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comparison kraken2.xml @ 9:cbe396d9773e draft default tip

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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 11:31:00 +0000
parents e150ae930235
children
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8:e150ae930235 9:cbe396d9773e
41 --minimum-base-quality '${min_base_quality}' 41 --minimum-base-quality '${min_base_quality}'
42 --minimum-hit-groups '${minimum_hit_groups}' 42 --minimum-hit-groups '${minimum_hit_groups}'
43 43
44 $use_names 44 $use_names
45 45
46 #if $report.create_report: 46 #if $report.create_report == "true":
47 --report '${report_output}' 47 --report '${report_output}'
48 $report.use_mpa_style 48 $report.use_mpa_style
49 $report.report_zero_counts 49 $report.report_zero_counts
50 $report.report_minimizer_data 50 $report.report_minimizer_data
51 #end if 51 #end if
95 <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]"/>
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)"/> 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)"/>
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" /> 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" />
98 <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)"/>
99 <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"/>
100 100 <conditional name="report">
101 <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">
102 <param name="create_report" type="boolean" label="Print a report with aggregrate counts/clade to file" help="--report" /> 102 <option value="true">Yes</option>
103 <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>
104 <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>
105 <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">
106 </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" />
107 107 <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>
108 <expand macro="input_database"/> 112 <expand macro="input_database"/>
109 </inputs> 113 </inputs>
110 <outputs> 114 <outputs>
111 <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 ${on_string}: Classified reads">
112 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> 116 <filter>split_reads and single_paired['single_paired_selector'] == "no"</filter>
113 </data> 117 </data>
114 <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads"> 118 <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
115 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> 119 <filter>split_reads and single_paired['single_paired_selector'] == "no"</filter>
116 </data> 120 </data>
117 <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report"> 121 <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report">
118 <filter>(report['create_report'])</filter> 122 <filter>report['create_report'] == "true"</filter>
119 </data> 123 </data>
120
121 <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs"> 124 <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs">
122 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> 125 <filter>split_reads and single_paired['single_paired_selector'] == "collection"</filter>
123 </collection> 126 </collection>
124 <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs"> 127 <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs">
125 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> 128 <filter>split_reads and "collection" in single_paired['single_paired_selector'] == "collection"</filter>
126 </collection> 129 </collection>
127 130
128 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> 131 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
129 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> 132 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
130 </outputs> 133 </outputs>
193 <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastqsanger"/> 196 <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastqsanger"/>
194 </collection> 197 </collection>
195 </param> 198 </param>
196 </conditional> 199 </conditional>
197 <param name="use_names" value="true"/> 200 <param name="use_names" value="true"/>
198 <section name="report"> 201 <conditional name="report">
199 <param name="create_report" value="true"/> 202 <param name="create_report" value="true"/>
200 <param name="report_minimizer_data" value="true"/> 203 <param name="report_minimizer_data" value="true"/>
201 </section> 204 </conditional>
202 <param name="kraken2_database" value="test_entry"/> 205 <param name="kraken2_database" value="test_entry"/>
203 <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/> 206 <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/>
204 </test> 207 </test>
205 </tests> 208 </tests>
206 <help> 209 <help>