Mercurial > repos > pjbriggs > macs21
annotate macs21_wrapper.xml @ 5:9f6d5cae9181 draft
Uploaded yet another attempt to fix tool dependencies!
| author | pjbriggs |
|---|---|
| date | Mon, 20 Apr 2015 11:12:28 -0400 |
| parents | a881c5b7162c |
| children | 344dd37d1704 |
| rev | line source |
|---|---|
| 2 | 1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-2"> |
| 0 | 2 <requirements> |
| 3 <requirement type="package" version="2.7">python</requirement> | |
| 2 | 4 <requirement type="package" version="1.9">numpy</requirement> |
| 0 | 5 <requirement type="package" version="2.1.0.20140616">macs2</requirement> |
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6 <requirement type="package" version="1.0">ucsc_tools_for_macs21</requirement> |
| 0 | 7 </requirements> |
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8 <description>Model-based Analysis of ChIP-Seq</description> |
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9 <command interpreter="python"> |
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10 macs21_wrapper.py |
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11 ## |
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12 ## Major command |
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13 $major_command.major_command_selector |
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14 ## |
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15 ## ChIP-seq input |
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16 $major_command.input_chipseq_file1 |
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17 ## |
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18 ## ChIP-seq control |
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19 #if str($major_command.input_control_file1) != 'None' |
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20 -c $major_command.input_control_file1 |
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21 #end if |
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22 ## |
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23 ## Call peaks |
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24 #if str($major_command.major_command_selector) == 'callpeak' |
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25 --format=$major_command.input_chipseq_file1.extension |
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26 --name="$experiment_name" |
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27 --bw=$major_command.bw |
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28 ## |
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29 ## Genome size |
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30 #if str($major_command.genome_size.gsize) == '' |
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31 --gsize=$major_command.genome_size.user_defined_gsize |
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32 #else: |
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33 --gsize=$major_command.genome_size.gsize |
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34 #end if |
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35 ## |
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36 ## Broad peaks |
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37 #if str($major_command.broad_options.broad_regions) == 'broad' |
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38 --broad --broad-cutoff=$major_command.broad_options.broad_cutoff |
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39 #end if |
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40 ## |
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41 ## (no)model options |
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42 #if str($major_command.nomodel_type.nomodel_type_selector) == 'nomodel' |
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43 --nomodel --extsize=$major_command.nomodel_type.extsize |
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44 #end if |
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45 ## |
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46 ## pq value select options |
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47 #if str($major_command.pq_options.pq_options_selector) == 'qvalue' |
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48 --qvalue=$major_command.pq_options.qvalue |
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49 #else |
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50 --pvalue=$major_command.pq_options.pvalue |
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51 #end if |
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52 ## |
| 2 | 53 ## Bedgraph options |
| 54 #if $major_command.bdg_options.bdg == True | |
| 55 -B $major_command.bdg_options.spmr | |
| 56 #end if | |
| 57 ## | |
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58 ## Advanced options |
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59 #if str($major_command.advanced_options.advanced_options_selector) == 'on' |
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60 --mfold $major_command.advanced_options.mfoldlo $major_command.advanced_options.mfoldhi |
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61 $major_command.advanced_options.nolambda |
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62 $major_command.advanced_options.call_summits |
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63 #if str($major_command.advanced_options.keep_duplicates.keep_dup) == '' |
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64 --keep-dup $major_command.advanced_options.keep_duplicates.maximum_tags |
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65 #else |
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66 --keep-dup $major_command.advanced_options.keep_duplicates.keep_dup |
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67 #end if |
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68 #else |
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69 ## Defaults if advanced options not set |
| 2 | 70 --mfold 10 30 --keep-dup 1 |
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71 #end if |
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72 ## |
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73 ## Output files |
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74 --output-summits=$output_summits_bed_file |
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75 --output-extra-files=$output_extra_files |
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76 --output-extra-files-path=$output_extra_files.files_path |
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77 ## |
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78 ## Narrow/broad peak outputs |
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79 #if str($major_command.broad_options.broad_regions) == 'broad' |
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80 --output-broadpeaks=$output_broadpeaks_file |
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81 --output-gappedpeaks=$output_gappedpeaks_file |
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82 #else |
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83 --output-narrowpeaks=$output_narrowpeaks_file |
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84 #end if |
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85 ## |
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86 ## Bedgraph outputs |
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87 #if str($major_command.bdg_options.bdg) == 'True' |
| 2 | 88 --output-pileup=$output_treat_pileup_file |
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89 --output-lambda-bedgraph=$output_lambda_bedgraph_file |
| 2 | 90 #if str($major_command.bdg_options.make_bigwig) == 'True' |
| 91 --output-bigwig=$output_bigwig_file | |
| 92 --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${major_command.input_chipseq_file1.dbkey}.len | |
| 93 #end if | |
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94 #end if |
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95 ## |
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96 ## XLS/interval output |
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97 #if str($major_command.xls_to_interval) == 'True' |
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98 --output-xls-to-interval=$output_xls_to_interval_peaks_file |
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99 #else |
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100 --output-peaks=$output_peaks_file |
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101 #end if |
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102 #end if |
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103 ## |
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104 ## Compare .bdg files |
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105 #if str($major_command.major_command_selector) == 'bdgcmp' |
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106 -m $major_command.bdgcmp_options.bdgcmp_options_selector |
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107 -p $major_command.pseudocount |
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108 --output-bdgcmp $output_bdgcmp_file |
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109 #end if |
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110 </command> |
| 0 | 111 <inputs> |
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112 <!--experiment name used as base for output file names --> |
| 0 | 113 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50" |
| 114 label="Experiment Name"/> | |
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115 <!--select a major MACS2 command--> |
| 0 | 116 <conditional name="major_command"> |
| 117 <param name="major_command_selector" type="select" label="Select action to be performed"> | |
| 118 <option value="callpeak">Peak Calling</option> | |
| 119 <option value="bdgcmp">Compare .bdg Files</option> | |
| 120 </param> | |
| 121 <!--callpeak option of macs2--> | |
| 122 <when value="callpeak"> | |
| 123 <!--choose 'broad' or 'narrow' regions--> | |
| 124 <conditional name="broad_options"> | |
| 125 <param name="broad_regions" type="select" label="Type of region to call" | |
| 126 help="Broad regions are formed by linking nearby enriched regions"> | |
| 127 <option value="" selected="true">Narrow regions</option> | |
| 128 <option value="broad">Broad regions</option> | |
| 129 </param> | |
| 130 <when value="broad"> | |
| 131 <param name="broad_cutoff" type="float" | |
| 132 label="Cutoff for broad regions" | |
| 133 value="0.1" help="default: 0.1 (--broad-cutoff)"/> | |
| 134 </when> | |
| 135 </conditional> | |
| 136 <param name="input_chipseq_file1" type="data" format="bed,sam,bam" | |
| 137 label="ChIP-seq read file" /> | |
| 138 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" | |
| 139 label="ChIP-seq control read file" /> | |
| 140 <conditional name="genome_size"> | |
| 141 <param name="gsize" type="select" label="Effective genome size" | |
| 142 help="Either pre-defined (for common organisms), or user-defined (--gsize)"> | |
| 143 <option value="hs" selected="true">Human (2.7e9)</option> | |
| 144 <option value="mm">Mouse (1.87e9)</option> | |
| 145 <option value="ce">C. elegans (9e7)</option> | |
| 146 <option value="dm">Fruitfly (1.2e8)</option> | |
| 147 <option value="">User-defined</option> | |
| 148 </param> | |
| 149 <when value=""> | |
| 150 <!-- User-defined effective genome size --> | |
| 151 <param name="user_defined_gsize" type="float" value="" | |
| 152 label="Enter effective genome size (number of bases)" | |
| 153 help="e.g. '1.0e+9' or '1000000000'" /> | |
| 154 </when> | |
| 155 </conditional> | |
| 156 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> | |
| 157 <param name="xls_to_interval" label="Include XLS file from MACS" | |
| 158 type="boolean" truevalue="True" falsevalue="False" checked="True" | |
| 159 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."/> | |
| 160 | |
| 161 <conditional name="bdg_options"> | |
| 162 <param name="bdg" | |
| 2 | 163 label="Save treatment and control lambda pileups in bedGraph" |
| 0 | 164 type="boolean" truevalue="-B" falsevalue="" checked="False" /> |
| 165 <when value="-B"> | |
| 166 <param name="spmr" | |
| 167 type="boolean" truevalue="--SPMR" falsevalue="" checked="False" | |
| 168 label="Save signal per million reads for fragment pileup profiles" | |
| 169 help="(--SPMR)" /> | |
| 2 | 170 <param name="make_bigwig" type="boolean" checked="True" |
| 171 truevalue="True" falsevalue="" | |
| 172 label="Also generate bigWig file from bedGraph" | |
| 173 help="bigWig file can used in subsequent analyses e.g. CEAS" /> | |
| 0 | 174 </when> |
| 175 <when value=""> | |
| 176 <!-- Display nothing --> | |
| 177 </when> | |
| 178 </conditional> | |
| 179 | |
| 180 <conditional name="pq_options"> | |
| 181 <param name="pq_options_selector" type="select" | |
| 182 label="Select p-value or q-value" help="default uses q-value"> | |
| 183 <option value="qvalue">q-value</option> | |
| 184 <option value="pvalue">p-value</option> | |
| 185 </param> | |
| 186 <when value="pvalue"> | |
| 187 <param name="pvalue" type="float" | |
| 188 label="p-value cutoff for binding region detection" | |
| 189 value="1e-2" help="default: 1e-2 (--pvalue)"/> | |
| 190 </when> | |
| 191 <when value="qvalue"> | |
| 192 <param name="qvalue" type="float" | |
| 193 label="q-value cutoff for binding region detection" | |
| 194 value="0.01" help="default: 0.01 (--qvalue)"/> | |
| 195 </when> | |
| 196 </conditional> | |
| 197 <conditional name="advanced_options"> | |
| 198 <param name="advanced_options_selector" type="select" | |
| 199 label="Display advanced options"> | |
| 200 <option value="off">Hide</option> | |
| 201 <option value="on">Display</option> | |
| 202 </param> | |
| 203 <when value="on"> | |
| 204 <param name="mfoldlo" type="integer" | |
| 205 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)" | |
| 206 value="10" help="(--mfold)"/> | |
| 207 <param name="mfoldhi" type="integer" | |
| 208 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" | |
| 209 value="30" help="(--mfold)"/> | |
| 210 <param name="nolambda" | |
| 211 label="Use fixed background lambda as local lambda for every binding region" | |
| 212 type="boolean" truevalue="--nolambda" falsevalue="" checked="False" | |
| 213 help="(--nolambda)"/> | |
| 214 <param name="call_summits" | |
| 215 label="Detect subpeaks within binding region" | |
| 216 type="boolean" truevalue="--call-summits" falsevalue="" checked="False" | |
| 217 help="(--call-summits)"/> | |
| 218 <conditional name="keep_duplicates"> | |
| 219 <param name="keep_dup" type="select" | |
| 220 label="Use of duplicate reads"> | |
| 221 <option value="auto">Automatically calculate maximum number of duplicates to keep (auto)</option> | |
| 222 <option value="all">Use all duplicates (all)</option> | |
| 223 <option value="" selected="true">Manually specify maxium number of duplicates</option> | |
| 224 </param> | |
| 225 <when value=""> | |
| 226 <param name="maximum_tags" type="integer" value="1" | |
| 227 label="Maxium number of duplicated tags to keep at each location"/> | |
| 228 </when> | |
| 229 </conditional> | |
| 230 </when> | |
| 231 <when value="off"> | |
| 232 <!--display nothing--> | |
| 233 </when> | |
| 234 </conditional> | |
| 235 <conditional name="nomodel_type"> | |
| 236 <param name="nomodel_type_selector" type="select" label="Build Model"> | |
| 237 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> | |
| 238 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option> | |
| 239 </param> | |
| 240 <when value="nomodel"> | |
| 241 <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)"/> | |
| 242 </when> | |
| 243 </conditional> | |
| 244 </when> | |
| 245 | |
| 246 <!--callpeak option of macs2--> | |
| 247 <when value="bdgcmp"> | |
| 248 <param name="input_chipseq_file1" type="data" format="bed,sam,bam" | |
| 249 label="ChIP-seq read file" /> | |
| 250 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" | |
| 251 label="ChIP-seq control read file" /> | |
| 252 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" | |
| 253 help="default: 0.00001 (-p)"/> | |
| 254 <conditional name="bdgcmp_options"> | |
| 255 <param name="bdgcmp_options_selector" type="select" | |
| 256 label="Select action to be performed"> | |
| 257 <option value="ppois">ppois</option> | |
| 258 <option value="qpois">qpois</option> | |
| 259 <option value="subtract">subtract</option> | |
| 260 <option value="logFE">logFE</option> | |
| 261 <option value="FE">FE</option> | |
| 262 <option value="logLR">logLR</option> | |
| 263 </param> | |
| 264 </conditional> | |
| 265 </when> | |
| 266 </conditional> | |
| 267 </inputs> | |
| 268 | |
| 269 <outputs> | |
| 270 <!--callpeaks output--> | |
| 271 <data name="output_extra_files" format="html" | |
| 272 label="${tool.name}: callpeak on ${on_string} (html report)"> | |
| 273 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 274 </data> | |
| 275 <data name="output_summits_bed_file" format="bed" | |
| 276 label="${tool.name}: callpeak on ${on_string} (summits: bed)"> | |
| 277 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 278 </data> | |
| 279 <data name="output_peaks_file" format="xls" | |
| 280 label="${tool.name}: callpeak on ${on_string} (peaks: xls)"> | |
| 281 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 282 <filter>major_command['xls_to_interval'] is False</filter> | |
| 283 </data> | |
| 284 <data name="output_narrowpeaks_file" format="interval" | |
| 285 label="${tool.name}: callpeak on ${on_string} (peaks: narrowPeak)"> | |
| 286 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 287 <filter>major_command['broad_options']['broad_regions'] == ''</filter> | |
| 288 </data> | |
| 289 <data name="output_broadpeaks_file" format="interval" | |
| 290 label="${tool.name}: callpeak on ${on_string} (peaks: broadPeak)"> | |
| 291 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 292 <filter>major_command['broad_options']['broad_regions'] == 'broad'</filter> | |
| 293 </data> | |
| 294 <data name="output_gappedpeaks_file" format="interval" | |
| 295 label="${tool.name}: callpeak on ${on_string} (peaks: gappedPeak)"> | |
| 296 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 297 <filter>major_command['broad_options']['broad_regions'] == 'broad'</filter> | |
| 298 </data> | |
| 299 <data name="output_xls_to_interval_peaks_file" format="interval" | |
| 300 label="${tool.name}: callpeak on ${on_string} (peaks: interval)"> | |
| 301 <filter>major_command['xls_to_interval'] is True</filter> | |
| 302 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 303 </data> | |
| 304 <data name="output_treat_pileup_file" format="bedgraph" | |
| 305 label="${tool.name}: callpeak on ${on_string} (treat pileup: bedGraph)"> | |
| 306 <filter>major_command['bdg_options']['bdg'] is True</filter> | |
| 307 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 308 </data> | |
| 309 <data name="output_lambda_bedgraph_file" format="bedgraph" | |
| 310 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)"> | |
| 311 <filter>major_command['bdg_options']['bdg'] is True</filter> | |
| 312 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 313 </data> | |
| 2 | 314 <data name="output_bigwig_file" format="bigwig" |
| 315 label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)"> | |
| 316 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 317 <filter>major_command['bdg_options']['bdg'] is True</filter> | |
| 318 <filter>major_command['bdg_options']['make_bigwig'] is True</filter> | |
| 319 </data> | |
| 0 | 320 <!--bdgcmp output--> |
| 321 <data name="output_bdgcmp_file" format="bdg" | |
| 322 label="${tool.name}: bdgcmp on ${on_string} (bdg)"> | |
| 323 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter> | |
| 324 </data> | |
| 325 </outputs> | |
| 326 <tests> | |
| 327 <!--none yet for macs2--> | |
| 328 </tests> | |
| 329 <help> | |
| 330 | |
| 331 .. class:: warningmark | |
| 332 | |
| 333 **This is a modified version of the standard Galaxy toolshed "MACS2" tool, | |
| 334 which has been customised for users at the University of Manchester to work | |
| 335 with MACS 2.1.0.** | |
| 336 | |
| 337 It is based on the 16:14f378e35191 revision of the tool at | |
| 338 | |
| 339 * http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 | |
| 340 | |
| 341 ------ | |
| 342 | |
| 343 **What it does** | |
| 344 | |
| 345 With the improvement of sequencing techniques, chromatin immunoprecipitation | |
| 346 followed by high throughput sequencing (ChIP-Seq) is getting popular to study | |
| 347 genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq | |
| 348 analysis method, we present a novel algorithm, named Model-based Analysis of | |
| 349 ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures | |
| 350 the influence of genome complexity to evaluate the significance of enriched | |
| 351 ChIP regions, and MACS improves the spatial resolution of binding sites through | |
| 352 combining the information of both sequencing tag position and orientation. MACS | |
| 353 can be easily used for ChIP-Seq data alone, or with control sample with the | |
| 354 increase of specificity. | |
| 355 | |
| 356 View the original MACS2 documentation: | |
| 357 https://github.com/taoliu/MACS/blob/master/README.rst | |
| 358 | |
| 359 ------ | |
| 360 | |
| 361 **Usage** | |
| 362 | |
| 363 **Peak Calling**: Main MACS2 Function to Call peaks from alignment results. | |
| 364 | |
| 365 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. | |
| 366 | |
| 367 | |
| 368 ------ | |
| 369 | |
| 370 **Citation** | |
| 371 | |
| 372 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. | |
| 373 | |
| 374 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. | |
| 375 </help> | |
| 376 </tool> |