data>
121 <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report"> 121 <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report">
122 <filter>(report['create_report'])</filter> 122 <filter>report['create_report'] == "true"</filter>
123 </data> 123 </data>
124
125 <data name="out1" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified forward reads" from_work_dir="un_out_1.*">
126 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
127 </data>
128 <data name="out2" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified reverse reads" from_work_dir="un_out_2.*">
129 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
130 </data>
131 <data name="out3" format_source="forward_input" label="${tool.name} on ${on_string}: Classified forward reads" from_work_dir="cl_out_1.*">
132 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
133 </data>
134 <data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*">
135 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
136 </data>
137
138 <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs"> 124 <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs">
139 <data name="forward" from_work_dir="un_out_1.*"/> 125 <filter>split_reads and single_paired['single_paired_selector'] == "collection"</filter>
140 <data name="reverse" from_work_dir="un_out_2.*"/>
141 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
142 </collection> 126 </collection>
143 <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs"> 127 <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs">
144 <data name="forward" from_work_dir="cl_out_1.*"/> 128 <filter>split_reads and "collection" in single_paired['single_paired_selector'] == "collection"</filter>
145 <data name="reverse" from_work_dir="cl_out_2.*"/>
146 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
147 </collection> 129 </collection>
148 130
149 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> 131 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
150 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> 132 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
151 </outputs> 133 </outputs>
152 <tests> 134 <tests>
153 <test expect_num_outputs="1"> 135 <test expect_num_outputs="1">
154 <param name="single_paired_selector" value="no"/> 136 <conditional name="single_paired">
155 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/> 137 <param name="single_paired_selector" value="no"/>
138 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
139 </conditional>
156 <param name="split_reads" value="false"/> 140 <param name="split_reads" value="false"/>
157 <param name="quick" value="no"/> 141 <param name="quick" value="no"/>
158 <param name="confidence" value=".2"/> 142 <param name="confidence" value=".2"/>
159 <param name="kraken2_database" value="test_entry"/> 143 <param name="kraken2_database" value="test_entry"/>
160 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> 144 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
161 </test> 145 </test>
162 <test expect_num_outputs="5"> 146
163 <param name="single_paired_selector" value="yes"/> 147 <test expect_num_outputs="3">
164 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> 148 <conditional name="single_paired">
165 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> 149 <param name="single_paired_selector" value="no"/>
150 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
151 </conditional>
152 <param name="split_reads" value="true"/>
153 <param name="quick" value="no"/>
154 <param name="confidence" value=".2"/>
155 <param name="kraken2_database" value="test_entry"/>
156 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
157 <output name="classified_out_s" file="kraken_test1_cl.fas" ftype="fasta"/>
158 <output name="unclassified_out_s" file="kraken_test1_un.fas" ftype="fasta"/>
159 </test>
160
161 <test expect_num_outputs="7">
162 <conditional name="single_paired">
163 <param name="single_paired_selector" value="collection"/>
164 <param name="input_pair">
165 <collection type="paired">
166 <element name="forward" value="kraken_test2_R1.fastq.gz" ftype="fastqsanger.gz"/>
167 <element name="reverse" value="kraken_test2_R2.fastq.gz" ftype="fastqsanger.gz"/>
168 </collection>
169 </param>
170 <param name="single_paired_selector" value="collection"/>
171 </conditional>
166 <param name="split_reads" value="true"/> 172 <param name="split_reads" value="true"/>
167 <param name="quick" value="no"/> 173 <param name="quick" value="no"/>
168 <param name="confidence" value="0"/> 174 <param name="confidence" value="0"/>
169 <param name="kraken2_database" value="test_entry"/> 175 <param name="kraken2_database" value="test_entry"/>
170 <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/>
171 <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/>
172 <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/>
173 <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/>
174 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
175 </test>
176 <!-- same test but collection in/output -->
177 <test expect_num_outputs="7">
178 <param name="single_paired_selector" value="collection"/>
179 <param name="input_pair">
180 <collection type="paired">
181 <element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>
182 <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>
183 </collection>
184 </param>
185 <param name="split_reads" value="true"/>
186 <param name="quick" value="no"/>
187 <param name="confidence" value="0"/>
188 <param name="kraken2_database" value="test_entry"/>
189 <output_collection name="out_unclassified_paired" type="paired"> 176 <output_collection name="out_unclassified_paired" type="paired">
190 <element name="forward" file="un_test2_output_1.fastq" ftype="fastq"/> 177 <element name="forward" file="un_test2_output_1.fastq" ftype="fastqsanger.gz" decompress="true"/>
191 <element name="reverse" file="un_test2_output_2.fastq" ftype="fastq"/> 178 <element name="reverse" file="un_test2_output_2.fastq" ftype="fastqsanger.gz" decompress="true"/>
192 </output_collection> 179 </output_collection>
193 <output_collection name="out_classified_paired" type="paired"> 180 <output_collection name="out_classified_paired" type="paired">
194 <element name="forward" file="cl_test2_output_1.fastq" ftype="fastq"/> 181 <element name="forward" file="cl_test2_output_1.fastq" ftype="fastqsanger.gz" decompress="true"/>
195 <element name="reverse" file="cl_test2_output_2.fastq" ftype="fastq"/> 182 <element name="reverse" file="cl_test2_output_2.fastq" ftype="fastqsanger.gz" decompress="true"/>
196 </output_collection> 183 </output_collection>
197 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> 184 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
198 </test> 185 <assert_command>
186 <has_text text="gzip -c"/>
187 </assert_command>
188 </test>
189
199 <test expect_num_outputs="2"> 190 <test expect_num_outputs="2">
200 <param name="single_paired_selector" value="yes"/> 191 <conditional name="single_paired">
201 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> 192 <param name="single_paired_selector" value="collection"/>
202 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> 193 <param name="input_pair">
203 <param name="use-names" value="true"/> 194 <collection type="paired">
204 <section name="report"> 195 <element name="forward" value="kraken_test2_R1.fastq" ftype="fastqsanger"/>
196 <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastqsanger"/>
197 </collection>
198 </param>
199 </conditional>
200 <param name="use_names" value="true"/>
201 <conditional name="report">
205 <param name="create_report" value="true"/> 202 <param name="create_report" value="true"/>
206 <param name="report_minimizer_data" value="true"/> 203 <param name="report_minimizer_data" value="true"/>
207 </section> 204 </conditional>
208 <param name="kraken2_database" value="test_entry"/> 205 <param name="kraken2_database" value="test_entry"/>
209 <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/> 206 <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/>
210 </test> 207 </test>
211 </tests> 208 </tests>
212 <help> 209 <help>