Mercurial > repos > iuc > bcftools_convert_from_vcf

comparison bcftools_convert_from_vcf.xml @ 20:d58d2e8c7a57 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 012656fd329f
comparison
equal deleted inserted replaced
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>