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comparison macs21_wrapper.xml @ 20:4d41e5cda4e6 draft

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author pjbriggs
date Mon, 19 Mar 2018 05:50:30 -0400
parents 51303ba3fbbe
children dfb939015935
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19:51303ba3fbbe 20:4d41e5cda4e6
99 --output-peaks=$output_peaks_file 99 --output-peaks=$output_peaks_file
100 #end if 100 #end if
101 ]]></command> 101 ]]></command>
102 <inputs> 102 <inputs>
103 <!--experiment name used as base for output file names --> 103 <!--experiment name used as base for output file names -->
104 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50" 104 <param name="experiment_name" type="text" value="MACS2.1 in Galaxy" size="50"
105 label="Experiment Name"/> 105 label="Experiment Name"/>
106 <!--choose 'broad' or 'narrow' regions--> 106 <!--choose 'broad' or 'narrow' regions-->
107 <conditional name="broad_options"> 107 <conditional name="broad_options">
108 <param name="broad_regions" type="select" label="Type of region to call" 108 <param name="broad_regions" type="select" label="Type of region to call"
109 help="Broad regions are formed by linking nearby enriched regions"> 109 help="Broad regions are formed by linking nearby enriched regions">
277 </outputs> 277 </outputs>
278 <tests> 278 <tests>
279 <!-- Peak calling without bigwig output --> 279 <!-- Peak calling without bigwig output -->
280 <test> 280 <test>
281 <!-- Inputs --> 281 <!-- Inputs -->
282 <param name="experiment_name" value="test_MACS2.1.0" /> 282 <param name="experiment_name" value="test_MACS2.1.1" />
283 <param name="broad_regions" value="" /> 283 <param name="broad_regions" value="" />
284 <param name="format" value="BED" /> 284 <param name="format" value="BED" />
285 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" 285 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
286 ftype="bed" /> 286 ftype="bed" />
287 <param name="input_control_file1" value="test_region_Input.bed" 287 <param name="input_control_file1" value="test_region_Input.bed"
303 <param name="advanced_options|keep_duplicates" value="" /> 303 <param name="advanced_options|keep_duplicates" value="" />
304 <param name="advanced_options|maximum_tags" value="1" /> 304 <param name="advanced_options|maximum_tags" value="1" />
305 <param name="nomodel_type_selector" value="nomodel" /> 305 <param name="nomodel_type_selector" value="nomodel" />
306 <param name="nomodel_type|extsize" value="243" /> 306 <param name="nomodel_type|extsize" value="243" />
307 <!-- Outputs --> 307 <!-- Outputs -->
308 <output name="output_extra_files" file="test_MACS2.1.0_html_report.zip" 308 <output name="output_extra_files" file="test_MACS2.1.1_html_report.zip"
309 compare="sim_size" delta="1500" /> 309 compare="sim_size" delta="1500" />
310 <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" /> 310 <output name="output_summits_bed_file" file="test_MACS2.1.1_summits.bed" />
311 <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" /> 311 <output name="output_narrowpeaks_file" file="test_MACS2.1.1_peaks_narrowPeak.interval" />
312 <output name="output_xls_to_interval_peaks_file" 312 <output name="output_xls_to_interval_peaks_file"
313 file="test_MACS2.1.0_peaks.xls.re_match" 313 file="test_MACS2.1.1_peaks.xls.re_match"
314 compare="re_match" lines_diff="1" /> 314 compare="re_match" lines_diff="1" />
315 <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" /> 315 <output name="output_treat_pileup_file" file="test_MACS2.1.1_treat_pileup.bdg" />
316 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" /> 316 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.1_control_lambda.bdg" />
317 </test> 317 </test>
318 <!-- Peak calling with bigwig output --> 318 <!-- Peak calling with bigwig output -->
319 <test> 319 <test>
320 <!-- Inputs --> 320 <!-- Inputs -->
321 <param name="experiment_name" value="test_MACS2.1.0" /> 321 <param name="experiment_name" value="test_MACS2.1.1" />
322 <param name="broad_regions" value="" /> 322 <param name="broad_regions" value="" />
323 <param name="format" value="BED" /> 323 <param name="format" value="BED" />
324 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" 324 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
325 ftype="bed" /> 325 ftype="bed" />
326 <param name="input_control_file1" value="test_region_Input.bed" 326 <param name="input_control_file1" value="test_region_Input.bed"
342 <param name="advanced_options|keep_duplicates" value="" /> 342 <param name="advanced_options|keep_duplicates" value="" />
343 <param name="advanced_options|maximum_tags" value="1" /> 343 <param name="advanced_options|maximum_tags" value="1" />
344 <param name="nomodel_type_selector" value="nomodel" /> 344 <param name="nomodel_type_selector" value="nomodel" />
345 <param name="nomodel_type|extsize" value="243" /> 345 <param name="nomodel_type|extsize" value="243" />
346 <!-- Outputs --> 346 <!-- Outputs -->
347 <output name="output_extra_files" file="test_MACS2.1.0_bw_html_report.zip" 347 <output name="output_extra_files" file="test_MACS2.1.1_bw_html_report.zip"
348 compare="sim_size" delta="2500" /> 348 compare="sim_size" delta="2500" />
349 <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" /> 349 <output name="output_summits_bed_file" file="test_MACS2.1.1_summits.bed" />
350 <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" /> 350 <output name="output_narrowpeaks_file" file="test_MACS2.1.1_peaks_narrowPeak.interval" />
351 <output name="output_xls_to_interval_peaks_file" 351 <output name="output_xls_to_interval_peaks_file"
352 file="test_MACS2.1.0_peaks.xls.re_match" 352 file="test_MACS2.1.1_peaks.xls.re_match"
353 compare="re_match" lines_diff="1" /> 353 compare="re_match" lines_diff="1" />
354 <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" /> 354 <output name="output_treat_pileup_file" file="test_MACS2.1.1_treat_pileup.bdg" />
355 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" /> 355 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.1_control_lambda.bdg" />
356 <output name="output_bigwig_file" file="test_MACS2.1.0_treat_pileup.bw" 356 <output name="output_bigwig_file" file="test_MACS2.1.1_treat_pileup.bw"
357 compare="sim_size" /> 357 compare="sim_size" />
358 </test> 358 </test>
359 </tests> 359 </tests>
360 <help> 360 <help>
361 **What it does** 361 **What it does**
362 362
363 MACS (Model-based Analysis of ChIP-seq) 2.1.0 provides algorithms for identifying 363 MACS (Model-based Analysis of ChIP-seq) 2.1.1 provides algorithms for identifying
364 transcript factor binding sites. The program can be used either for ChIP-Seq data alone, 364 transcript factor binding sites. The program can be used either for ChIP-Seq data alone,
365 or with control sample data to improve specificity. 365 or with control sample data to improve specificity.
366 366
367 View the MACS2 documentation at: 367 View the MACS2 documentation at:
368 https://github.com/taoliu/MACS/blob/master/README.rst 368 https://github.com/taoliu/MACS/blob/master/README.rst