Mercurial > repos > iuc > kraken2
comparison kraken2.xml @ 6:cdee7158adf3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 3c6cc780d2d8ea156d167289cc2576fc3e43d2fd
| author | iuc |
|---|---|
| date | Thu, 06 Jun 2024 09:03:24 +0000 |
| parents | 20e2f64aa1fe |
| children |
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| 5:20e2f64aa1fe | 6:cdee7158adf3 |
|---|---|
| 133 </data> | 133 </data> |
| 134 <data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*"> | 134 <data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*"> |
| 135 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> | 135 <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter> |
| 136 </data> | 136 </data> |
| 137 | 137 |
| 138 <data name="out1_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified forward read collection" from_work_dir="un_out_1.*"> | 138 <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs"> |
| 139 <data name="forward" from_work_dir="un_out_1.*"/> | |
| 140 <data name="reverse" from_work_dir="un_out_2.*"/> | |
| 139 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> | 141 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> |
| 140 </data> | 142 </collection> |
| 141 <data name="out2_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified reverse read collection" from_work_dir="un_out_2.*"> | 143 <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs"> |
| 142 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> | 144 <data name="forward" from_work_dir="cl_out_1.*"/> |
| 143 </data> | 145 <data name="reverse" from_work_dir="cl_out_2.*"/> |
| 144 <data name="out3_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified forward read collection" from_work_dir="cl_out_1.*"> | |
| 145 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> | 146 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> |
| 146 </data> | 147 </collection> |
| 147 <data name="out4_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified reverse read collection" from_work_dir="cl_out_2.*"> | |
| 148 <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter> | |
| 149 </data> | |
| 150 | 148 |
| 151 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> | 149 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> |
| 152 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> | 150 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> |
| 153 </outputs> | 151 </outputs> |
| 154 <tests> | 152 <tests> |
| 171 <param name="kraken2_database" value="test_entry"/> | 169 <param name="kraken2_database" value="test_entry"/> |
| 172 <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/> | 170 <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/> |
| 173 <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/> | 171 <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/> |
| 174 <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/> | 172 <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/> |
| 175 <output name="out4" file="cl_test2_output_2.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"> | |
| 190 <element name="forward" file="un_test2_output_1.fastq" ftype="fastq"/> | |
| 191 <element name="reverse" file="un_test2_output_2.fastq" ftype="fastq"/> | |
| 192 </output_collection> | |
| 193 <output_collection name="out_classified_paired" type="paired"> | |
| 194 <element name="forward" file="cl_test2_output_1.fastq" ftype="fastq"/> | |
| 195 <element name="reverse" file="cl_test2_output_2.fastq" ftype="fastq"/> | |
| 196 </output_collection> | |
| 176 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> | 197 <output name="output" file="kraken_test2_output.tab" ftype="tabular"/> |
| 177 </test> | 198 </test> |
| 178 <test expect_num_outputs="2"> | 199 <test expect_num_outputs="2"> |
| 179 <param name="single_paired_selector" value="yes"/> | 200 <param name="single_paired_selector" value="yes"/> |
| 180 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> | 201 <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/> |