Mercurial > repos > pjbriggs > macs21
annotate macs21_wrapper.xml @ 18:4e85d68a2347 draft
Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2.
| author | pjbriggs |
|---|---|
| date | Wed, 22 Mar 2017 11:24:52 -0400 |
| parents | f346287fe52c |
| children | 51303ba3fbbe |
| rev | line source |
|---|---|
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1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-6"> |
| 9 | 2 <description>Model-based Analysis of ChIP-Seq: peak calling</description> |
| 0 | 3 <requirements> |
| 4 <requirement type="package" version="2.7">python</requirement> | |
| 2 | 5 <requirement type="package" version="1.9">numpy</requirement> |
| 0 | 6 <requirement type="package" version="2.1.0.20140616">macs2</requirement> |
| 6 | 7 <requirement type="package" version="3.1.2">R</requirement> |
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8 <requirement type="package" version="2.0">ucsc_tools_for_macs21</requirement> |
| 0 | 9 </requirements> |
| 9 | 10 <version_command>macs2 --version</version_command> |
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11 <command interpreter="python"> |
| 9 | 12 macs21_wrapper.py callpeak |
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13 ## |
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14 ## ChIP-seq input |
| 9 | 15 $input_chipseq_file1 |
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16 ## |
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17 ## ChIP-seq control |
| 9 | 18 #if str($input_control_file1) != 'None' |
| 19 -c $input_control_file1 | |
| 20 #end if | |
| 21 ## | |
| 17 | 22 --format=$format |
| 9 | 23 --name="$experiment_name" |
| 24 --bw=$bw | |
| 25 ## | |
| 26 ## Genome size | |
| 27 #if str($genome_size.gsize) == '' | |
| 28 --gsize=$genome_size.user_defined_gsize | |
| 29 #else: | |
| 30 --gsize=$genome_size.gsize | |
| 31 #end if | |
| 32 ## | |
| 33 ## Broad peaks | |
| 34 #if str($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 | |
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48 #end if |
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49 ## |
| 9 | 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 | |
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62 #else |
| 9 | 63 --keep-dup $advanced_options.keep_duplicates.keep_dup |
| 2 | 64 #end if |
| 9 | 65 #else |
| 66 ## Defaults if advanced options not set | |
| 67 --mfold 10 30 --keep-dup 1 | |
| 68 #end if | |
| 69 ## | |
| 70 ## Output files | |
| 71 --output-summits=$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 | |
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90 #end if |
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91 #end if |
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92 ## |
| 9 | 93 ## XLS/interval output |
| 94 #if str($xls_to_interval) == 'True' | |
| 95 --output-xls-to-interval=$output_xls_to_interval_peaks_file | |
| 96 #else | |
| 97 --output-peaks=$output_peaks_file | |
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98 #end if |
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99 </command> |
| 0 | 100 <inputs> |
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101 <!--experiment name used as base for output file names --> |
| 0 | 102 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50" |
| 103 label="Experiment Name"/> | |
| 9 | 104 <!--choose 'broad' or 'narrow' regions--> |
| 105 <conditional name="broad_options"> | |
| 106 <param name="broad_regions" type="select" label="Type of region to call" | |
| 107 help="Broad regions are formed by linking nearby enriched regions"> | |
| 108 <option value="" selected="true">Narrow regions</option> | |
| 109 <option value="broad">Broad regions</option> | |
| 110 </param> | |
| 111 <when value="broad"> | |
| 112 <param name="broad_cutoff" type="float" | |
| 113 label="Cutoff for broad regions" | |
| 114 value="0.1" help="default: 0.1 (--broad-cutoff)"/> | |
| 115 </when> | |
| 116 </conditional> | |
| 17 | 117 <param name="format" type="select" label="Format of input read data" |
| 118 help="Specify the format of the input data and whether or not it is paired end (--format)"> | |
| 119 <option value="BAMPE" selected="true">BAM (paired-end)</option> | |
| 120 <option value="BAM">BAM (single-end)</option> | |
| 121 <option value="BEDPE">BED (paired-end)</option> | |
| 122 <option value="BED">BED (single-end)</option> | |
| 123 <option value="SAMPE">SAM (paired-end)</option> | |
| 124 <option value="SAM">SAM (single-end)</option> | |
| 125 </param> | |
| 9 | 126 <param name="input_chipseq_file1" type="data" format="bed,sam,bam" |
| 127 label="ChIP-seq read file" /> | |
| 128 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" | |
| 129 label="ChIP-seq control read file" /> | |
| 130 <conditional name="genome_size"> | |
| 131 <param name="gsize" type="select" label="Effective genome size" | |
| 132 help="Either pre-defined (for common organisms), or user-defined (--gsize)"> | |
| 133 <option value="hs" selected="true">Human (2.7e9)</option> | |
| 134 <option value="mm">Mouse (1.87e9)</option> | |
| 135 <option value="ce">C. elegans (9e7)</option> | |
| 136 <option value="dm">Fruitfly (1.2e8)</option> | |
| 137 <option value="">User-defined</option> | |
| 0 | 138 </param> |
| 9 | 139 <when value=""> |
| 140 <!-- User-defined effective genome size --> | |
| 141 <param name="user_defined_gsize" type="float" value="" | |
| 142 label="Enter effective genome size (number of bases)" | |
| 143 help="e.g. '1.0e+9' or '1000000000'" /> | |
| 144 </when> | |
| 145 </conditional> | |
| 146 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> | |
| 147 <param name="xls_to_interval" label="Include XLS file from MACS" | |
| 148 type="boolean" truevalue="True" falsevalue="False" checked="True" | |
| 149 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."/> | |
| 150 | |
| 151 <conditional name="bdg_options"> | |
| 152 <param name="bdg" | |
| 153 label="Save treatment and control lambda pileups in bedGraph" | |
| 154 type="boolean" truevalue="-B" falsevalue="" checked="False" /> | |
| 155 <when value="-B"> | |
| 156 <param name="spmr" | |
| 157 type="boolean" truevalue="--SPMR" falsevalue="" checked="False" | |
| 158 label="Save signal per million reads for fragment pileup profiles" | |
| 159 help="(--SPMR)" /> | |
| 160 <param name="make_bigwig" type="boolean" checked="True" | |
| 161 truevalue="True" falsevalue="" | |
| 162 label="Also generate bigWig file from bedGraph" | |
| 163 help="bigWig file can used in subsequent analyses e.g. CEAS" /> | |
| 164 </when> | |
| 165 <when value=""> | |
| 166 <!-- Display nothing --> | |
| 167 </when> | |
| 168 </conditional> | |
| 169 | |
| 170 <conditional name="pq_options"> | |
| 171 <param name="pq_options_selector" type="select" | |
| 172 label="Select p-value or q-value" help="default uses q-value"> | |
| 173 <option value="qvalue">q-value</option> | |
| 174 <option value="pvalue">p-value</option> | |
| 175 </param> | |
| 176 <when value="pvalue"> | |
| 177 <param name="pvalue" type="float" | |
| 178 label="p-value cutoff for binding region detection" | |
| 179 value="1e-2" help="default: 1e-2 (--pvalue)"/> | |
| 180 </when> | |
| 181 <when value="qvalue"> | |
| 182 <param name="qvalue" type="float" | |
| 183 label="q-value cutoff for binding region detection" | |
| 184 value="0.01" help="default: 0.01 (--qvalue)"/> | |
| 185 </when> | |
| 186 </conditional> | |
| 187 <conditional name="advanced_options"> | |
| 188 <param name="advanced_options_selector" | |
| 189 type="boolean" truevalue="on" falsevalue="off" checked="False" | |
| 190 label="Use advanced options?" /> | |
| 191 <when value="on"> | |
| 192 <param name="mfoldlo" type="integer" | |
| 193 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)" | |
| 194 value="10" help="(--mfold)"/> | |
| 195 <param name="mfoldhi" type="integer" | |
| 196 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" | |
| 197 value="30" help="(--mfold)"/> | |
| 198 <param name="nolambda" | |
| 199 label="Use fixed background lambda as local lambda for every binding region" | |
| 200 type="boolean" truevalue="--nolambda" falsevalue="" checked="False" | |
| 201 help="(--nolambda)"/> | |
| 202 <param name="call_summits" | |
| 203 label="Detect subpeaks within binding region" | |
| 204 type="boolean" truevalue="--call-summits" falsevalue="" checked="False" | |
| 205 help="(--call-summits)"/> | |
| 206 <conditional name="keep_duplicates"> | |
| 207 <param name="keep_dup" type="select" | |
| 208 label="Use of duplicate reads"> | |
| 209 <option value="auto">Automatically calculate maximum number of duplicates to keep (auto)</option> | |
| 210 <option value="all">Use all duplicates (all)</option> | |
| 211 <option value="" selected="true">Manually specify maxium number of duplicates</option> | |
| 0 | 212 </param> |
| 213 <when value=""> | |
| 9 | 214 <param name="maximum_tags" type="integer" value="1" |
| 215 label="Maxium number of duplicated tags to keep at each location"/> | |
| 0 | 216 </when> |
| 217 </conditional> | |
| 9 | 218 </when> |
| 219 <when value="off"> | |
| 220 <!--display nothing--> | |
| 0 | 221 </when> |
| 9 | 222 </conditional> |
| 223 <conditional name="nomodel_type"> | |
| 224 <param name="nomodel_type_selector" type="select" label="Build Model"> | |
| 225 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> | |
| 226 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option> | |
| 227 </param> | |
| 228 <when value="nomodel"> | |
| 229 <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)"/> | |
| 0 | 230 </when> |
| 231 </conditional> | |
| 232 </inputs> | |
| 233 | |
| 234 <outputs> | |
| 235 <!--callpeaks output--> | |
| 236 <data name="output_extra_files" format="html" | |
| 237 label="${tool.name}: callpeak on ${on_string} (html report)"> | |
| 238 </data> | |
| 239 <data name="output_summits_bed_file" format="bed" | |
| 240 label="${tool.name}: callpeak on ${on_string} (summits: bed)"> | |
| 241 </data> | |
| 242 <data name="output_peaks_file" format="xls" | |
| 243 label="${tool.name}: callpeak on ${on_string} (peaks: xls)"> | |
| 9 | 244 <filter>xls_to_interval is False</filter> |
| 0 | 245 </data> |
| 246 <data name="output_narrowpeaks_file" format="interval" | |
| 247 label="${tool.name}: callpeak on ${on_string} (peaks: narrowPeak)"> | |
| 9 | 248 <filter>broad_options['broad_regions'] == ''</filter> |
| 0 | 249 </data> |
| 250 <data name="output_broadpeaks_file" format="interval" | |
| 251 label="${tool.name}: callpeak on ${on_string} (peaks: broadPeak)"> | |
| 9 | 252 <filter>broad_options['broad_regions'] == 'broad'</filter> |
| 0 | 253 </data> |
| 254 <data name="output_gappedpeaks_file" format="interval" | |
| 255 label="${tool.name}: callpeak on ${on_string} (peaks: gappedPeak)"> | |
| 9 | 256 <filter>broad_options['broad_regions'] == 'broad'</filter> |
| 0 | 257 </data> |
| 258 <data name="output_xls_to_interval_peaks_file" format="interval" | |
| 259 label="${tool.name}: callpeak on ${on_string} (peaks: interval)"> | |
| 9 | 260 <filter>xls_to_interval is True</filter> |
| 0 | 261 </data> |
| 262 <data name="output_treat_pileup_file" format="bedgraph" | |
| 263 label="${tool.name}: callpeak on ${on_string} (treat pileup: bedGraph)"> | |
| 9 | 264 <filter>bdg_options['bdg'] is True</filter> |
| 0 | 265 </data> |
| 266 <data name="output_lambda_bedgraph_file" format="bedgraph" | |
| 267 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)"> | |
| 9 | 268 <filter>bdg_options['bdg'] is True</filter> |
| 0 | 269 </data> |
| 2 | 270 <data name="output_bigwig_file" format="bigwig" |
| 271 label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)"> | |
| 9 | 272 <filter>bdg_options['bdg'] is True</filter> |
| 273 <filter>bdg_options['make_bigwig'] is True</filter> | |
| 0 | 274 </data> |
| 275 </outputs> | |
| 276 <tests> | |
| 9 | 277 <!-- Peak calling without bigwig output --> |
| 278 <test> | |
| 279 <!-- Inputs --> | |
| 280 <param name="experiment_name" value="test_MACS2.1.0" /> | |
| 281 <param name="broad_regions" value="" /> | |
| 17 | 282 <param name="format" value="BED" /> |
| 9 | 283 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" |
| 284 ftype="bed" /> | |
| 285 <param name="input_control_file1" value="test_region_Input.bed" | |
| 286 ftype="bed" /> | |
| 287 <param name="gsize" value="" /> | |
| 288 <param name="user_defined_gsize" value="775000000.0" /> | |
| 289 <param name="bw" value="300" /> | |
| 290 <param name="xls_to_interval" value="true" /> | |
| 291 <param name="bdg_options|bdg" value="-B" /> | |
| 292 <param name="bdg_options|spmr" value="--SPMR" /> | |
| 293 <param name="bdg_options|make_bigwig" value="false" /> | |
| 294 <param name="pq_options_selector" value="qvalue" /> | |
| 295 <param name="qvalue" value="0.05" /> | |
| 296 <param name="advanced_options_selector" value="true" /> | |
| 297 <param name="advanced_options|mfoldlo" value="5" /> | |
| 298 <param name="advanced_options|mfoldhi" value="50" /> | |
| 299 <param name="advanced_options|nolambda" value="" /> | |
| 300 <param name="advanced_options|call_summits" value="" /> | |
| 301 <param name="advanced_options|keep_duplicates" value="" /> | |
| 302 <param name="advanced_options|maximum_tags" value="1" /> | |
| 303 <param name="nomodel_type_selector" value="nomodel" /> | |
| 304 <param name="nomodel_type|extsize" value="243" /> | |
| 305 <!-- Outputs --> | |
| 306 <output name="output_extra_files" file="test_MACS2.1.0_html_report.zip" | |
| 307 compare="sim_size" delta="1500" /> | |
| 308 <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" /> | |
| 309 <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" /> | |
| 310 <output name="output_xls_to_interval_peaks_file" | |
| 311 file="test_MACS2.1.0_peaks.xls.re_match" | |
| 312 compare="re_match" lines_diff="1" /> | |
| 313 <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" /> | |
| 314 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" /> | |
| 315 </test> | |
| 316 <!-- Peak calling with bigwig output --> | |
| 317 <test> | |
| 318 <!-- Inputs --> | |
| 319 <param name="experiment_name" value="test_MACS2.1.0" /> | |
| 320 <param name="broad_regions" value="" /> | |
| 17 | 321 <param name="format" value="BED" /> |
| 9 | 322 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" |
| 323 ftype="bed" /> | |
| 324 <param name="input_control_file1" value="test_region_Input.bed" | |
| 325 ftype="bed" /> | |
| 326 <param name="gsize" value="" /> | |
| 327 <param name="user_defined_gsize" value="775000000.0" /> | |
| 328 <param name="bw" value="300" /> | |
| 329 <param name="xls_to_interval" value="true" /> | |
| 330 <param name="bdg_options|bdg" value="-B" /> | |
| 331 <param name="bdg_options|spmr" value="--SPMR" /> | |
| 332 <param name="bdg_options|make_bigwig" value="true" /> | |
| 333 <param name="pq_options_selector" value="qvalue" /> | |
| 334 <param name="qvalue" value="0.05" /> | |
| 335 <param name="advanced_options_selector" value="true" /> | |
| 336 <param name="advanced_options|mfoldlo" value="5" /> | |
| 337 <param name="advanced_options|mfoldhi" value="50" /> | |
| 338 <param name="advanced_options|nolambda" value="" /> | |
| 339 <param name="advanced_options|call_summits" value="" /> | |
| 340 <param name="advanced_options|keep_duplicates" value="" /> | |
| 341 <param name="advanced_options|maximum_tags" value="1" /> | |
| 342 <param name="nomodel_type_selector" value="nomodel" /> | |
| 343 <param name="nomodel_type|extsize" value="243" /> | |
| 344 <!-- Outputs --> | |
| 345 <output name="output_extra_files" file="test_MACS2.1.0_bw_html_report.zip" | |
| 346 compare="sim_size" delta="2500" /> | |
| 347 <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" /> | |
| 348 <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" /> | |
| 349 <output name="output_xls_to_interval_peaks_file" | |
| 350 file="test_MACS2.1.0_peaks.xls.re_match" | |
| 351 compare="re_match" lines_diff="1" /> | |
| 352 <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" /> | |
| 353 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" /> | |
| 354 <output name="output_bigwig_file" file="test_MACS2.1.0_treat_pileup.bw" | |
| 355 compare="sim_size" /> | |
| 356 </test> | |
| 0 | 357 </tests> |
| 358 <help> | |
| 359 **What it does** | |
| 360 | |
| 9 | 361 MACS (Model-based Analysis of ChIP-seq) 2.1.0 provides algorithms for identifying |
| 362 transcript factor binding sites. The program can be used either for ChIP-Seq data alone, | |
| 363 or with control sample data to improve specificity. | |
| 0 | 364 |
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365 View the MACS2 documentation at: |
| 0 | 366 https://github.com/taoliu/MACS/blob/master/README.rst |
| 367 | |
| 368 ------ | |
| 369 | |
| 370 **Usage** | |
| 371 | |
| 9 | 372 The tool interfaces with the **callpeak** function in MACS, which calls peaks from |
| 373 alignment results. | |
| 0 | 374 |
| 375 ------ | |
| 376 | |
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377 **Credits** |
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378 |
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379 This Galaxy tool was based on the MACS2 tool hosted in the Galaxy toolshed at |
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380 |
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381 * http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 |
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383 (specifically the 16:14f378e35191 revision of the tool) which is credited to Ziru |
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384 Zhou. This version is a reimplemented version developed within the Bioinformatics |
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385 Core Facility at the University of Manchester, which uses more up-to-date Galaxy |
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386 syntax and adds some extra features. |
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387 |
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388 The tool runs Tao Liu's MACS2 software: |
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389 |
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390 * https://github.com/taoliu/MACS |
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391 |
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392 The reference for MACS is: |
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394 * Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, |
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395 Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). |
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396 Genome Biol. 2008;9(9):R137. |
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397 |
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398 Please kindly acknowledge both this Galaxy tool and the MACS2 package if you |
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399 use it. |
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401 <citations> |
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402 <!-- |
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403 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set |
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404 Can be either DOI or Bibtex |
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405 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex |
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406 --> |
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407 <citation type="doi">10.1186/gb-2008-9-9-r137</citation> |
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408 </citations> |
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