Model-based Analysis of ChIP-Seq macs_wrapper.py $options_file $output_bed_file $output_extra_files $output_extra_files.files_path macs macs Paired End (requires elandmulti format) Single End Save Do not create wig file (faster) Do not build the shifting model Build the shifting model Produce a diagnosis report Do not produce report (faster) xls_to_interval is True xls_to_interval is True input_type['input_control_file1'] is not None wig_type['wig_type_selector']=='wig' wig_type['wig_type_selector'] == 'wig' input_type['input_control_file1'] is not None <% import simplejson %> #set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'lambdaset': str( $lambdaset ), 'futurefdr':str( $futurefdr ) } #if str( $xls_to_interval ) == 'create': #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 ) } #else: #set $__options['xls_to_interval'] = False #end if ##treatment/tag input files and format #set $__options['input_chipseq'] = [ str( $input_type['input_chipseq_file1'] ) ] #if $input_type['input_type_selector'] == 'paired_end': #set $_hole = __options['input_chipseq'].append( str( $input_type['input_chipseq_file2'] ) ) #set $__options['format'] = 'ELANDMULTIPET' #else: #set $__options['format'] = $input_type['input_chipseq_file1'].extension.upper() #end if ##control/input files #set $__options['input_control'] = [] #if str( $input_type['input_control_file1'] ) != 'None': #set $_hole = __options['input_control'].append( str( $input_type['input_control_file1'] ) ) #end if #if $input_type['input_type_selector'] == 'paired_end' and str( $input_type['input_control_file2'] ) != 'None': #set $_hole = __options['input_control'].append( str( $input_type['input_control_file2'] ) ) #end if ##wig options #if $wig_type['wig_type_selector'] == 'wig': #set $__options['wig'] = {} #set $__options['wig']['wigextend'] = str( $wig_type['wigextend'] ) #set $__options['wig']['space'] = str( $wig_type['space'] ) #set $__options['wig']['output_treatment_file'] = str( $output_treatment_wig_file ) #if $input_type['input_control_file1'] is not None: #set $__options['wig']['output_control_file'] = str( $output_control_wig_file ) #end if #end if ##model options #if $nomodel_type['nomodel_type_selector'] == 'nomodel': #set $__options['nomodel'] = str( $nomodel_type['shiftsize'] ) #end if ##diag options #if $diag_type['diag_type_selector'] == 'diag': #set $__options['diag'] = { 'fe-min':str( $diag_type['fe-min'] ), 'fe-max':str( $diag_type['fe-max'] ), 'fe-step':str( $diag_type['fe-step'] ) } #end if ${ simplejson.dumps( __options ) }

**What it does** This tool allows ChIP-seq peak calling using MACS. Depending upon selected options, 2 to 6 history items will be created; the first output will be a standard BED file and the last will be an HTML report containing links to download additional files generated by MACS. Up to two each of wig and interval files can be optionally created; the interval files are parsed from the xls output. View the original MACS documentation: http://liulab.dfci.harvard.edu/MACS/00README.html.