Mercurial > repos > iuc > bcftools_stats
comparison bcftools_stats.xml @ 20:bf8325a07ce7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
author | iuc |
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date | Tue, 16 Jul 2024 17:04:38 +0000 |
parents | a2f8dc22d7c0 |
children | 591cc8518033 |
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19:a2f8dc22d7c0 | 20:bf8325a07ce7 |
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155 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title"> | 155 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title"> |
156 <validator type="regex" message="">^\w.*\w$</validator> | 156 <validator type="regex" message="">^\w.*\w$</validator> |
157 </param> | 157 </param> |
158 </inputs> | 158 </inputs> |
159 <outputs> | 159 <outputs> |
160 <data name="output_file" format="txt"/> | 160 <data name="output_file" format="txt" label="${tool.name} on ${on_string}: txt" /> |
161 <data name="output_pdf" format="pdf" from_work_dir="plot_tmp/summary.pdf"> | 161 <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF" from_work_dir="plot_tmp/summary.pdf"> |
162 <filter>plot_title</filter> | 162 <filter>plot_title</filter> |
163 </data> | 163 </data> |
164 </outputs> | 164 </outputs> |
165 <tests> | 165 <tests> |
166 <test> | 166 <test expect_num_outputs="1"> |
167 <param name="input_file" ftype="vcf" value="stats.b.vcf" /> | 167 <param name="input_file" ftype="vcf" value="stats.b.vcf" /> |
168 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> | 168 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> |
169 <output name="output_file"> | 169 <output name="output_file"> |
170 <assert_contents> | 170 <assert_contents> |
171 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> | 171 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> |
172 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/> | 172 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/> |
173 </assert_contents> | 173 </assert_contents> |
174 </output> | 174 </output> |
175 </test> | 175 </test> |
176 <test> | 176 <test expect_num_outputs="1"> |
177 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> | 177 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> |
178 <section name="sec_default"> | 178 <section name="sec_default"> |
179 <expand macro="test_using_reference" select_from="cached" ref="mpileup" /> | 179 <expand macro="test_using_reference" select_from="cached" ref="mpileup" /> |
180 </section> | 180 </section> |
181 <output name="output_file"> | 181 <output name="output_file"> |
184 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/> | 184 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/> |
185 <has_text_matching expression="ST\t0\tA>C\t16"/> | 185 <has_text_matching expression="ST\t0\tA>C\t16"/> |
186 </assert_contents> | 186 </assert_contents> |
187 </output> | 187 </output> |
188 </test> | 188 </test> |
189 <test> | 189 <test expect_num_outputs="2"> |
190 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> | 190 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> |
191 <param name="plot_title" value="Plot for mpileup.vcf" /> | 191 <param name="plot_title" value="Plot for mpileup.vcf" /> |
192 <output name="output_file"> | 192 <output name="output_file"> |
193 <assert_contents> | 193 <assert_contents> |
194 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> | 194 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> |
197 </assert_contents> | 197 </assert_contents> |
198 </output> | 198 </output> |
199 <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" /> | 199 <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" /> |
200 </test> | 200 </test> |
201 <!-- Test region overlap option--> | 201 <!-- Test region overlap option--> |
202 <test> | 202 <test expect_num_outputs="1"> |
203 <param name="input_file" ftype="vcf" value="stats.b.vcf" /> | 203 <param name="input_file" ftype="vcf" value="stats.b.vcf" /> |
204 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> | 204 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> |
205 <section name="sec_restrict"> | 205 <section name="sec_restrict"> |
206 <param name="regions_overlap" value="1"/> | 206 <param name="regions_overlap" value="1"/> |
207 </section> | 207 </section> |
214 <assert_command> | 214 <assert_command> |
215 <has_text text="--regions-overlap" /> | 215 <has_text text="--regions-overlap" /> |
216 </assert_command> | 216 </assert_command> |
217 </test> | 217 </test> |
218 <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605 | 218 <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605 |
219 <test> | 219 <test expect_num_outputs="1"> |
220 <param name="input_file" value="mpileup.vcf.gz" /> | 220 <param name="input_file" value="mpileup.vcf.gz" /> |
221 <output name="output_file"> | 221 <output name="output_file"> |
222 <assert_contents> | 222 <assert_contents> |
223 <has_text_matching expression="bcftools stats input0.vcf.gz"/> | 223 <has_text_matching expression="bcftools stats input0.vcf.gz"/> |
224 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> | 224 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> |
226 </assert_contents> | 226 </assert_contents> |
227 </output> | 227 </output> |
228 </test> | 228 </test> |
229 --> | 229 --> |
230 <!-- Test modification in samples option --> | 230 <!-- Test modification in samples option --> |
231 <test> | 231 <test expect_num_outputs="1"> |
232 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> | 232 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> |
233 <section name="sec_restrict"> | 233 <section name="sec_restrict"> |
234 <param name="samples" value="-" /> | 234 <param name="samples" value="-" /> |
235 </section> | 235 </section> |
236 <output name="output_file"> | 236 <output name="output_file"> |