Mercurial > repos > iuc > bcftools_stats

comparison bcftools_stats.xml @ 22:afeffe9e655d 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 16:43:04 +0000
parents b6bb8672fa3e
children 913c052dfc71
comparison
equal deleted inserted replaced
21:b6bb8672fa3e 22:afeffe9e655d
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">