Mercurial > repos > iuc > cnvkit_batch
comparison batch.xml @ 3:97d2b6742760 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5
| author | iuc |
|---|---|
| date | Fri, 13 Dec 2024 23:59:44 +0000 |
| parents | ec07e22c41f8 |
| children |
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| 2:ec07e22c41f8 | 3:97d2b6742760 |
|---|---|
| 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"> |
| 188 <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"> |
| 189 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> | 193 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> |
| 190 </output> | 194 </output> |
| 191 </test> | 195 </test> |
| 192 <test expect_num_outputs="13"> | 196 <test expect_num_outputs="13"> |
| 193 <conditional name="reference_source"> | 197 <conditional name="CNV_reference"> |
| 194 <param name="ref_selector" value="cached"/> | 198 <conditional name="reference_source"> |
| 195 <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" /> | |
| 196 </conditional> | 206 </conditional> |
| 197 <param name="CNV_reference_availabel" value="no" /> | 207 <section name="output_section"> |
| 198 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> | 208 <param name="scatter" value="1"/> |
| 199 <param name="normal" ftype="bam" value="normal.bam" /> | 209 <param name="diagram" value="1"/> |
| 200 <param name="targets" ftype="bed" value="capture.bed" /> | 210 </section> |
| 201 <param name="scatter" value="1"/> | |
| 202 <param name="diagram" value="1"/> | |
| 203 <output name="out_sample_bintest" file="tumor.bintest.cns" /> | 211 <output name="out_sample_bintest" file="tumor.bintest.cns" /> |
| 204 <output name="out_sample_antitargetcoverage"> | 212 <output name="out_sample_antitargetcoverage"> |
| 205 <assert_contents><has_text text="chromosome"/></assert_contents> | 213 <assert_contents><has_text text="chromosome"/></assert_contents> |
| 206 </output> | 214 </output> |
| 207 <output name="out_sample_call"> | 215 <output name="out_sample_call"> |
| 231 <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"> |
| 232 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> | 240 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> |
| 233 </output> | 241 </output> |
| 234 </test> | 242 </test> |
| 235 <test expect_num_outputs="10"> | 243 <test expect_num_outputs="10"> |
| 236 <param name="CNV_reference_availabel" value="yes" /> | 244 <conditional name="CNV_reference"> |
| 237 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> | 245 <param name="CNV_reference_availabel" value="yes" /> |
| 238 <param name="reference" ftype="tabular" value="reference.cnn" /> | 246 <param name="input_sample_file" ftype="bam" value="tumor.bam" /> |
| 239 <param name="scatter" value="1"/> | 247 <param name="reference" ftype="tabular" value="reference.cnn" /> |
| 240 <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> | |
| 241 <output name="out_sample_bintest" file="tumor.bintest.cns" /> | 253 <output name="out_sample_bintest" file="tumor.bintest.cns" /> |
| 242 <output name="out_sample_antitargetcoverage"> | 254 <output name="out_sample_antitargetcoverage"> |
| 243 <assert_contents><has_text text="chromosome"/></assert_contents> | 255 <assert_contents><has_text text="chromosome"/></assert_contents> |
| 244 </output> | 256 </output> |
| 245 <output name="out_sample_call"> | 257 <output name="out_sample_call"> |