# HG changeset patch # User modencode-dcc # Date 1358451399 18000 # Node ID 6ed68e907ff646d69e8a29b9a1f763b9f789c6e7 # Parent 1c5611e52fd01ffddda0d44d61a050cae3456dba Uploaded diff -r 1c5611e52fd0 -r 6ed68e907ff6 spp_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spp_wrapper.xml Thu Jan 17 14:36:39 2013 -0500 @@ -0,0 +1,201 @@ + + SPP cross-correlation analysis package + spp_wrapper.py $options_file $output_narrow_peak $output_region_peak $output_peakshift_file $output_rdata_file $output_plot_file $output_default_file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + major_command['save_narrowpeak_file'] is True + major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' + + + major_command['save_plot_file'] is True + + + major_command['save_regionpeak_file'] is True + major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' + + + major_command['save_peakshift_file'] is True + major_command['major_command_selector'] == 'cross_correlation' or major_command['major_command_selector'] == 'custom' or major_command['major_command_selector'] == 'idr' + + + major_command['save_rdata_file'] is True + major_command['major_command_selector'] == 'peak_calling' or major_command['major_command_selector'] == 'custom' + + + + + <% +import simplejson +%> +#set $__options ={ 'experiment_name':str($experiment_name), 'chip_file':str($major_command.input_chipseq_file1) } + +#if str( $major_command.input_control_file1 ) != 'None': + #set $__options['input_file'] = str( $major_command.input_control_file1 ) +#end if + +##============================================================================= +#if str($major_command.major_command_selector) == 'cross_correlation': + #set $__options['action'] = str( "cross_correlation" ) + #set $__options['rf'] = str( $major_command.replace ) + + #set $__options['out'] = str( $major_command.save_peakshift_file ) + #set $__options['savp'] = str( $major_command.save_plot_file ) +#end if +##============================================================================= +#if str($major_command.major_command_selector) == 'peak_calling': + #set $__options['action'] = str( "peak_calling" ) + #set $__options['fdr'] = str( $major_command.fdr ) + #set $__options['npeak'] = str( $major_command.num_peaks ) + #set $__options['rf'] = str( $major_command.replace ) + + #set $__options['savr'] = str( $major_command.save_regionpeak_file ) + #set $__options['savd'] = str( $major_command.save_rdata_file ) + #set $__options['savn'] = str( $major_command.save_narrowpeak_file ) + #set $__options['savp'] = str( $major_command.save_plot_file ) +#end if +##============================================================================= +#if str($major_command.major_command_selector) == 'idr': + #set $__options['action'] = str( "idr" ) + #set $__options['npeak'] = int( $major_command.num_peaks ) + #set $__options['rf'] = str( $major_command.replace ) + + #set $__options['savr'] = str( $major_command.save_regionpeak_file ) + #set $__options['out'] = str( $major_command.save_peakshift_file ) + #set $__options['savp'] = str( $major_command.save_plot_file ) +#end if +##============================================================================= +#if str($major_command.major_command_selector) == 'custom': + #set $__options['action'] = str( "custom" ) + #set $__options['s'] = str( $major_command.strand_shift ) + #set $__options['x'] = str( $major_command.excluded_strand_shift ) + #set $__options['npeak'] = int( $major_command.num_peaks ) + #set $__options['fdr'] = int( $major_command.fdr ) + #set $__options['rf'] = str( $major_command.replace ) + + #if str($major_command.user_defined_strpeak) == '': + #set $__options['speak'] = str( $major_command.user_defined_strpeak ) + #else: + #set $__options['speak'] = "-speak=$major_command.user_defined_strpeak" + #end if + + #if str($major_command.filter_char) == '': + #set $__options['filtchr'] = str( $major_command.filter_char ) + #else: + #set $__options['filtchr'] = "-filtchr=$major_command.filter_char" + #end if + + #set $__options['out'] = str( $major_command.save_peakshift_file ) + #set $__options['savr'] = str( $major_command.save_regionpeak_file ) + #set $__options['savd'] = str( $major_command.save_rdata_file ) + #set $__options['savn'] = str( $major_command.save_narrowpeak_file ) + #set $__options['savp'] = str( $major_command.save_plot_file ) +#end if + +${ simplejson.dumps( __options ) } + + + + + + +**What it does** + +This tool allows ChIP-seq peak calling using SPP + +This set of programs operate on mapped Illumina single-end read datasets in tagAlign or BAM format. + +View the modified SPP documentation: http://code.google.com/p/phantompeakqualtools/ + +------ + +**Usage** + +**Determine strand cross-correlation peak**: Compute the predominant insert-size (fragment length) based on strand cross-correlation peak. + +**Peak calling**: Call Peaks and regions for punctate binding datasets. + +**IDR analysis**: Compute Data quality measures based on relative phantom peak. + +**Custom settings**: Enables all options available to SPP for custom analysis. + +------ + +**Citation** + +Anshul Kundaje, Computer Science Dept., Stanford University, ENCODE Consortium, Personal Communication, Oct 2010 +Kharchenko PK, Tolstorukov MY, Park PJ, Design and analysis of ChIP-seq experiments for DNA-binding proteins Nat Biotechnol. 2008 Dec;26(12):1351-9 + +Integration of SPP with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org. + +