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annotate macs21_wrapper.xml @ 23:c7646ff9b5c9 draft default tip
planemo upload commit a2f39c10087e77bde5b5db5d04305f72b8eb2af2
| author | pjbriggs |
|---|---|
| date | Tue, 27 Jun 2023 07:37:07 +0000 |
| parents | dfb939015935 |
| children |
| rev | line source |
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1 <tool id="macs2_1_peakcalling" name="MACS2.1.2" version="2.1.2-galaxy1"> |
| 9 | 2 <description>Model-based Analysis of ChIP-Seq: peak calling</description> |
| 0 | 3 <requirements> |
| 4 <requirement type="package" version="2.7">python</requirement> | |
| 22 | 5 <requirement type="package" version="2.1.2">macs2</requirement> |
| 6 <requirement type="package" version="3.5">R</requirement> | |
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7 <requirement type="package" version="377">ucsc-fetchchromsizes</requirement> |
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8 <requirement type="package" version="377">ucsc-bedclip</requirement> |
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9 <requirement type="package" version="377">ucsc-bedsort</requirement> |
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10 <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement> |
| 0 | 11 </requirements> |
| 9 | 12 <version_command>macs2 --version</version_command> |
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13 <command><![CDATA[ |
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14 python $__tool_directory__/macs21_wrapper.py callpeak |
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15 ## |
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16 ## ChIP-seq input |
| 9 | 17 $input_chipseq_file1 |
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18 ## |
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19 ## ChIP-seq control |
| 9 | 20 #if str($input_control_file1) != 'None' |
| 21 -c $input_control_file1 | |
| 22 #end if | |
| 23 ## | |
| 17 | 24 --format=$format |
| 9 | 25 --name="$experiment_name" |
| 26 --bw=$bw | |
| 27 ## | |
| 28 ## Genome size | |
| 29 #if str($genome_size.gsize) == '' | |
| 30 --gsize=$genome_size.user_defined_gsize | |
| 31 #else: | |
| 32 --gsize=$genome_size.gsize | |
| 33 #end if | |
| 34 ## | |
| 35 ## Broad peaks | |
| 36 #if str($broad_options.broad_regions) == 'broad' | |
| 37 --broad --broad-cutoff=$broad_options.broad_cutoff | |
| 38 #end if | |
| 39 ## | |
| 40 ## (no)model options | |
| 41 #if str($nomodel_type.nomodel_type_selector) == 'nomodel' | |
| 42 --nomodel --extsize=$nomodel_type.extsize | |
| 43 #end if | |
| 44 ## | |
| 45 ## pq value select options | |
| 46 #if str($pq_options.pq_options_selector) == 'qvalue' | |
| 47 --qvalue=$pq_options.qvalue | |
| 48 #else | |
| 49 --pvalue=$pq_options.pvalue | |
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50 #end if |
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51 ## |
| 9 | 52 ## Bedgraph options |
| 53 #if $bdg_options.bdg | |
| 54 -B $bdg_options.spmr | |
| 55 #end if | |
| 56 ## | |
| 57 ## Advanced options | |
| 58 #if $advanced_options.advanced_options_selector | |
| 59 --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi | |
| 60 $advanced_options.nolambda | |
| 61 $advanced_options.call_summits | |
| 62 #if str($advanced_options.keep_duplicates.keep_dup) == '' | |
| 63 --keep-dup $advanced_options.keep_duplicates.maximum_tags | |
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64 #else |
| 9 | 65 --keep-dup $advanced_options.keep_duplicates.keep_dup |
| 2 | 66 #end if |
| 9 | 67 #else |
| 68 ## Defaults if advanced options not set | |
| 69 --mfold 10 30 --keep-dup 1 | |
| 70 #end if | |
| 71 ## | |
| 72 ## Output files | |
| 73 --output-summits=$output_summits_bed_file | |
| 74 --output-extra-files=$output_extra_files | |
| 75 --output-extra-files-path=$output_extra_files.files_path | |
| 76 ## | |
| 77 ## Narrow/broad peak outputs | |
| 78 #if str($broad_options.broad_regions) == 'broad' | |
| 79 --output-broadpeaks=$output_broadpeaks_file | |
| 80 --output-gappedpeaks=$output_gappedpeaks_file | |
| 81 #else | |
| 82 --output-narrowpeaks=$output_narrowpeaks_file | |
| 83 #end if | |
| 84 ## | |
| 85 ## Bedgraph outputs | |
| 86 #if $bdg_options.bdg | |
| 87 --output-pileup=$output_treat_pileup_file | |
| 88 --output-lambda-bedgraph=$output_lambda_bedgraph_file | |
| 89 #if $bdg_options.make_bigwig | |
| 90 --output-bigwig=$output_bigwig_file | |
| 91 --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${input_chipseq_file1.dbkey}.len | |
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92 #end if |
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93 #end if |
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94 ## |
| 9 | 95 ## XLS/interval output |
| 96 #if str($xls_to_interval) == 'True' | |
| 97 --output-xls-to-interval=$output_xls_to_interval_peaks_file | |
| 98 #else | |
| 99 --output-peaks=$output_peaks_file | |
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100 #end if |
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101 ]]></command> |
| 0 | 102 <inputs> |
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103 <!--experiment name used as base for output file names --> |
| 20 | 104 <param name="experiment_name" type="text" value="MACS2.1 in Galaxy" size="50" |
| 0 | 105 label="Experiment Name"/> |
| 9 | 106 <!--choose 'broad' or 'narrow' regions--> |
| 107 <conditional name="broad_options"> | |
| 108 <param name="broad_regions" type="select" label="Type of region to call" | |
| 109 help="Broad regions are formed by linking nearby enriched regions"> | |
| 110 <option value="" selected="true">Narrow regions</option> | |
| 111 <option value="broad">Broad regions</option> | |
| 112 </param> | |
| 113 <when value="broad"> | |
| 114 <param name="broad_cutoff" type="float" | |
| 115 label="Cutoff for broad regions" | |
| 116 value="0.1" help="default: 0.1 (--broad-cutoff)"/> | |
| 117 </when> | |
| 118 </conditional> | |
| 17 | 119 <param name="format" type="select" label="Format of input read data" |
| 120 help="Specify the format of the input data and whether or not it is paired end (--format)"> | |
| 121 <option value="BAMPE" selected="true">BAM (paired-end)</option> | |
| 122 <option value="BAM">BAM (single-end)</option> | |
| 123 <option value="BEDPE">BED (paired-end)</option> | |
| 124 <option value="BED">BED (single-end)</option> | |
| 125 <option value="SAMPE">SAM (paired-end)</option> | |
| 126 <option value="SAM">SAM (single-end)</option> | |
| 127 </param> | |
| 9 | 128 <param name="input_chipseq_file1" type="data" format="bed,sam,bam" |
| 129 label="ChIP-seq read file" /> | |
| 130 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" | |
| 131 label="ChIP-seq control read file" /> | |
| 132 <conditional name="genome_size"> | |
| 133 <param name="gsize" type="select" label="Effective genome size" | |
| 134 help="Either pre-defined (for common organisms), or user-defined (--gsize)"> | |
| 135 <option value="hs" selected="true">Human (2.7e9)</option> | |
| 136 <option value="mm">Mouse (1.87e9)</option> | |
| 137 <option value="ce">C. elegans (9e7)</option> | |
| 138 <option value="dm">Fruitfly (1.2e8)</option> | |
| 139 <option value="">User-defined</option> | |
| 0 | 140 </param> |
| 9 | 141 <when value=""> |
| 142 <!-- User-defined effective genome size --> | |
| 143 <param name="user_defined_gsize" type="float" value="" | |
| 144 label="Enter effective genome size (number of bases)" | |
| 145 help="e.g. '1.0e+9' or '1000000000'" /> | |
| 146 </when> | |
| 147 </conditional> | |
| 148 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> | |
| 149 <param name="xls_to_interval" label="Include XLS file from MACS" | |
| 150 type="boolean" truevalue="True" falsevalue="False" checked="True" | |
| 151 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."/> | |
| 152 | |
| 153 <conditional name="bdg_options"> | |
| 154 <param name="bdg" | |
| 155 label="Save treatment and control lambda pileups in bedGraph" | |
| 156 type="boolean" truevalue="-B" falsevalue="" checked="False" /> | |
| 157 <when value="-B"> | |
| 158 <param name="spmr" | |
| 159 type="boolean" truevalue="--SPMR" falsevalue="" checked="False" | |
| 160 label="Save signal per million reads for fragment pileup profiles" | |
| 161 help="(--SPMR)" /> | |
| 162 <param name="make_bigwig" type="boolean" checked="True" | |
| 163 truevalue="True" falsevalue="" | |
| 164 label="Also generate bigWig file from bedGraph" | |
| 165 help="bigWig file can used in subsequent analyses e.g. CEAS" /> | |
| 166 </when> | |
| 167 <when value=""> | |
| 168 <!-- Display nothing --> | |
| 169 </when> | |
| 170 </conditional> | |
| 171 | |
| 172 <conditional name="pq_options"> | |
| 173 <param name="pq_options_selector" type="select" | |
| 174 label="Select p-value or q-value" help="default uses q-value"> | |
| 175 <option value="qvalue">q-value</option> | |
| 176 <option value="pvalue">p-value</option> | |
| 177 </param> | |
| 178 <when value="pvalue"> | |
| 179 <param name="pvalue" type="float" | |
| 180 label="p-value cutoff for binding region detection" | |
| 181 value="1e-2" help="default: 1e-2 (--pvalue)"/> | |
| 182 </when> | |
| 183 <when value="qvalue"> | |
| 184 <param name="qvalue" type="float" | |
| 185 label="q-value cutoff for binding region detection" | |
| 186 value="0.01" help="default: 0.01 (--qvalue)"/> | |
| 187 </when> | |
| 188 </conditional> | |
| 189 <conditional name="advanced_options"> | |
| 190 <param name="advanced_options_selector" | |
| 191 type="boolean" truevalue="on" falsevalue="off" checked="False" | |
| 192 label="Use advanced options?" /> | |
| 193 <when value="on"> | |
| 194 <param name="mfoldlo" type="integer" | |
| 195 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)" | |
| 196 value="10" help="(--mfold)"/> | |
| 197 <param name="mfoldhi" type="integer" | |
| 198 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" | |
| 199 value="30" help="(--mfold)"/> | |
| 200 <param name="nolambda" | |
| 201 label="Use fixed background lambda as local lambda for every binding region" | |
| 202 type="boolean" truevalue="--nolambda" falsevalue="" checked="False" | |
| 203 help="(--nolambda)"/> | |
| 204 <param name="call_summits" | |
| 205 label="Detect subpeaks within binding region" | |
| 206 type="boolean" truevalue="--call-summits" falsevalue="" checked="False" | |
| 207 help="(--call-summits)"/> | |
| 208 <conditional name="keep_duplicates"> | |
| 209 <param name="keep_dup" type="select" | |
| 210 label="Use of duplicate reads"> | |
| 211 <option value="auto">Automatically calculate maximum number of duplicates to keep (auto)</option> | |
| 212 <option value="all">Use all duplicates (all)</option> | |
| 213 <option value="" selected="true">Manually specify maxium number of duplicates</option> | |
| 0 | 214 </param> |
| 215 <when value=""> | |
| 9 | 216 <param name="maximum_tags" type="integer" value="1" |
| 217 label="Maxium number of duplicated tags to keep at each location"/> | |
| 0 | 218 </when> |
| 219 </conditional> | |
| 9 | 220 </when> |
| 221 <when value="off"> | |
| 222 <!--display nothing--> | |
| 0 | 223 </when> |
| 9 | 224 </conditional> |
| 225 <conditional name="nomodel_type"> | |
| 226 <param name="nomodel_type_selector" type="select" label="Build Model"> | |
| 227 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> | |
| 228 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option> | |
| 229 </param> | |
| 230 <when value="nomodel"> | |
| 231 <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 | 232 </when> |
| 233 </conditional> | |
| 234 </inputs> | |
| 235 | |
| 236 <outputs> | |
| 237 <!--callpeaks output--> | |
| 238 <data name="output_extra_files" format="html" | |
| 239 label="${tool.name}: callpeak on ${on_string} (html report)"> | |
| 240 </data> | |
| 241 <data name="output_summits_bed_file" format="bed" | |
| 242 label="${tool.name}: callpeak on ${on_string} (summits: bed)"> | |
| 243 </data> | |
| 244 <data name="output_peaks_file" format="xls" | |
| 245 label="${tool.name}: callpeak on ${on_string} (peaks: xls)"> | |
| 9 | 246 <filter>xls_to_interval is False</filter> |
| 0 | 247 </data> |
| 248 <data name="output_narrowpeaks_file" format="interval" | |
| 249 label="${tool.name}: callpeak on ${on_string} (peaks: narrowPeak)"> | |
| 9 | 250 <filter>broad_options['broad_regions'] == ''</filter> |
| 0 | 251 </data> |
| 252 <data name="output_broadpeaks_file" format="interval" | |
| 253 label="${tool.name}: callpeak on ${on_string} (peaks: broadPeak)"> | |
| 9 | 254 <filter>broad_options['broad_regions'] == 'broad'</filter> |
| 0 | 255 </data> |
| 256 <data name="output_gappedpeaks_file" format="interval" | |
| 257 label="${tool.name}: callpeak on ${on_string} (peaks: gappedPeak)"> | |
| 9 | 258 <filter>broad_options['broad_regions'] == 'broad'</filter> |
| 0 | 259 </data> |
| 260 <data name="output_xls_to_interval_peaks_file" format="interval" | |
| 261 label="${tool.name}: callpeak on ${on_string} (peaks: interval)"> | |
| 9 | 262 <filter>xls_to_interval is True</filter> |
| 0 | 263 </data> |
| 264 <data name="output_treat_pileup_file" format="bedgraph" | |
| 265 label="${tool.name}: callpeak on ${on_string} (treat pileup: bedGraph)"> | |
| 9 | 266 <filter>bdg_options['bdg'] is True</filter> |
| 0 | 267 </data> |
| 268 <data name="output_lambda_bedgraph_file" format="bedgraph" | |
| 269 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)"> | |
| 9 | 270 <filter>bdg_options['bdg'] is True</filter> |
| 0 | 271 </data> |
| 2 | 272 <data name="output_bigwig_file" format="bigwig" |
| 273 label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)"> | |
| 9 | 274 <filter>bdg_options['bdg'] is True</filter> |
| 275 <filter>bdg_options['make_bigwig'] is True</filter> | |
| 0 | 276 </data> |
| 277 </outputs> | |
| 278 <tests> | |
| 9 | 279 <!-- Peak calling without bigwig output --> |
| 280 <test> | |
| 281 <!-- Inputs --> | |
| 22 | 282 <param name="experiment_name" value="test_MACS2.1.2" /> |
| 9 | 283 <param name="broad_regions" value="" /> |
| 17 | 284 <param name="format" value="BED" /> |
| 9 | 285 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" |
| 286 ftype="bed" /> | |
| 287 <param name="input_control_file1" value="test_region_Input.bed" | |
| 288 ftype="bed" /> | |
| 289 <param name="gsize" value="" /> | |
| 290 <param name="user_defined_gsize" value="775000000.0" /> | |
| 291 <param name="bw" value="300" /> | |
| 292 <param name="xls_to_interval" value="true" /> | |
| 293 <param name="bdg_options|bdg" value="-B" /> | |
| 294 <param name="bdg_options|spmr" value="--SPMR" /> | |
| 295 <param name="bdg_options|make_bigwig" value="false" /> | |
| 296 <param name="pq_options_selector" value="qvalue" /> | |
| 297 <param name="qvalue" value="0.05" /> | |
| 298 <param name="advanced_options_selector" value="true" /> | |
| 299 <param name="advanced_options|mfoldlo" value="5" /> | |
| 300 <param name="advanced_options|mfoldhi" value="50" /> | |
| 301 <param name="advanced_options|nolambda" value="" /> | |
| 302 <param name="advanced_options|call_summits" value="" /> | |
| 303 <param name="advanced_options|keep_duplicates" value="" /> | |
| 304 <param name="advanced_options|maximum_tags" value="1" /> | |
| 305 <param name="nomodel_type_selector" value="nomodel" /> | |
| 306 <param name="nomodel_type|extsize" value="243" /> | |
| 307 <!-- Outputs --> | |
| 22 | 308 <output name="output_extra_files" file="test_MACS2.1.2_html_report.zip" |
| 9 | 309 compare="sim_size" delta="1500" /> |
| 22 | 310 <output name="output_summits_bed_file" file="test_MACS2.1.2_summits.bed" /> |
| 311 <output name="output_narrowpeaks_file" file="test_MACS2.1.2_peaks_narrowPeak.interval" /> | |
| 9 | 312 <output name="output_xls_to_interval_peaks_file" |
| 22 | 313 file="test_MACS2.1.2_peaks.xls.re_match" |
| 9 | 314 compare="re_match" lines_diff="1" /> |
| 22 | 315 <output name="output_treat_pileup_file" file="test_MACS2.1.2_treat_pileup.bdg" /> |
| 316 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.2_control_lambda.bdg" /> | |
| 9 | 317 </test> |
| 318 <!-- Peak calling with bigwig output --> | |
| 319 <test> | |
| 320 <!-- Inputs --> | |
| 22 | 321 <param name="experiment_name" value="test_MACS2.1.2" /> |
| 9 | 322 <param name="broad_regions" value="" /> |
| 17 | 323 <param name="format" value="BED" /> |
| 9 | 324 <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" |
| 325 ftype="bed" /> | |
| 326 <param name="input_control_file1" value="test_region_Input.bed" | |
| 327 ftype="bed" /> | |
| 328 <param name="gsize" value="" /> | |
| 329 <param name="user_defined_gsize" value="775000000.0" /> | |
| 330 <param name="bw" value="300" /> | |
| 331 <param name="xls_to_interval" value="true" /> | |
| 332 <param name="bdg_options|bdg" value="-B" /> | |
| 333 <param name="bdg_options|spmr" value="--SPMR" /> | |
| 334 <param name="bdg_options|make_bigwig" value="true" /> | |
| 335 <param name="pq_options_selector" value="qvalue" /> | |
| 336 <param name="qvalue" value="0.05" /> | |
| 337 <param name="advanced_options_selector" value="true" /> | |
| 338 <param name="advanced_options|mfoldlo" value="5" /> | |
| 339 <param name="advanced_options|mfoldhi" value="50" /> | |
| 340 <param name="advanced_options|nolambda" value="" /> | |
| 341 <param name="advanced_options|call_summits" value="" /> | |
| 342 <param name="advanced_options|keep_duplicates" value="" /> | |
| 343 <param name="advanced_options|maximum_tags" value="1" /> | |
| 344 <param name="nomodel_type_selector" value="nomodel" /> | |
| 345 <param name="nomodel_type|extsize" value="243" /> | |
| 346 <!-- Outputs --> | |
| 22 | 347 <output name="output_extra_files" file="test_MACS2.1.2_bw_html_report.zip" |
| 9 | 348 compare="sim_size" delta="2500" /> |
| 22 | 349 <output name="output_summits_bed_file" file="test_MACS2.1.2_summits.bed" /> |
| 350 <output name="output_narrowpeaks_file" file="test_MACS2.1.2_peaks_narrowPeak.interval" /> | |
| 9 | 351 <output name="output_xls_to_interval_peaks_file" |
| 22 | 352 file="test_MACS2.1.2_peaks.xls.re_match" |
| 9 | 353 compare="re_match" lines_diff="1" /> |
| 22 | 354 <output name="output_treat_pileup_file" file="test_MACS2.1.2_treat_pileup.bdg" /> |
| 355 <output name="output_lambda_bedgraph_file" file="test_MACS2.1.2_control_lambda.bdg" /> | |
| 356 <output name="output_bigwig_file" file="test_MACS2.1.2_treat_pileup.bw" | |
| 9 | 357 compare="sim_size" /> |
| 358 </test> | |
| 0 | 359 </tests> |
| 360 <help> | |
| 361 **What it does** | |
| 362 | |
| 22 | 363 MACS (Model-based Analysis of ChIP-seq) 2.1.2 provides algorithms for identifying |
| 9 | 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. | |
| 0 | 366 |
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367 View the MACS2 documentation at: |
| 0 | 368 https://github.com/taoliu/MACS/blob/master/README.rst |
| 369 | |
| 370 ------ | |
| 371 | |
| 372 **Usage** | |
| 373 | |
| 9 | 374 The tool interfaces with the **callpeak** function in MACS, which calls peaks from |
| 375 alignment results. | |
| 0 | 376 |
| 377 ------ | |
| 378 | |
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379 **Credits** |
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380 |
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381 This Galaxy tool was based on the MACS2 tool hosted in the Galaxy toolshed at |
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382 |
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383 * http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 |
| 0 | 384 |
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385 (specifically the 16:14f378e35191 revision of the tool) which is credited to Ziru |
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386 Zhou. This version is a reimplemented version developed within the Bioinformatics |
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387 Core Facility at the University of Manchester, which uses more up-to-date Galaxy |
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388 syntax and adds some extra features. |
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389 |
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390 The tool runs Tao Liu's MACS2 software: |
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391 |
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392 * https://github.com/taoliu/MACS |
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393 |
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394 The reference for MACS is: |
| 0 | 395 |
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396 * Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, |
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397 Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). |
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398 Genome Biol. 2008;9(9):R137. |
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399 |
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400 Please kindly acknowledge both this Galaxy tool and the MACS2 package if you |
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401 use it. |
| 0 | 402 </help> |
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403 <citations> |
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404 <!-- |
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405 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set |
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406 Can be either DOI or Bibtex |
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407 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex |
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408 --> |
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409 <citation type="doi">10.1186/gb-2008-9-9-r137</citation> |
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410 </citations> |
| 0 | 411 </tool> |