Mercurial > repos > iuc > kraken2
comparison kraken2.xml @ 5:20e2f64aa1fe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit b5beeef6c90fe39ce3ace531877d632725839ee4
| author | iuc |
|---|---|
| date | Fri, 09 Feb 2024 21:43:22 +0000 |
| parents | e674066930b2 |
| children | cdee7158adf3 |
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| 4:e674066930b2 | 5:20e2f64aa1fe |
|---|---|
| 4 assign taxonomic labels to sequencing reads | 4 assign taxonomic labels to sequencing reads |
| 5 </description> | 5 </description> |
| 6 <macros> | 6 <macros> |
| 7 <import>macros.xml</import> | 7 <import>macros.xml</import> |
| 8 </macros> | 8 </macros> |
| 9 <xrefs> | |
| 10 <xref type="bio.tools">kraken2</xref> | |
| 11 </xrefs> | |
| 9 <requirements> | 12 <requirements> |
| 10 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> | 13 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> |
| 11 </requirements> | 14 </requirements> |
| 12 <version_command>kraken2 --version</version_command> | 15 <version_command>kraken2 --version</version_command> |
| 13 <command detect_errors="exit_code"> | 16 <command detect_errors="exit_code"> |
| 113 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> | 116 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> |
| 114 </data> | 117 </data> |
| 115 <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"> |
| 116 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> | 119 <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter> |
| 117 </data> | 120 </data> |
| 118 <data name="report_output" format="tabular" label="Report: ${tool.name} on ${on_string}"> | 121 <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report"> |
| 119 <filter>(report['create_report'])</filter> | 122 <filter>(report['create_report'])</filter> |
| 120 </data> | 123 </data> |
| 121 | 124 |
| 122 <data name="out1" format_source="forward_input" label="Unclassified forward" from_work_dir="un_out_1.*"> | 125 <data name="out1" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified forward reads" from_work_dir="un_out_1.*"> |
| 123 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> | 126 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> |
| 124 </data> | 127 </data> |
| 125 <data name="out2" format_source="forward_input" label="Unclassified reverse" from_work_dir="un_out_2.*"> | 128 <data name="out2" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified reverse reads" from_work_dir="un_out_2.*"> |
| 126 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> | 129 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> |
| 127 </data> | 130 </data> |
| 128 <data name="out3" format_source="forward_input" label="Classified forward" from_work_dir="cl_out_1.*"> | 131 <data name="out3" format_source="forward_input" label="${tool.name} on ${on_string}: Classified forward reads" from_work_dir="cl_out_1.*"> |
| 129 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> | 132 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> |
| 130 </data> | 133 </data> |
| 131 <data name="out4" format_source="forward_input" label="Classified reverse" from_work_dir="cl_out_2.*"> | 134 <data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*"> |
| 132 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> | 135 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> |
| 133 </data> | 136 </data> |
| 134 | 137 |
| 135 <data name="out1_1" format_source="input_pair['forward']" label="Unclassified forward" from_work_dir="un_out_1.*"> | 138 <data name="out1_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified forward read collection" from_work_dir="un_out_1.*"> |
| 136 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> | 139 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> |
| 137 </data> | 140 </data> |
| 138 <data name="out2_1" format_source="input_pair['forward']" label="Unclassified reverse" from_work_dir="un_out_2.*"> | 141 <data name="out2_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified reverse read collection" from_work_dir="un_out_2.*"> |
| 139 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> | 142 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> |
| 140 </data> | 143 </data> |
| 141 <data name="out3_1" format_source="input_pair['forward']" label="Classified forward" from_work_dir="cl_out_1.*"> | 144 <data name="out3_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified forward read collection" from_work_dir="cl_out_1.*"> |
| 142 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> | 145 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> |
| 143 </data> | 146 </data> |
| 144 <data name="out4_1" format_source="input_pair['forward']" label="Classified reverse" from_work_dir="cl_out_2.*"> | 147 <data name="out4_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified reverse read collection" from_work_dir="cl_out_2.*"> |
| 145 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> | 148 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> |
| 146 </data> | 149 </data> |
| 147 | 150 |
| 148 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> | 151 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> |
| 149 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> | 152 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> |
| 150 </outputs> | 153 </outputs> |
| 151 <tests> | 154 <tests> |
| 152 <test> | 155 <test expect_num_outputs="1"> |
| 153 <param name="single_paired_selector" value="no"/> | 156 <param name="single_paired_selector" value="no"/> |
| 154 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/> | 157 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/> |
| 155 <param name="split_reads" value="false"/> | 158 <param name="split_reads" value="false"/> |
| 156 <param name="quick" value="no"/> | 159 <param name="quick" value="no"/> |
| 157 <param name="confidence" value=".2"/> | 160 <param name="confidence" value=".2"/> |
| 158 <param name="kraken2_database" value="test_entry"/> | 161 <param name="kraken2_database" value="test_entry"/> |
| 159 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> | 162 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> |
| 160 </test> | 163 </test> |
| 161 <test> | 164 <test expect_num_outputs="5"> |
| 162 <param name="single_paired_selector" value="yes"/> | 165 <param name="single_paired_selector" value="yes"/> |
| 163 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> | 166 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> |
| 164 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> | 167 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> |
| 165 <param name="split_reads" value="true"/> | 168 <param name="split_reads" value="true"/> |
| 166 <param name="quick" value="no"/> | 169 <param name="quick" value="no"/> |
| 169 <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/> | 172 <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/> |
| 170 <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/> | 173 <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/> |
| 171 <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/> | 174 <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/> |
| 172 <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/> | 175 <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/> |
| 173 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> | 176 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> |
| 174 | |
| 175 </test> | 177 </test> |
| 176 <test> | 178 <test expect_num_outputs="2"> |
| 177 <param name="single_paired_selector" value="yes"/> | 179 <param name="single_paired_selector" value="yes"/> |
| 178 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> | 180 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> |
| 179 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> | 181 <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/> |
| 180 <param name="use-names" value="true"/> | 182 <param name="use-names" value="true"/> |
| 181 <section name="report"> | 183 <section name="report"> |