Mercurial > repos > iuc > merqury

comparison merqury.xml @ 4:09c589057ee8 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/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4
author iuc
date Thu, 10 Aug 2023 22:57:52 +0000
parents f8113c25bc6b
children eb7b00ec347d
comparison
equal deleted inserted replaced
3:f8113c25bc6b 4:09c589057ee8
162 <option value="plots" selected="true">Plots</option> 162 <option value="plots" selected="true">Plots</option>
163 <option value="sizes">Size files</option> 163 <option value="sizes">Size files</option>
164 <option value="stats" selected="true">Stats file</option> 164 <option value="stats" selected="true">Stats file</option>
165 <option value="bed">BED: hap-mer tracks</option> 165 <option value="bed">BED: hap-mer tracks</option>
166 <option value="wig">WIG: hap-mer tracks</option> 166 <option value="wig">WIG: hap-mer tracks</option>
167 <option value="hist">Histogram files</option>
167 <option value="log">Log file</option> 168 <option value="log">Log file</option>
168 </param> 169 </param>
169 <param name="output_add_headers" type="boolean" value="false" label="Add column header on tabular outputs" /> 170 <param name="output_add_headers" type="boolean" value="false" label="Add column header on tabular outputs" />
170 </inputs> 171 </inputs>
171 <outputs> 172 <outputs>
194 <filter>"stats" in output_selector</filter> 195 <filter>"stats" in output_selector</filter>
195 </collection> 196 </collection>
196 <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file"> 197 <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file">
197 <filter>"log" in output_selector</filter> 198 <filter>"log" in output_selector</filter>
198 </data> 199 </data>
200 <collection name="hist_files" type="list" label="${tool.name} on ${on_string}: histograms">
201 <discover_datasets pattern="(?P&lt;name&gt;.+)\.hist" format="tabular" directory="output_files"/>
202 <filter>"hist" in output_selector</filter>
203 </collection>
199 </outputs> 204 </outputs>
200 <tests> 205 <tests>
201 <!--Test 01: trio mode--> 206 <!--Test 01: trio mode-->
202 <test expect_num_outputs="1"> 207 <test expect_num_outputs="1">
203 <conditional name="mode"> 208 <conditional name="mode">
215 <output_collection name="sizes_files" type="list" count="2"> 220 <output_collection name="sizes_files" type="list" count="2">
216 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/> 221 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
217 </output_collection> 222 </output_collection>
218 </test> 223 </test>
219 <!--Test 02: standard mode with tabular headers --> 224 <!--Test 02: standard mode with tabular headers -->
220 <test expect_num_outputs="6"> 225 <test expect_num_outputs="7">
221 <conditional name="mode"> 226 <conditional name="mode">
222 <param name="options" value="default"/> 227 <param name="options" value="default"/>
223 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/> 228 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
224 <conditional name="assembly_options"> 229 <conditional name="assembly_options">
225 <param name="number_assemblies" value="one"/> 230 <param name="number_assemblies" value="one"/>
226 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/> 231 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
227 </conditional> 232 </conditional>
228 </conditional> 233 </conditional>
229 <param name="label" value="output_02"/> 234 <param name="label" value="output_02"/>
230 <param name="output_selector" value="stats,plots,bed,sizes,qv,wig"/> 235 <param name="output_selector" value="stats,plots,bed,sizes,qv,wig,hist"/>
231 <output_collection name="png_files" type="list" count="6"> 236 <output_collection name="png_files" type="list" count="6">
232 <element name="output_02.assembly.spectra-cn.fl"> 237 <element name="output_02.assembly.spectra-cn.fl">
233 <assert_contents> 238 <assert_contents>
234 <has_size value="71874" delta="100"/> 239 <has_size value="71874" delta="100"/>
235 </assert_contents> 240 </assert_contents>
282 <assert_contents> 287 <assert_contents>
283 <has_size value="0"/> 288 <has_size value="0"/>
284 </assert_contents> 289 </assert_contents>
285 </element> 290 </element>
286 </output_collection> 291 </output_collection>
292 <output_collection name="hist_files" type="list" count="4">
293 <element name="output_02.spectra-asm" file="output_02.spectra-asm.hist" ftype="tabular"/>
294 <element name="output_02.dist_only" file="output_02.dist_only.hist" ftype="tabular"/>
295 <element name="output_02.assembly.spectra-cn" file="output_02.assembly.spectra-cn.hist" ftype="tabular"/>
296 <element name="output_02.assembly.only" file="output_02.assembly.only.hist" ftype="tabular"/>
297 </output_collection>
287 </test> 298 </test>
288 <!--Test 03: Standard mode two assemblies--> 299 <!--Test 03: Standard mode two assemblies-->
289 <test expect_num_outputs="2"> 300 <test expect_num_outputs="2">
290 <conditional name="mode"> 301 <conditional name="mode">
291 <param name="options" value="default"/> 302 <param name="options" value="default"/>