Mercurial > repos > stemcellcommons > macs2
annotate macs2_wrapper.xml @ 21:eed6c8dcef5d draft default tip
Add option to call broad peaks.
| author | stemcellcommons |
|---|---|
| date | Wed, 16 Apr 2014 15:30:35 -0400 |
| parents | db2805f9df66 |
| children |
| rev | line source |
|---|---|
|
17
e047d7bbace9
Remove MACS2 external dependency. Change tool name and version number.
Ilya Sytchev <isytchev@hsph.harvard.edu>
parents:
10
diff
changeset
|
1 <tool id="macs2_peakcalling" name="MACS2" version="2.0.10"> |
| 10 | 2 <description>Model-based Analysis of ChIP-Seq</description> |
| 3 <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command> | |
| 21 | 4 <version_command>macs2 --version</version_command> |
| 10 | 5 <inputs> |
| 6 <!--experiment name and option of selecting paired or single end will always be present--> | |
| 7 <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/> | |
| 8 | |
| 9 <!--select one of the 7 major commands offered by macs2--> | |
| 10 <conditional name="major_command"> | |
| 11 <param name="major_command_selector" type="select" label="Select action to be performed"> | |
| 21 | 12 <option value="callpeak">Peak Calling</option> |
| 13 <!--<option value="filterdup">filterdup</option> | |
| 14 <option value="randsample">randsample</option>--> | |
| 15 <option value="bdgcmp">Compare .bdg Files</option> | |
| 16 <!--<option value="bdgdiff">bdgdiff</option> | |
| 17 <option value="bdgpeakcall">bdgpeakcall</option> | |
| 18 <option value="bdgbroadcall">bdgbroadcall</option>--> | |
| 10 | 19 </param> |
| 20 <!--callpeak option of macs2--> | |
| 21 <when value="callpeak"> | |
| 21 | 22 <!--may need to add a few more formats at later time--> |
| 10 | 23 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" /> |
| 24 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" /> | |
| 21 | 25 <param name="gsize" type="float" label="Effective genome size" value="2.7e+9" help="Human: 3.3e+9, Mouse: 3.0e+9, Fly: 1.9e+8, Worm: 1.3e+8 (--gsize)"/> |
| 26 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> | |
| 27 <param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="True" falsevalue="False" checked="False"/> | |
| 28 <param name="bdg" label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" type="boolean" truevalue="-B" falsevalue="" checked="False" help="files located in html report"/> | |
| 10 | 29 |
| 21 | 30 <conditional name="pq_options"> |
| 31 <param name="pq_options_selector" type="select" label="Select p-value or q-value" help="default uses q-value"> | |
| 32 <option value="qvalue">q-value</option> | |
| 33 <option value="pvalue">p-value</option> | |
| 34 </param> | |
| 35 <when value="pvalue"> | |
| 36 <param name="pvalue" type="float" label="p-value cutoff for peak detection" value="1e-2" help="default: 1e-2 (--pvalue)"/> | |
| 37 </when> | |
| 38 <when value="qvalue"> | |
| 39 <param name="qvalue" type="float" label="q-value cutoff for peak detection" value="5e-2" help="default: 5e-2 (--qvalue)"/> | |
| 40 </when> | |
| 41 </conditional> | |
| 42 <conditional name="advanced_options"> | |
| 43 <param name="advanced_options_selector" type="select" label="Display advanced options"> | |
| 44 <option value="off">Hide</option> | |
| 45 <option value="on">Display</option> | |
| 46 </param> | |
| 47 <when value="on"> | |
| 10 | 48 <param name="mfoldlo" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)" value="10" help="(--mfold)"/> |
| 21 | 49 <param name="mfoldhi" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)" value="30" help="(--mfold)"/> |
| 50 <param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming (--nolambda)"/> | |
| 51 <conditional name="broad_options"> | |
| 52 <param name="broad_options_selector" type="select" label="Composite broad regions" help="put nearby highly enriched regions into a broad region with loose cutoff (--broad)"> | |
| 53 <option value="nobroad" selected="true">No broad regions</option> | |
| 54 <option value="broad">Broad regions</option> | |
| 55 </param> | |
| 56 <when value="broad"> | |
| 57 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" help="value is either p-value or q-value as specified above (--broad-cutoff)"/> | |
| 58 </when> | |
| 59 <when value="nobroad"/> | |
| 60 </conditional> | |
| 61 </when> | |
| 62 <when value="off"> | |
| 63 <!--display nothing--> | |
| 64 </when> | |
| 65 </conditional> | |
| 66 <conditional name="nomodel_type"> | |
| 10 | 67 <param name="nomodel_type_selector" type="select" label="Build Model"> |
| 21 | 68 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> |
| 10 | 69 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option> |
| 70 </param> | |
| 71 <when value="nomodel"> | |
| 72 <param name="shiftsize" type="integer" label="Arbitrary shift size in bp" value="100" help="(--shiftsize)"/> | |
| 73 </when> | |
| 74 </conditional> | |
| 75 </when> | |
| 76 | |
| 77 <!--callpeak option of macs2--> | |
| 78 <when value="bdgcmp"> | |
| 79 <param name="input_chipseq_file1" type="data" format="bam" label="ChIP-Seq Tag File" /> | |
| 80 <param name="input_control_file1" type="data" format="bam" optional="True" label="ChIP-Seq Control File" /> | |
| 21 | 81 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001" help="default: 0.00001 (-p)"/> |
| 10 | 82 |
| 83 <conditional name="bdgcmp_options"> | |
| 84 <param name="bdgcmp_options_selector" type="select" label="Select action to be performed"> | |
| 21 | 85 <option value="ppois">ppois</option> |
| 86 <option value="qpois">qpois</option> | |
| 87 <option value="subtract">subtract</option> | |
| 88 <option value="logFE">logFE</option> | |
| 89 <option value="FE">FE</option> | |
| 90 <option value="logLR">logLR</option> | |
| 10 | 91 </param> |
| 21 | 92 </conditional> |
| 10 | 93 </when> |
| 94 </conditional> | |
| 95 </inputs> | |
| 96 | |
| 97 <outputs> | |
| 98 <!--callpeaks output--> | |
| 99 <data name="output_bed_file" format="bed" label="${tool.name}: callpeak on ${on_string} (peaks: bed)"> | |
| 100 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 101 </data> | |
| 102 <data name="output_extra_files" format="html" label="${tool.name}: callpeak on ${on_string} (html report)"> | |
| 103 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 104 </data> | |
| 105 <data name="output_peaks_file" format="xls" label="${tool.name}: callpeak on ${on_string} (peaks: xls)"> | |
| 106 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 107 </data> | |
| 108 <data name="output_narrowpeaks_file" format="txt" label="${tool.name}: callpeak on ${on_string} (peaks: encodePeak)"> | |
| 109 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 110 </data> | |
| 111 <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name}: callpeak on ${on_string} (peaks: interval)"> | |
| 112 <filter>major_command['xls_to_interval'] is True</filter> | |
| 113 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 114 </data> | |
| 115 <data name="output_xls_to_interval_negative_peaks_file" format="interval" label="${tool.name}: callpeak on ${on_string} (negative peaks: interval)"> | |
| 116 <filter>major_command['xls_to_interval'] is True</filter> | |
| 117 <filter>major_command['input_control_file1'] is not None</filter> | |
| 118 <filter>major_command['major_command_selector'] == 'callpeak'</filter> | |
| 119 </data> | |
| 120 <!--bdgcmp output--> | |
| 121 <data name="output_bdgcmp_file" format="bdg" label="${tool.name}: bdgcmp on ${on_string} (bdg)"> | |
| 122 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter> | |
| 123 </data> | |
| 124 </outputs> | |
| 125 <configfiles> | |
| 126 | |
| 127 <configfile name="outputs_file"><% | |
| 20 | 128 import json |
| 10 | 129 %> |
| 130 ##======================================================================================= | |
| 131 #set $__outputs = { 'command':str( $major_command.major_command_selector ) } | |
| 132 #if str( $major_command.major_command_selector ) == 'callpeak': | |
| 21 | 133 #set $__outputs['output_bed_file'] = str( $output_bed_file ) |
| 134 #set $__outputs['output_extra_file'] = str( $output_extra_files ) | |
| 135 #set $__outputs['output_extra_file_path'] = str( $output_extra_files.files_path ) | |
| 136 #set $__outputs['output_peaks_file'] = str( $output_peaks_file ) | |
| 137 #set $__outputs['output_narrowpeaks_file'] = str( $output_narrowpeaks_file ) | |
| 138 #set $__outputs['output_xls_to_interval_peaks_file'] = str( $output_xls_to_interval_peaks_file ) | |
| 139 #set $__outputs['output_xls_to_interval_negative_peaks_file'] = str( $output_xls_to_interval_negative_peaks_file ) | |
| 10 | 140 #end if |
| 141 ##======================================================================================= | |
| 142 #if str( $major_command.major_command_selector ) == 'bdgcmp': | |
| 21 | 143 #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file ) |
| 10 | 144 #end if |
| 145 | |
| 20 | 146 ${ json.dumps( __outputs ) } |
| 10 | 147 </configfile> |
| 148 <configfile name="options_file"><% | |
| 20 | 149 import json |
| 10 | 150 %> |
| 151 ##======================================================================================= | |
| 152 #set $__options = { 'experiment_name':str( $experiment_name ) } | |
| 153 ##treatment/tag input files and format | |
| 154 #set $__options['input_chipseq'] = [ str( $major_command.input_chipseq_file1 ) ] | |
| 155 #set $__options['format'] = $major_command.input_chipseq_file1.extension.upper() | |
| 156 | |
| 157 ##control/input files | |
| 158 #set $__options['input_control'] = [] | |
| 159 #if str( $major_command.input_control_file1 ) != 'None': | |
| 21 | 160 #set $_hole = __options['input_control'].append( str( $major_command.input_control_file1 ) ) |
| 10 | 161 #end if |
| 162 | |
| 163 #if str( $major_command.major_command_selector ) == 'callpeak': | |
| 21 | 164 #set $__options['command'] = str( "callpeak" ) |
| 165 #set $__options['gsize'] = int( $major_command.gsize ) | |
| 166 #set $__options['bw'] = str( $major_command.bw ) | |
| 167 #set $__options['bdg'] = str( $major_command.bdg ) | |
| 168 #set $__options['xls_to_interval'] = str( $major_command.xls_to_interval ) | |
| 10 | 169 |
| 21 | 170 ##advanced options |
| 171 #if str( $major_command.advanced_options.advanced_options_selector ) == 'on': | |
| 172 #set $__options['mfoldlo'] = int( $major_command.advanced_options.mfoldlo ) | |
| 173 #set $__options['mfoldhi'] = int( $major_command.advanced_options.mfoldhi ) | |
| 174 #set $__options['nolambda'] = str( $major_command.advanced_options.nolambda ) | |
| 175 #if str($major_command.advanced_options.broad_options.broad_options_selector) == 'broad' | |
| 176 #set $__options['broad_cutoff'] = str($major_command.advanced_options.broad_options.broad_cutoff) | |
| 177 #end if | |
| 178 #else: | |
| 179 #set $__options['mfoldlo'] = int( "10" ) | |
| 180 #set $__options['mfoldhi'] = int( "30" ) | |
| 181 #set $__options['nolambda'] = str( "" ) | |
| 182 #end if | |
| 183 | |
| 184 ##enable xls file options | |
| 185 ##if str( $major_command.xls_to_interval ) == 'create': | |
| 186 ##set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) } | |
| 187 ##end if | |
| 188 | |
| 189 ##pq value select options | |
| 190 #if str( $major_command.pq_options.pq_options_selector ) == 'qvalue': | |
| 191 #set $__options['qvalue'] = str( $major_command.pq_options.qvalue ) | |
| 192 #else: | |
| 193 #set $__options['pvalue'] = str( $major_command.pq_options.pvalue ) | |
| 194 #end if | |
| 195 | |
| 196 ##model options | |
| 197 #if str( $major_command.nomodel_type.nomodel_type_selector ) == 'nomodel': | |
| 198 #set $__options['nomodel'] = str( $major_command.nomodel_type.shiftsize ) | |
| 199 #end if | |
| 10 | 200 #end if |
| 201 ##======================================================================================= | |
| 202 #if str( $major_command.major_command_selector ) == 'bdgcmp': | |
| 21 | 203 #set $__options['command'] = str( "bdgcmp" ) |
| 204 #set $__options['pseudocount'] = float( str( $major_command.pseudocount ) ) | |
| 205 #set $__options['m'] = str( $major_command.bdgcmp_options.bdgcmp_options_selector ) | |
| 10 | 206 #end if |
| 207 ##======================================================================================= | |
| 208 | |
| 20 | 209 ${ json.dumps( __options ) } |
| 10 | 210 </configfile> |
| 211 </configfiles> | |
| 212 <tests> | |
| 21 | 213 <!--none yet for macs2--> |
| 10 | 214 </tests> |
| 215 <help> | |
| 216 **What it does** | |
| 217 | |
| 218 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) | |
| 219 is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for | |
| 220 identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of | |
| 221 binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. | |
| 222 | |
| 223 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README | |
| 224 | |
| 225 ------ | |
| 226 | |
| 227 **Usage** | |
| 228 | |
| 229 **Peak Calling**: Main MACS2 Function to Call peaks from alignment results. | |
| 230 | |
| 231 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. | |
| 232 | |
| 233 | |
| 234 ------ | |
| 235 | |
| 236 **Citation** | |
| 237 | |
| 238 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. | |
| 239 | |
| 240 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. | |
| 241 </help> | |
|
17
e047d7bbace9
Remove MACS2 external dependency. Change tool name and version number.
Ilya Sytchev <isytchev@hsph.harvard.edu>
parents:
10
diff
changeset
|
242 </tool> |