Mercurial > repos > iuc > cnvkit_batch

comparison batch.xml @ 2:0d371963d4b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5
author iuc
date Fri, 13 Dec 2024 23:53:57 +0000
parents 0c60bd0f4de6
children 004311c34527
comparison
equal deleted inserted replaced
1:0c60bd0f4de6 2:0d371963d4b9
145 <filter>output_section['scatter']</filter> 145 <filter>output_section['scatter']</filter>
146 </data> 146 </data>
147 </outputs> 147 </outputs>
148 <tests> 148 <tests>
149 <test expect_num_outputs="13"> 149 <test expect_num_outputs="13">
150 <conditional name="reference_source"> 150 <conditional name="CNV_reference">
151 <param name="ref_selector" value="history"/> 151 <conditional name="reference_source">
152 <param name="fasta" ftype="fasta" value="genome.fasta" /> 152 <param name="ref_selector" value="history"/>
153 <param name="fasta" ftype="fasta" value="genome.fasta" />
154 </conditional>
155 <param name="CNV_reference_availabel" value="no" />
156 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
157 <param name="normal" ftype="bam" value="normal.bam" />
158 <param name="targets" ftype="bed" value="capture.bed" />
153 </conditional> 159 </conditional>
154 <param name="CNV_reference_availabel" value="no" /> 160 <section name="output_section">
155 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> 161 <param name="scatter" value="1"/>
156 <param name="normal" ftype="bam" value="normal.bam" /> 162 <param name="diagram" value="1"/>
157 <param name="targets" ftype="bed" value="capture.bed" /> 163 </section>
158 <param name="scatter" value="1"/>
159 <param name="diagram" value="1"/>
160 <output name="out_sample_bintest" file="tumor.bintest.cns" /> 164 <output name="out_sample_bintest" file="tumor.bintest.cns" />
161 <output name="out_sample_antitargetcoverage"> 165 <output name="out_sample_antitargetcoverage">
162 <assert_contents><has_text text="chromosome"/></assert_contents> 166 <assert_contents><has_text text="chromosome"/></assert_contents>
163 </output> 167 </output>
164 <output name="out_sample_call"> 168 <output name="out_sample_call">
174 <assert_contents><has_text text="chromosome"/></assert_contents> 178 <assert_contents><has_text text="chromosome"/></assert_contents>
175 </output> 179 </output>
176 <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 180 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
177 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" /> 181 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
178 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" /> 182 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
179 <output name="out_reference_cnn" file="reference.cnn" /> 183 <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
184 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
185 </output>
180 <output name="out_capture_target"> 186 <output name="out_capture_target">
181 <assert_contents><has_text_matching expression="chrM"/></assert_contents> 187 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
182 </output> 188 </output>
183 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size"> 189 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
184 <assert_contents><has_size value="13000" delta="3000" /></assert_contents> 190 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
186 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size"> 192 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
187 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> 193 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
188 </output> 194 </output>
189 </test> 195 </test>
190 <test expect_num_outputs="13"> 196 <test expect_num_outputs="13">
191 <conditional name="reference_source"> 197 <conditional name="CNV_reference">
192 <param name="ref_selector" value="cached"/> 198 <conditional name="reference_source">
193 <param name="fasta" value="test_buildid"/> 199 <param name="ref_selector" value="cached"/>
200 <param name="fasta" value="test_buildid"/>
201 </conditional>
202 <param name="CNV_reference_availabel" value="no" />
203 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
204 <param name="normal" ftype="bam" value="normal.bam" />
205 <param name="targets" ftype="bed" value="capture.bed" />
194 </conditional> 206 </conditional>
195 <param name="CNV_reference_availabel" value="no" /> 207 <section name="output_section">
196 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> 208 <param name="scatter" value="1"/>
197 <param name="normal" ftype="bam" value="normal.bam" /> 209 <param name="diagram" value="1"/>
198 <param name="targets" ftype="bed" value="capture.bed" /> 210 </section>
199 <param name="scatter" value="1"/>
200 <param name="diagram" value="1"/>
201 <output name="out_sample_bintest" file="tumor.bintest.cns" /> 211 <output name="out_sample_bintest" file="tumor.bintest.cns" />
202 <output name="out_sample_antitargetcoverage"> 212 <output name="out_sample_antitargetcoverage">
203 <assert_contents><has_text text="chromosome"/></assert_contents> 213 <assert_contents><has_text text="chromosome"/></assert_contents>
204 </output> 214 </output>
205 <output name="out_sample_call"> 215 <output name="out_sample_call">
215 <assert_contents><has_text text="chromosome"/></assert_contents> 225 <assert_contents><has_text text="chromosome"/></assert_contents>
216 </output> 226 </output>
217 <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 227 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
218 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" /> 228 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
219 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" /> 229 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
220 <output name="out_reference_cnn" file="reference.cnn" /> 230 <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
231 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
232 </output>
221 <output name="out_capture_target"> 233 <output name="out_capture_target">
222 <assert_contents><has_text_matching expression="chrM"/></assert_contents> 234 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
223 </output> 235 </output>
224 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size"> 236 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
225 <assert_contents><has_size value="13000" delta="3000" /></assert_contents> 237 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
227 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size"> 239 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
228 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> 240 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
229 </output> 241 </output>
230 </test> 242 </test>
231 <test expect_num_outputs="10"> 243 <test expect_num_outputs="10">
232 <param name="CNV_reference_availabel" value="yes" /> 244 <conditional name="CNV_reference">
233 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> 245 <param name="CNV_reference_availabel" value="yes" />
234 <param name="reference" ftype="tabular" value="reference.cnn" /> 246 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
235 <param name="scatter" value="1"/> 247 <param name="reference" ftype="tabular" value="reference.cnn" />
236 <param name="diagram" value="1"/> 248 </conditional>
249 <section name="output_section">
250 <param name="scatter" value="1"/>
251 <param name="diagram" value="1"/>
252 </section>
237 <output name="out_sample_bintest" file="tumor.bintest.cns" /> 253 <output name="out_sample_bintest" file="tumor.bintest.cns" />
238 <output name="out_sample_antitargetcoverage"> 254 <output name="out_sample_antitargetcoverage">
239 <assert_contents><has_text text="chromosome"/></assert_contents> 255 <assert_contents><has_text text="chromosome"/></assert_contents>
240 </output> 256 </output>
241 <output name="out_sample_call"> 257 <output name="out_sample_call">