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comparison macs21_wrapper.xml @ 9:7aecd0908b3c draft

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Uploaded version 2.1.0-4.
author pjbriggs
date Mon, 15 Jun 2015 06:06:48 -0400
parents 78c15c0a96ae
children f346287fe52c
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8:78c15c0a96ae 9:7aecd0908b3c
1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-2"> 1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-4">
2 <description>Model-based Analysis of ChIP-Seq: peak calling</description>
2 <requirements> 3 <requirements>
3 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="2.7">python</requirement>
4 <requirement type="package" version="1.9">numpy</requirement> 5 <requirement type="package" version="1.9">numpy</requirement>
5 <requirement type="package" version="2.1.0.20140616">macs2</requirement> 6 <requirement type="package" version="2.1.0.20140616">macs2</requirement>
6 <requirement type="package" version="3.1.2">R</requirement> 7 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="package" version="1.0">ucsc_tools_for_macs21</requirement> 8 <requirement type="package" version="1.0">ucsc_tools_for_macs21</requirement>
8 </requirements> 9 </requirements>
9 <description>Model-based Analysis of ChIP-Seq</description> 10 <version_command>macs2 --version</version_command>
10 <command interpreter="python"> 11 <command interpreter="python">
11 macs21_wrapper.py 12 macs21_wrapper.py callpeak
12 ##
13 ## Major command
14 $major_command.major_command_selector
15 ## 13 ##
16 ## ChIP-seq input 14 ## ChIP-seq input
17 $major_command.input_chipseq_file1 15 $input_chipseq_file1
18 ## 16 ##
19 ## ChIP-seq control 17 ## ChIP-seq control
20 #if str($major_command.input_control_file1) != 'None' 18 #if str($input_control_file1) != 'None'
21 -c $major_command.input_control_file1 19 -c $input_control_file1
22 #end if 20 #end if
23 ## 21 ##
24 ## Call peaks 22 --format=$input_chipseq_file1.extension
25 #if str($major_command.major_command_selector) == 'callpeak' 23 --name="$experiment_name"
26 --format=$major_command.input_chipseq_file1.extension 24 --bw=$bw
27 --name="$experiment_name" 25 ##
28 --bw=$major_command.bw 26 ## Genome size
29 ## 27 #if str($genome_size.gsize) == ''
30 ## Genome size 28 --gsize=$genome_size.user_defined_gsize
31 #if str($major_command.genome_size.gsize) == '' 29 #else:
32 --gsize=$major_command.genome_size.user_defined_gsize 30 --gsize=$genome_size.gsize
33 #else: 31 #end if
34 --gsize=$major_command.genome_size.gsize 32 ##
33 ## Broad peaks
34 #if str($broad_options.broad_regions) == 'broad'
35 --broad --broad-cutoff=$broad_options.broad_cutoff
36 #end if
37 ##
38 ## (no)model options
39 #if str($nomodel_type.nomodel_type_selector) == 'nomodel'
40 --nomodel --extsize=$nomodel_type.extsize
41 #end if
42 ##
43 ## pq value select options
44 #if str($pq_options.pq_options_selector) == 'qvalue'
45 --qvalue=$pq_options.qvalue
46 #else
47 --pvalue=$pq_options.pvalue
48 #end if
49 ##
50 ## Bedgraph options
51 #if $bdg_options.bdg
52 -B $bdg_options.spmr
53 #end if
54 ##
55 ## Advanced options
56 #if $advanced_options.advanced_options_selector
57 --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi
58 $advanced_options.nolambda
59 $advanced_options.call_summits
60 #if str($advanced_options.keep_duplicates.keep_dup) == ''
61 --keep-dup $advanced_options.keep_duplicates.maximum_tags
62 #else
63 --keep-dup $advanced_options.keep_duplicates.keep_dup
35 #end if 64 #end if
36 ## 65 #else
37 ## Broad peaks 66 ## Defaults if advanced options not set
38 #if str($major_command.broad_options.broad_regions) == 'broad' 67 --mfold 10 30 --keep-dup 1
39 --broad --broad-cutoff=$major_command.broad_options.broad_cutoff 68 #end if
69 ##
70 ## Output files
71 --output-summits=$output_summits_bed_file
72 --output-extra-files=$output_extra_files
73 --output-extra-files-path=$output_extra_files.files_path
74 ##
75 ## Narrow/broad peak outputs
76 #if str($broad_options.broad_regions) == 'broad'
77 --output-broadpeaks=$output_broadpeaks_file
78 --output-gappedpeaks=$output_gappedpeaks_file
79 #else
80 --output-narrowpeaks=$output_narrowpeaks_file
81 #end if
82 ##
83 ## Bedgraph outputs
84 #if $bdg_options.bdg
85 --output-pileup=$output_treat_pileup_file
86 --output-lambda-bedgraph=$output_lambda_bedgraph_file
87 #if $bdg_options.make_bigwig
88 --output-bigwig=$output_bigwig_file
89 --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${input_chipseq_file1.dbkey}.len
40 #end if 90 #end if
41 ## 91 #end if
42 ## (no)model options 92 ##
43 #if str($major_command.nomodel_type.nomodel_type_selector) == 'nomodel' 93 ## XLS/interval output
44 --nomodel --extsize=$major_command.nomodel_type.extsize 94 #if str($xls_to_interval) == 'True'
45 #end if 95 --output-xls-to-interval=$output_xls_to_interval_peaks_file
46 ## 96 #else
47 ## pq value select options 97 --output-peaks=$output_peaks_file
48 #if str($major_command.pq_options.pq_options_selector) == 'qvalue'
49 --qvalue=$major_command.pq_options.qvalue
50 #else
51 --pvalue=$major_command.pq_options.pvalue
52 #end if
53 ##
54 ## Bedgraph options
55 #if $major_command.bdg_options.bdg == True
56 -B $major_command.bdg_options.spmr
57 #end if
58 ##
59 ## Advanced options
60 #if str($major_command.advanced_options.advanced_options_selector) == 'on'
61 --mfold $major_command.advanced_options.mfoldlo $major_command.advanced_options.mfoldhi
62 $major_command.advanced_options.nolambda
63 $major_command.advanced_options.call_summits
64 #if str($major_command.advanced_options.keep_duplicates.keep_dup) == ''
65 --keep-dup $major_command.advanced_options.keep_duplicates.maximum_tags
66 #else
67 --keep-dup $major_command.advanced_options.keep_duplicates.keep_dup
68 #end if
69 #else
70 ## Defaults if advanced options not set
71 --mfold 10 30 --keep-dup 1
72 #end if
73 ##
74 ## Output files
75 --output-summits=$output_summits_bed_file
76 --output-extra-files=$output_extra_files
77 --output-extra-files-path=$output_extra_files.files_path
78 ##
79 ## Narrow/broad peak outputs
80 #if str($major_command.broad_options.broad_regions) == 'broad'
81 --output-broadpeaks=$output_broadpeaks_file
82 --output-gappedpeaks=$output_gappedpeaks_file
83 #else
84 --output-narrowpeaks=$output_narrowpeaks_file
85 #end if
86 ##
87 ## Bedgraph outputs
88 #if str($major_command.bdg_options.bdg) == 'True'
89 --output-pileup=$output_treat_pileup_file
90 --output-lambda-bedgraph=$output_lambda_bedgraph_file
91 #if str($major_command.bdg_options.make_bigwig) == 'True'
92 --output-bigwig=$output_bigwig_file
93 --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${major_command.input_chipseq_file1.dbkey}.len
94 #end if
95 #end if
96 ##
97 ## XLS/interval output
98 #if str($major_command.xls_to_interval) == 'True'
99 --output-xls-to-interval=$output_xls_to_interval_peaks_file
100 #else
101 --output-peaks=$output_peaks_file
102 #end if
103 #end if
104 ##
105 ## Compare .bdg files
106 #if str($major_command.major_command_selector) == 'bdgcmp'
107 -m $major_command.bdgcmp_options.bdgcmp_options_selector
108 -p $major_command.pseudocount
109 --output-bdgcmp $output_bdgcmp_file
110 #end if 98 #end if
111 </command> 99 </command>
112 <inputs> 100 <inputs>
113 <!--experiment name used as base for output file names --> 101 <!--experiment name used as base for output file names -->
114 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50" 102 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50"
115 label="Experiment Name"/> 103 label="Experiment Name"/>
116 <!--select a major MACS2 command--> 104 <!--choose 'broad' or 'narrow' regions-->
117 <conditional name="major_command"> 105 <conditional name="broad_options">
118 <param name="major_command_selector" type="select" label="Select action to be performed"> 106 <param name="broad_regions" type="select" label="Type of region to call"
119 <option value="callpeak">Peak Calling</option> 107 help="Broad regions are formed by linking nearby enriched regions">
120 <option value="bdgcmp">Compare .bdg Files</option> 108 <option value="" selected="true">Narrow regions</option>
109 <option value="broad">Broad regions</option>
121 </param> 110 </param>
122 <!--callpeak option of macs2--> 111 <when value="broad">
123 <when value="callpeak"> 112 <param name="broad_cutoff" type="float"
124 <!--choose 'broad' or 'narrow' regions--> 113 label="Cutoff for broad regions"
125 <conditional name="broad_options"> 114 value="0.1" help="default: 0.1 (--broad-cutoff)"/>
126 <param name="broad_regions" type="select" label="Type of region to call" 115 </when>
127 help="Broad regions are formed by linking nearby enriched regions"> 116 </conditional>
128 <option value="" selected="true">Narrow regions</option> 117 <param name="input_chipseq_file1" type="data" format="bed,sam,bam"
129 <option value="broad">Broad regions</option> 118 label="ChIP-seq read file" />
119 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True"
120 label="ChIP-seq control read file" />
121 <conditional name="genome_size">
122 <param name="gsize" type="select" label="Effective genome size"
123 help="Either pre-defined (for common organisms), or user-defined (--gsize)">
124 <option value="hs" selected="true">Human (2.7e9)</option>
125 <option value="mm">Mouse (1.87e9)</option>
126 <option value="ce">C. elegans (9e7)</option>
127 <option value="dm">Fruitfly (1.2e8)</option>
128 <option value="">User-defined</option>
129 </param>
130 <when value="">
131 <!-- User-defined effective genome size -->
132 <param name="user_defined_gsize" type="float" value=""
133 label="Enter effective genome size (number of bases)"
134 help="e.g. '1.0e+9' or '1000000000'" />
135 </when>
136 </conditional>
137 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/>
138 <param name="xls_to_interval" label="Include XLS file from MACS"
139 type="boolean" truevalue="True" falsevalue="False" checked="True"
140 help="MACS2 XLS file will be output to the history in 'interval' format (suitable for subsequent analysis in Galaxy). Note that start positions are 1-based."/>
141
142 <conditional name="bdg_options">
143 <param name="bdg"
144 label="Save treatment and control lambda pileups in bedGraph"
145 type="boolean" truevalue="-B" falsevalue="" checked="False" />
146 <when value="-B">
147 <param name="spmr"
148 type="boolean" truevalue="--SPMR" falsevalue="" checked="False"
149 label="Save signal per million reads for fragment pileup profiles"
150 help="(--SPMR)" />
151 <param name="make_bigwig" type="boolean" checked="True"
152 truevalue="True" falsevalue=""
153 label="Also generate bigWig file from bedGraph"
154 help="bigWig file can used in subsequent analyses e.g. CEAS" />
155 </when>
156 <when value="">
157 <!-- Display nothing -->
158 </when>
159 </conditional>
160
161 <conditional name="pq_options">
162 <param name="pq_options_selector" type="select"
163 label="Select p-value or q-value" help="default uses q-value">
164 <option value="qvalue">q-value</option>
165 <option value="pvalue">p-value</option>
166 </param>
167 <when value="pvalue">
168 <param name="pvalue" type="float"
169 label="p-value cutoff for binding region detection"
170 value="1e-2" help="default: 1e-2 (--pvalue)"/>
171 </when>
172 <when value="qvalue">
173 <param name="qvalue" type="float"
174 label="q-value cutoff for binding region detection"
175 value="0.01" help="default: 0.01 (--qvalue)"/>
176 </when>
177 </conditional>
178 <conditional name="advanced_options">
179 <param name="advanced_options_selector"
180 type="boolean" truevalue="on" falsevalue="off" checked="False"
181 label="Use advanced options?" />
182 <when value="on">
183 <param name="mfoldlo" type="integer"
184 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)"
185 value="10" help="(--mfold)"/>
186 <param name="mfoldhi" type="integer"
187 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)"
188 value="30" help="(--mfold)"/>
189 <param name="nolambda"
190 label="Use fixed background lambda as local lambda for every binding region"
191 type="boolean" truevalue="--nolambda" falsevalue="" checked="False"
192 help="(--nolambda)"/>
193 <param name="call_summits"
194 label="Detect subpeaks within binding region"
195 type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
196 help="(--call-summits)"/>
197 <conditional name="keep_duplicates">
198 <param name="keep_dup" type="select"
199 label="Use of duplicate reads">
200 <option value="auto">Automatically calculate maximum number of duplicates to keep (auto)</option>
201 <option value="all">Use all duplicates (all)</option>
202 <option value="" selected="true">Manually specify maxium number of duplicates</option>
130 </param> 203 </param>
131 <when value="broad"> 204 <when value="">
132 <param name="broad_cutoff" type="float" 205 <param name="maximum_tags" type="integer" value="1"
133 label="Cutoff for broad regions" 206 label="Maxium number of duplicated tags to keep at each location"/>
134 value="0.1" help="default: 0.1 (--broad-cutoff)"/>
135 </when> 207 </when>
136 </conditional> 208 </conditional>
137 <param name="input_chipseq_file1" type="data" format="bed,sam,bam" 209 </when>
138 label="ChIP-seq read file" /> 210 <when value="off">
139 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" 211 <!--display nothing-->
140 label="ChIP-seq control read file" /> 212 </when>
141 <conditional name="genome_size"> 213 </conditional>
142 <param name="gsize" type="select" label="Effective genome size" 214 <conditional name="nomodel_type">
143 help="Either pre-defined (for common organisms), or user-defined (--gsize)"> 215 <param name="nomodel_type_selector" type="select" label="Build Model">
144 <option value="hs" selected="true">Human (2.7e9)</option> 216 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option>
145 <option value="mm">Mouse (1.87e9)</option> 217 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option>
146 <option value="ce">C. elegans (9e7)</option> 218 </param>
147 <option value="dm">Fruitfly (1.2e8)</option> 219 <when value="nomodel">
148 <option value="">User-defined</option> 220 <param name="extsize" type="integer" label="Arbitrary extension size in bp" value="200" help="Used as fragment size to extend each read towards 3' end (--extsize)"/>
149 </param>
150 <when value="">
151 <!-- User-defined effective genome size -->
152 <param name="user_defined_gsize" type="float" value=""
153 label="Enter effective genome size (number of bases)"
154 help="e.g. '1.0e+9' or '1000000000'" />
155 </when>
156 </conditional>
157 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/>
158 <param name="xls_to_interval" label="Include XLS file from MACS"
159 type="boolean" truevalue="True" falsevalue="False" checked="True"
160 help="MACS2 XLS file will be output to the history in 'interval' format (suitable for subsequent analysis in Galaxy). Note that start positions are 1-based."/>
161
162 <conditional name="bdg_options">
163 <param name="bdg"
164 label="Save treatment and control lambda pileups in bedGraph"
165 type="boolean" truevalue="-B" falsevalue="" checked="False" />
166 <when value="-B">
167 <param name="spmr"
168 type="boolean" truevalue="--SPMR" falsevalue="" checked="False"
169 label="Save signal per million reads for fragment pileup profiles"
170 help="(--SPMR)" />
171 <param name="make_bigwig" type="boolean" checked="True"
172 truevalue="True" falsevalue=""
173 label="Also generate bigWig file from bedGraph"
174 help="bigWig file can used in subsequent analyses e.g. CEAS" />
175 </when>
176 <when value="">
177 <!-- Display nothing -->
178 </when>
179 </conditional>
180
181 <conditional name="pq_options">
182 <param name="pq_options_selector" type="select"
183 label="Select p-value or q-value" help="default uses q-value">
184 <option value="qvalue">q-value</option>
185 <option value="pvalue">p-value</option>
186 </param>
187 <when value="pvalue">
188 <param name="pvalue" type="float"
189 label="p-value cutoff for binding region detection"
190 value="1e-2" help="default: 1e-2 (--pvalue)"/>
191 </when>
192 <when value="qvalue">
193 <param name="qvalue" type="float"
194 label="q-value cutoff for binding region detection"
195 value="0.01" help="default: 0.01 (--qvalue)"/>
196 </when>
197 </conditional>
198 <conditional name="advanced_options">
199 <param name="advanced_options_selector" type="select"
200 label="Display advanced options">
201 <option value="off">Hide</option>
202 <option value="on">Display</option>
203 </param>
204 <when value="on">
205 <param name="mfoldlo" type="integer"
206 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)"
207 value="10" help="(--mfold)"/>
208 <param name="mfoldhi" type="integer"
209 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)"
210 value="30" help="(--mfold)"/>
211 <param name="nolambda"
212 label="Use fixed background lambda as local lambda for every binding region"
213 type="boolean" truevalue="--nolambda" falsevalue="" checked="False"
214 help="(--nolambda)"/>
215 <param name="call_summits"
216 label="Detect subpeaks within binding region"
217 type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
218 help="(--call-summits)"/>
219 <conditional name="keep_duplicates">
220 <param name="keep_dup" type="select"
221 label="Use of duplicate reads">
222 <option value="auto">Automatically calculate maximum number of duplicates to keep (auto)</option>
223 <option value="all">Use all duplicates (all)</option>
224 <option value="" selected="true">Manually specify maxium number of duplicates</option>
225 </param>
226 <when value="">
227 <param name="maximum_tags" type="integer" value="1"
228 label="Maxium number of duplicated tags to keep at each location"/>
229 </when>
230 </conditional>
231 </when>
232 <when value="off">
233 <!--display nothing-->
234 </when>
235 </conditional>
236 <conditional name="nomodel_type">
237 <param name="nomodel_type_selector" type="select" label="Build Model">
238 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option>
239 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option>
240 </param>
241 <when value="nomodel">
242 <param name="extsize" type="integer" label="Arbitrary extension size in bp" value="200" help="Used as fragment size to extend each read towards 3' end (--extsize)"/>
243 </when>
244 </conditional>
245 </when>
246
247 <!--callpeak option of macs2-->
248 <when value="bdgcmp">
249 <param name="input_chipseq_file1" type="data" format="bed,sam,bam"
250 label="ChIP-seq read file" />
251 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True"
252 label="ChIP-seq control read file" />
253 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001"
254 help="default: 0.00001 (-p)"/>
255 <conditional name="bdgcmp_options">
256 <param name="bdgcmp_options_selector" type="select"
257 label="Select action to be performed">
258 <option value="ppois">ppois</option>
259 <option value="qpois">qpois</option>
260 <option value="subtract">subtract</option>
261 <option value="logFE">logFE</option>
262 <option value="FE">FE</option>
263 <option value="logLR">logLR</option>
264 </param>
265 </conditional>
266 </when> 221 </when>
267 </conditional> 222 </conditional>
268 </inputs> 223 </inputs>
269 224
270 <outputs> 225 <outputs>
271 <!--callpeaks output--> 226 <!--callpeaks output-->
272 <data name="output_extra_files" format="html" 227 <data name="output_extra_files" format="html"
273 label="${tool.name}: callpeak on ${on_string} (html report)"> 228 label="${tool.name}: callpeak on ${on_string} (html report)">
274 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
275 </data> 229 </data>
276 <data name="output_summits_bed_file" format="bed" 230 <data name="output_summits_bed_file" format="bed"
277 label="${tool.name}: callpeak on ${on_string} (summits: bed)"> 231 label="${tool.name}: callpeak on ${on_string} (summits: bed)">
278 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
279 </data> 232 </data>
280 <data name="output_peaks_file" format="xls" 233 <data name="output_peaks_file" format="xls"
281 label="${tool.name}: callpeak on ${on_string} (peaks: xls)"> 234 label="${tool.name}: callpeak on ${on_string} (peaks: xls)">
282 <filter>major_command['major_command_selector'] == 'callpeak'</filter> 235 <filter>xls_to_interval is False</filter>
283 <filter>major_command['xls_to_interval'] is False</filter>
284 </data> 236 </data>
285 <data name="output_narrowpeaks_file" format="interval" 237 <data name="output_narrowpeaks_file" format="interval"
286 label="${tool.name}: callpeak on ${on_string} (peaks: narrowPeak)"> 238 label="${tool.name}: callpeak on ${on_string} (peaks: narrowPeak)">
287 <filter>major_command['major_command_selector'] == 'callpeak'</filter> 239 <filter>broad_options['broad_regions'] == ''</filter>
288 <filter>major_command['broad_options']['broad_regions'] == ''</filter>
289 </data> 240 </data>
290 <data name="output_broadpeaks_file" format="interval" 241 <data name="output_broadpeaks_file" format="interval"
291 label="${tool.name}: callpeak on ${on_string} (peaks: broadPeak)"> 242 label="${tool.name}: callpeak on ${on_string} (peaks: broadPeak)">
292 <filter>major_command['major_command_selector'] == 'callpeak'</filter> 243 <filter>broad_options['broad_regions'] == 'broad'</filter>
293 <filter>major_command['broad_options']['broad_regions'] == 'broad'</filter>
294 </data> 244 </data>
295 <data name="output_gappedpeaks_file" format="interval" 245 <data name="output_gappedpeaks_file" format="interval"
296 label="${tool.name}: callpeak on ${on_string} (peaks: gappedPeak)"> 246 label="${tool.name}: callpeak on ${on_string} (peaks: gappedPeak)">
297 <filter>major_command['major_command_selector'] == 'callpeak'</filter> 247 <filter>broad_options['broad_regions'] == 'broad'</filter>
298 <filter>major_command['broad_options']['broad_regions'] == 'broad'</filter>
299 </data> 248 </data>
300 <data name="output_xls_to_interval_peaks_file" format="interval" 249 <data name="output_xls_to_interval_peaks_file" format="interval"
301 label="${tool.name}: callpeak on ${on_string} (peaks: interval)"> 250 label="${tool.name}: callpeak on ${on_string} (peaks: interval)">
302 <filter>major_command['xls_to_interval'] is True</filter> 251 <filter>xls_to_interval is True</filter>
303 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
304 </data> 252 </data>
305 <data name="output_treat_pileup_file" format="bedgraph" 253 <data name="output_treat_pileup_file" format="bedgraph"
306 label="${tool.name}: callpeak on ${on_string} (treat pileup: bedGraph)"> 254 label="${tool.name}: callpeak on ${on_string} (treat pileup: bedGraph)">
307 <filter>major_command['bdg_options']['bdg'] is True</filter> 255 <filter>bdg_options['bdg'] is True</filter>
308 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
309 </data> 256 </data>
310 <data name="output_lambda_bedgraph_file" format="bedgraph" 257 <data name="output_lambda_bedgraph_file" format="bedgraph"
311 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)"> 258 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)">
312 <filter>major_command['bdg_options']['bdg'] is True</filter> 259 <filter>bdg_options['bdg'] is True</filter>
313 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
314 </data> 260 </data>
315 <data name="output_bigwig_file" format="bigwig" 261 <data name="output_bigwig_file" format="bigwig"
316 label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)"> 262 label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)">
317 <filter>major_command['major_command_selector'] == 'callpeak'</filter> 263 <filter>bdg_options['bdg'] is True</filter>
318 <filter>major_command['bdg_options']['bdg'] is True</filter> 264 <filter>bdg_options['make_bigwig'] is True</filter>
319 <filter>major_command['bdg_options']['make_bigwig'] is True</filter>
320 </data>
321 <!--bdgcmp output-->
322 <data name="output_bdgcmp_file" format="bdg"
323 label="${tool.name}: bdgcmp on ${on_string} (bdg)">
324 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter>
325 </data> 265 </data>
326 </outputs> 266 </outputs>
327 <tests> 267 <tests>
328 <!--none yet for macs2--> 268 <!-- Peak calling without bigwig output -->
269 <test>
270 <!-- Inputs -->
271 <param name="experiment_name" value="test_MACS2.1.0" />
272 <param name="broad_regions" value="" />
273 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
274 ftype="bed" />
275 <param name="input_control_file1" value="test_region_Input.bed"
276 ftype="bed" />
277 <param name="gsize" value="" />
278 <param name="user_defined_gsize" value="775000000.0" />
279 <param name="bw" value="300" />
280 <param name="xls_to_interval" value="true" />
281 <param name="bdg_options|bdg" value="-B" />
282 <param name="bdg_options|spmr" value="--SPMR" />
283 <param name="bdg_options|make_bigwig" value="false" />
284 <param name="pq_options_selector" value="qvalue" />
285 <param name="qvalue" value="0.05" />
286 <param name="advanced_options_selector" value="true" />
287 <param name="advanced_options|mfoldlo" value="5" />
288 <param name="advanced_options|mfoldhi" value="50" />
289 <param name="advanced_options|nolambda" value="" />
290 <param name="advanced_options|call_summits" value="" />
291 <param name="advanced_options|keep_duplicates" value="" />
292 <param name="advanced_options|maximum_tags" value="1" />
293 <param name="nomodel_type_selector" value="nomodel" />
294 <param name="nomodel_type|extsize" value="243" />
295 <!-- Outputs -->
296 <output name="output_extra_files" file="test_MACS2.1.0_html_report.zip"
297 compare="sim_size" delta="1500" />
298 <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" />
299 <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" />
300 <output name="output_xls_to_interval_peaks_file"
301 file="test_MACS2.1.0_peaks.xls.re_match"
302 compare="re_match" lines_diff="1" />
303 <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" />
304 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" />
305 </test>
306 <!-- Peak calling with bigwig output -->
307 <test>
308 <!-- Inputs -->
309 <param name="experiment_name" value="test_MACS2.1.0" />
310 <param name="broad_regions" value="" />
311 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
312 ftype="bed" />
313 <param name="input_control_file1" value="test_region_Input.bed"
314 ftype="bed" />
315 <param name="gsize" value="" />
316 <param name="user_defined_gsize" value="775000000.0" />
317 <param name="bw" value="300" />
318 <param name="xls_to_interval" value="true" />
319 <param name="bdg_options|bdg" value="-B" />
320 <param name="bdg_options|spmr" value="--SPMR" />
321 <param name="bdg_options|make_bigwig" value="true" />
322 <param name="pq_options_selector" value="qvalue" />
323 <param name="qvalue" value="0.05" />
324 <param name="advanced_options_selector" value="true" />
325 <param name="advanced_options|mfoldlo" value="5" />
326 <param name="advanced_options|mfoldhi" value="50" />
327 <param name="advanced_options|nolambda" value="" />
328 <param name="advanced_options|call_summits" value="" />
329 <param name="advanced_options|keep_duplicates" value="" />
330 <param name="advanced_options|maximum_tags" value="1" />
331 <param name="nomodel_type_selector" value="nomodel" />
332 <param name="nomodel_type|extsize" value="243" />
333 <!-- Outputs -->
334 <output name="output_extra_files" file="test_MACS2.1.0_bw_html_report.zip"
335 compare="sim_size" delta="2500" />
336 <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" />
337 <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" />
338 <output name="output_xls_to_interval_peaks_file"
339 file="test_MACS2.1.0_peaks.xls.re_match"
340 compare="re_match" lines_diff="1" />
341 <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" />
342 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" />
343 <output name="output_bigwig_file" file="test_MACS2.1.0_treat_pileup.bw"
344 compare="sim_size" />
345 </test>
329 </tests> 346 </tests>
330 <help> 347 <help>
331 **What it does** 348 **What it does**
332 349
333 MACS (Model-based Analysis of ChIP-seq) provides algorithms for transcript 350 MACS (Model-based Analysis of ChIP-seq) 2.1.0 provides algorithms for identifying
334 factor binding sites. The program can be used either for ChIP-Seq data alone, 351 transcript factor binding sites. The program can be used either for ChIP-Seq data alone,
335 or with control sample datat to improve specificity. 352 or with control sample data to improve specificity.
336 353
337 View the MACS2 documentation at: 354 View the MACS2 documentation at:
338 https://github.com/taoliu/MACS/blob/master/README.rst 355 https://github.com/taoliu/MACS/blob/master/README.rst
339 356
340 ------ 357 ------
341 358
342 **Usage** 359 **Usage**
343 360
344 The tool interfaces with two main functions in MACS: 361 The tool interfaces with the **callpeak** function in MACS, which calls peaks from
345 362 alignment results.
346 * **callpeaks** (the main function) calls peaks from alignment results
347 * **bdgcmp** deducts noise by comparing two signal tracks in bedGraph format.
348 363
349 ------ 364 ------
350 365
351 **Credits** 366 **Credits**
352 367