Mercurial > repos > iuc > bcftools_convert_from_vcf
comparison bcftools_convert_from_vcf.xml @ 20:d58d2e8c7a57 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
| author | iuc |
|---|---|
| date | Tue, 16 Jul 2024 17:00:03 +0000 |
| parents | 9b29129fb491 |
| children |
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| 19:cacc9970727a | 20:d58d2e8c7a57 |
|---|---|
| 143 <filter>convert['convert_to'] == 'hap_legend_sample'</filter> | 143 <filter>convert['convert_to'] == 'hap_legend_sample'</filter> |
| 144 </data> | 144 </data> |
| 145 <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/> | 145 <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/> |
| 146 </outputs> | 146 </outputs> |
| 147 <tests> | 147 <tests> |
| 148 <test> | 148 <test expect_num_outputs="2"> |
| 149 <param name="input_file" ftype="vcf" value="convert.vcf" /> | 149 <param name="input_file" ftype="vcf" value="convert.vcf" /> |
| 150 <param name="convert_to" value="gen_sample" /> | 150 <param name="convert_to" value="gen_sample" /> |
| 151 <output name="output_gen"> | 151 <output name="output_gen"> |
| 152 <assert_contents> | 152 <assert_contents> |
| 153 <has_text text="X:2698560_G_A X:2698560_G_A 2698560 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0"/> | 153 <has_text text="X:2698560_G_A X:2698560_G_A 2698560 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0"/> |
| 157 <assert_contents> | 157 <assert_contents> |
| 158 <has_text text="NA00001 NA00001 0"/> | 158 <has_text text="NA00001 NA00001 0"/> |
| 159 </assert_contents> | 159 </assert_contents> |
| 160 </output> | 160 </output> |
| 161 </test> | 161 </test> |
| 162 <test> | 162 <test expect_num_outputs="2"> |
| 163 <param name="input_file" ftype="vcf" value="convert.vcf" /> | 163 <param name="input_file" ftype="vcf" value="convert.vcf" /> |
| 164 <param name="convert_to" value="gen_sample" /> | 164 <param name="convert_to" value="gen_sample" /> |
| 165 <param name="tag" value="GP" /> | 165 <param name="tag" value="GP" /> |
| 166 <param name="convert_3N6" value="True" /> | 166 <param name="convert_3N6" value="True" /> |
| 167 <output name="output_gen"> | 167 <output name="output_gen"> |
| 168 <assert_contents> | 168 <assert_contents> |
| 169 <has_text text="X:2698630_A_G X:2698630_A_G 2698630 A G 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000"/> | 169 <has_text text="X:2698630_A_G X:2698630_A_G 2698630 A G 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000"/> |
| 170 </assert_contents> | 170 </assert_contents> |
| 171 </output> | 171 </output> |
| 172 </test> | 172 </test> |
| 173 <test> | 173 <test expect_num_outputs="2"> |
| 174 <param name="input_file" ftype="vcf" value="check.vcf" /> | 174 <param name="input_file" ftype="vcf" value="check.vcf" /> |
| 175 <param name="convert_to" value="gen_sample" /> | 175 <param name="convert_to" value="gen_sample" /> |
| 176 <param name="tag" value="GT" /> | 176 <param name="tag" value="GT" /> |
| 177 <param name="convert_3N6" value="True" /> | 177 <param name="convert_3N6" value="True" /> |
| 178 <param name="vcf_ids" value="True" /> | 178 <param name="vcf_ids" value="True" /> |
| 180 <assert_contents> | 180 <assert_contents> |
| 181 <has_text text="1:3062915_GTTT_G id3D 3062915 GTTT G 0 1 0 0 1 0"/> | 181 <has_text text="1:3062915_GTTT_G id3D 3062915 GTTT G 0 1 0 0 1 0"/> |
| 182 </assert_contents> | 182 </assert_contents> |
| 183 </output> | 183 </output> |
| 184 </test> | 184 </test> |
| 185 <test> | 185 <test expect_num_outputs="2"> |
| 186 <param name="input_file" ftype="vcf" value="convert.vcf" /> | 186 <param name="input_file" ftype="vcf" value="convert.vcf" /> |
| 187 <param name="convert_to" value="hap_sample" /> | 187 <param name="convert_to" value="hap_sample" /> |
| 188 <output name="output_hap"> | 188 <output name="output_hap"> |
| 189 <assert_contents> | 189 <assert_contents> |
| 190 <has_text text="X X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/> | 190 <has_text text="X X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/> |
| 191 </assert_contents> | 191 </assert_contents> |
| 192 </output> | 192 </output> |
| 193 </test> | 193 </test> |
| 194 <test> | 194 <test expect_num_outputs="3"> |
| 195 <param name="input_file" ftype="vcf" value="convert.vcf" /> | 195 <param name="input_file" ftype="vcf" value="convert.vcf" /> |
| 196 <param name="convert_to" value="hap_legend_sample" /> | 196 <param name="convert_to" value="hap_legend_sample" /> |
| 197 <output name="output_hap"> | 197 <output name="output_hap"> |
| 198 <assert_contents> | 198 <assert_contents> |
| 199 <has_text text="1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/> | 199 <has_text text="1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/> |
| 210 <has_text text="NA00001 NA00001 NA00001 2"/> | 210 <has_text text="NA00001 NA00001 NA00001 2"/> |
| 211 </assert_contents> | 211 </assert_contents> |
| 212 </output> | 212 </output> |
| 213 </test> | 213 </test> |
| 214 <!-- Test keep-duplicates option --> | 214 <!-- Test keep-duplicates option --> |
| 215 <test> | 215 <test expect_num_outputs="3"> |
| 216 <param name="input_file" ftype="vcf" value="convert.vcf" /> | 216 <param name="input_file" ftype="vcf" value="convert.vcf" /> |
| 217 <param name="convert_to" value="hap_legend_sample" /> | 217 <param name="convert_to" value="hap_legend_sample" /> |
| 218 <param name="keep_duplicates" value="true"/> | 218 <param name="keep_duplicates" value="true"/> |
| 219 <output name="output_hap"> | 219 <output name="output_hap"> |
| 220 <assert_contents> | 220 <assert_contents> |
| 235 <assert_command> | 235 <assert_command> |
| 236 <has_text text="--keep-duplicates" /> | 236 <has_text text="--keep-duplicates" /> |
| 237 </assert_command> | 237 </assert_command> |
| 238 </test> | 238 </test> |
| 239 <!-- Test region overlap --> | 239 <!-- Test region overlap --> |
| 240 <test> | 240 <test expect_num_outputs="2"> |
| 241 <param name="input_file" ftype="vcf" value="convert.vcf" /> | 241 <param name="input_file" ftype="vcf" value="convert.vcf" /> |
| 242 <param name="convert_to" value="gen_sample" /> | 242 <param name="convert_to" value="gen_sample" /> |
| 243 <section name="sec_restrict"> | 243 <section name="sec_restrict"> |
| 244 <param name="regions_overlap" value="1"/> | 244 <param name="regions_overlap" value="1"/> |
| 245 </section> | 245 </section> |