Mercurial > repos > iuc > macs2

comparison macs2_callpeak.xml @ 13:01cded2297b7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 1cf6ca65ca6bbf3553d830f13be1760dcd667cae
author iuc
date Fri, 04 May 2018 21:39:56 -0400
parents 38769345062e
children c16dbe4e2db2
comparison
equal deleted inserted replaced
12:38769345062e 13:01cded2297b7
241 <expand macro="keep_duplicates" /> 241 <expand macro="keep_duplicates" />
242 </section> 242 </section>
243 </inputs> 243 </inputs>
244 <outputs> 244 <outputs>
245 <!--callpeaks output--> 245 <!--callpeaks output-->
246 <data name="output_tabular" format="tabular" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)"> 246 <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
247 <filter> outputs and 'peaks_tabular' in outputs</filter> 247 <filter> outputs and 'peaks_tabular' in outputs</filter>
248 </data> 248 </data>
249 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)"> 249 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
250 <filter> 250 <filter>
251 (( 251 ((
252 advanced_options['broad_options']['broad_options_selector'] == "broad" 252 advanced_options['broad_options']['broad_options_selector'] == "broad"
253 )) 253 ))
254 </filter> 254 </filter>
255 </data> 255 </data>
256 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)"> 256 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
257 <filter> 257 <filter>
258 (( 258 ((
259 advanced_options['broad_options']['broad_options_selector'] == "broad" 259 advanced_options['broad_options']['broad_options_selector'] == "broad"
260 )) 260 ))
261 </filter> 261 </filter>
262 </data> 262 </data>
263 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)"> 263 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
264 <filter> 264 <filter>
265 (( 265 ((
266 advanced_options['broad_options']['broad_options_selector'] == "nobroad" 266 advanced_options['broad_options']['broad_options_selector'] == "nobroad"
267 )) 267 ))
268 </filter> 268 </filter>
269 </data> 269 </data>
270 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)"> 270 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
271 <filter>outputs and 'summits' in outputs</filter> 271 <filter>outputs and 'summits' in outputs</filter>
272 </data> 272 </data>
273 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (plot)"> 273 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (plot)">
274 <filter> 274 <filter>
275 (( 275 ((
276 outputs and 'pdf' in outputs and 276 outputs and 'pdf' in outputs and
277 nomodel_type['nomodel_type_selector'] == "create_model" and 277 nomodel_type['nomodel_type_selector'] == "create_model" and
278 format != "BAMPE" 278 format != "BAMPE"
279 )) 279 ))
280 </filter> 280 </filter>
281 </data> 281 </data>
282 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)"> 282 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
283 <filter>outputs and 'bdg' in outputs</filter> 283 <filter>outputs and 'bdg' in outputs</filter>
284 </data> 284 </data>
285 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)"> 285 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
286 <filter>outputs and 'bdg' in outputs</filter> 286 <filter>outputs and 'bdg' in outputs</filter>
287 </data> 287 </data>
288 <data name="output_extra_files" format="html" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (html report)"> 288 <data name="output_extra_files" format="html" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (html report)">
289 <filter>outputs and 'html' in outputs</filter> 289 <filter>outputs and 'html' in outputs</filter>
290 </data> 290 </data>
291 </outputs> 291 </outputs>
292 <tests> 292 <tests>
293 <test expect_num_outputs="5"> 293 <test expect_num_outputs="5">