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comparison macs21_wrapper.xml @ 3:4124781932db draft

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Updated to MACS 2.1.1 and use conda for dependency resolution.
author pjbriggs
date Tue, 20 Mar 2018 11:25:04 -0400
parents 00d73c812399
children 11cf21ee4242
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2:00d73c812399 3:4124781932db
1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-6"> 1 <tool id="macs2_1_peakcalling" name="MACS2.1.1" version="2.1.1.0">
2 <description>Model-based Analysis of ChIP-Seq: peak calling</description> 2 <description>Model-based Analysis of ChIP-Seq: peak calling</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="2.7">python</requirement>
5 <requirement type="package" version="1.9">numpy</requirement> 5 <requirement type="package" version="2.1.1">macs2</requirement>
6 <requirement type="package" version="2.1.0.20140616">macs2</requirement> 6 <requirement type="package" version="3.4">R</requirement>
7 <requirement type="package" version="3.1.2">R</requirement> 7 <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
8 <requirement type="package" version="2.0">ucsc_tools_for_macs21</requirement> 8 <requirement type="package" version="357">ucsc-bedclip</requirement>
9 <requirement type="package" version="357">ucsc-bedsort</requirement>
10 <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
9 </requirements> 11 </requirements>
10 <version_command>macs2 --version</version_command> 12 <version_command>macs2 --version</version_command>
11 <command interpreter="python"> 13 <command><![CDATA[
12 macs21_wrapper.py callpeak 14 python $__tool_directory__/macs21_wrapper.py callpeak
13 ## 15 ##
14 ## ChIP-seq input 16 ## ChIP-seq input
15 $input_chipseq_file1 17 $input_chipseq_file1
16 ## 18 ##
17 ## ChIP-seq control 19 ## ChIP-seq control
94 #if str($xls_to_interval) == 'True' 96 #if str($xls_to_interval) == 'True'
95 --output-xls-to-interval=$output_xls_to_interval_peaks_file 97 --output-xls-to-interval=$output_xls_to_interval_peaks_file
96 #else 98 #else
97 --output-peaks=$output_peaks_file 99 --output-peaks=$output_peaks_file
98 #end if 100 #end if
99 </command> 101 ]]></command>
100 <inputs> 102 <inputs>
101 <!--experiment name used as base for output file names --> 103 <!--experiment name used as base for output file names -->
102 <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"
103 label="Experiment Name"/> 105 label="Experiment Name"/>
104 <!--choose 'broad' or 'narrow' regions--> 106 <!--choose 'broad' or 'narrow' regions-->
105 <conditional name="broad_options"> 107 <conditional name="broad_options">
106 <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"
107 help="Broad regions are formed by linking nearby enriched regions"> 109 help="Broad regions are formed by linking nearby enriched regions">
275 </outputs> 277 </outputs>
276 <tests> 278 <tests>
277 <!-- Peak calling without bigwig output --> 279 <!-- Peak calling without bigwig output -->
278 <test> 280 <test>
279 <!-- Inputs --> 281 <!-- Inputs -->
280 <param name="experiment_name" value="test_MACS2.1.0" /> 282 <param name="experiment_name" value="test_MACS2.1.1" />
281 <param name="broad_regions" value="" /> 283 <param name="broad_regions" value="" />
282 <param name="format" value="BED" /> 284 <param name="format" value="BED" />
283 <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"
284 ftype="bed" /> 286 ftype="bed" />
285 <param name="input_control_file1" value="test_region_Input.bed" 287 <param name="input_control_file1" value="test_region_Input.bed"
301 <param name="advanced_options|keep_duplicates" value="" /> 303 <param name="advanced_options|keep_duplicates" value="" />
302 <param name="advanced_options|maximum_tags" value="1" /> 304 <param name="advanced_options|maximum_tags" value="1" />
303 <param name="nomodel_type_selector" value="nomodel" /> 305 <param name="nomodel_type_selector" value="nomodel" />
304 <param name="nomodel_type|extsize" value="243" /> 306 <param name="nomodel_type|extsize" value="243" />
305 <!-- Outputs --> 307 <!-- Outputs -->
306 <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"
307 compare="sim_size" delta="1500" /> 309 compare="sim_size" delta="1500" />
308 <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" />
309 <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" />
310 <output name="output_xls_to_interval_peaks_file" 312 <output name="output_xls_to_interval_peaks_file"
311 file="test_MACS2.1.0_peaks.xls.re_match" 313 file="test_MACS2.1.1_peaks.xls.re_match"
312 compare="re_match" lines_diff="1" /> 314 compare="re_match" lines_diff="1" />
313 <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" />
314 <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" />
315 </test> 317 </test>
316 <!-- Peak calling with bigwig output --> 318 <!-- Peak calling with bigwig output -->
317 <test> 319 <test>
318 <!-- Inputs --> 320 <!-- Inputs -->
319 <param name="experiment_name" value="test_MACS2.1.0" /> 321 <param name="experiment_name" value="test_MACS2.1.1" />
320 <param name="broad_regions" value="" /> 322 <param name="broad_regions" value="" />
321 <param name="format" value="BED" /> 323 <param name="format" value="BED" />
322 <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"
323 ftype="bed" /> 325 ftype="bed" />
324 <param name="input_control_file1" value="test_region_Input.bed" 326 <param name="input_control_file1" value="test_region_Input.bed"
340 <param name="advanced_options|keep_duplicates" value="" /> 342 <param name="advanced_options|keep_duplicates" value="" />
341 <param name="advanced_options|maximum_tags" value="1" /> 343 <param name="advanced_options|maximum_tags" value="1" />
342 <param name="nomodel_type_selector" value="nomodel" /> 344 <param name="nomodel_type_selector" value="nomodel" />
343 <param name="nomodel_type|extsize" value="243" /> 345 <param name="nomodel_type|extsize" value="243" />
344 <!-- Outputs --> 346 <!-- Outputs -->
345 <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"
346 compare="sim_size" delta="2500" /> 348 compare="sim_size" delta="2500" />
347 <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" />
348 <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" />
349 <output name="output_xls_to_interval_peaks_file" 351 <output name="output_xls_to_interval_peaks_file"
350 file="test_MACS2.1.0_peaks.xls.re_match" 352 file="test_MACS2.1.1_peaks.xls.re_match"
351 compare="re_match" lines_diff="1" /> 353 compare="re_match" lines_diff="1" />
352 <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" />
353 <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" />
354 <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"
355 compare="sim_size" /> 357 compare="sim_size" />
356 </test> 358 </test>
357 </tests> 359 </tests>
358 <help> 360 <help>
359 **What it does** 361 **What it does**
360 362
361 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
362 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,
363 or with control sample data to improve specificity. 365 or with control sample data to improve specificity.
364 366
365 View the MACS2 documentation at: 367 View the MACS2 documentation at:
366 https://github.com/taoliu/MACS/blob/master/README.rst 368 https://github.com/taoliu/MACS/blob/master/README.rst