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comparison macs2_callpeak.xml @ 12:38769345062e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
author iuc
date Thu, 22 Mar 2018 09:43:37 -0400
parents cb785e26207c
children 01cded2297b7
comparison
equal deleted inserted replaced
11:cb785e26207c 12:38769345062e
1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3"> 1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3" profile="17.09">
2 <description>Call peaks from alignment results</description> 2 <description>Call peaks from alignment results</description>
3 <macros> 3 <macros>
4 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
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" label="${tool.name} on ${on_string} (Peaks in tabular format)"> 246 <data name="output_tabular" format="tabular" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
247 <filter> outputs and 'peaks_tabular' in outputs</filter> 247 <filter> outputs and 'peaks_tabular' in outputs</filter>
248 </data> 248 </data>
249 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)"> 249 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
250 <filter> 250 <filter>
251 (( 251 ((
252 advanced_options['broad_options']['broad_options_selector'] == "broad" 252 advanced_options['broad_options']['broad_options_selector'] == "broad"
253 )) 253 ))
254 </filter> 254 </filter>
255 </data> 255 </data>
256 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)"> 256 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
257 <filter> 257 <filter>
258 (( 258 ((
259 advanced_options['broad_options']['broad_options_selector'] == "broad" 259 advanced_options['broad_options']['broad_options_selector'] == "broad"
260 )) 260 ))
261 </filter> 261 </filter>
262 </data> 262 </data>
263 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)"> 263 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
264 <filter> 264 <filter>
265 (( 265 ((
266 advanced_options['broad_options']['broad_options_selector'] == "nobroad" 266 advanced_options['broad_options']['broad_options_selector'] == "nobroad"
267 )) 267 ))
268 </filter> 268 </filter>
269 </data> 269 </data>
270 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)"> 270 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
271 <filter>outputs and 'summits' in outputs</filter> 271 <filter>outputs and 'summits' in outputs</filter>
272 </data> 272 </data>
273 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)"> 273 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (plot)">
274 <filter> 274 <filter>
275 (( 275 ((
276 outputs and 'pdf' in outputs and 276 outputs and 'pdf' in outputs and
277 nomodel_type['nomodel_type_selector'] == "create_model" and 277 nomodel_type['nomodel_type_selector'] == "create_model" and
278 format != "BAMPE" 278 format != "BAMPE"
279 )) 279 ))
280 </filter> 280 </filter>
281 </data> 281 </data>
282 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)"> 282 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
283 <filter>outputs and 'bdg' in outputs</filter> 283 <filter>outputs and 'bdg' in outputs</filter>
284 </data> 284 </data>
285 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)"> 285 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
286 <filter>outputs and 'bdg' in outputs</filter> 286 <filter>outputs and 'bdg' in outputs</filter>
287 </data> 287 </data>
288 <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)"> 288 <data name="output_extra_files" format="html" default_identifier_source="input_treatment_file" label="${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">
347 347
348 **What it does** 348 **What it does**
349 349
350 **callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments. It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. 350 **callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments. It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.
351 351
352 .. _MACS2: https://github.com/taoliu/MACS
353
354 ----- 352 -----
355 353
356 **Inputs** 354 **Inputs**
357 355
358 MACS can be used for ChIP-Seq data (Treatment) alone, or with a Control sample with the increase of specificity (recommended). 356 MACS can be used for ChIP-Seq data (Treatment) alone, or with a Control sample with the increase of specificity (recommended).
369 367
370 hs: 2.7e9 368 hs: 2.7e9
371 mm: 1.87e9 369 mm: 1.87e9
372 ce: 9e7 370 ce: 9e7
373 dm: 1.2e8 371 dm: 1.2e8
372
373 Or see the **deepTools** website for updated information on calculating `Effective Genome Size`_.
374 374
375 ----- 375 -----
376 376
377 **Outputs** 377 **Outputs**
378 378
585 585
586 .. class:: warningmark 586 .. class:: warningmark
587 587
588 If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options. For more information, see the MACS2_ website. 588 If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options. For more information, see the MACS2_ website.
589 589
590 .. _MACS2: https://github.com/taoliu/MACS
591 .. _`Effective Genome Size`: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
590 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html 592 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html
591 593
592 @citation@ 594 @citation@
593 ]]></help> 595 ]]></help>
594 <expand macro="citations" /> 596 <expand macro="citations" />