# HG changeset patch # User jbrayet # Date 1453127445 18000 # Node ID da20d7c414b597d55493d81122aadcc3ed205ee9 # Parent 14ffe4d757203660229a60119f44186e5753d0c2 Uploaded diff -r 14ffe4d75720 -r da20d7c414b5 macs_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs_wrapper.xml Mon Jan 18 09:30:45 2016 -0500 @@ -0,0 +1,237 @@ + + Model-based Analysis of ChIP-Seq + + institutcuriengsintegration/macs:1.0 + + macs_wrapper.py $options_file $output_bed_file $output_extra_files $output_extra_files.files_path + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 json as 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 ), '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. + +------ + +**Citation** + +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. <http://www.ncbi.nlm.nih.gov/pubmed/18798982>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + +