Mercurial > repos > pjbriggs > macs21
changeset 0:06cb587a5e87 draft
Uploaded initial version 2.1.0-4.
| author | pjbriggs |
|---|---|
| date | Tue, 30 Jun 2015 08:16:18 -0400 |
| parents | |
| children | 02a01ea54722 |
| files | README.rst macs21_wrapper.py macs21_wrapper.xml test-data/test_MACS2.1.0_bw_html_report.zip test-data/test_MACS2.1.0_control_lambda.bdg test-data/test_MACS2.1.0_html_report.zip test-data/test_MACS2.1.0_peaks.xls test-data/test_MACS2.1.0_peaks.xls.re_match test-data/test_MACS2.1.0_peaks_narrowPeak.interval test-data/test_MACS2.1.0_summits.bed test-data/test_MACS2.1.0_treat_pileup.bdg test-data/test_MACS2.1.0_treat_pileup.bw test-data/test_region_IP.bed test-data/test_region_Input.bed tool_dependencies.xml |
| diffstat | 15 files changed, 1237 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,99 @@ +MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0) peak calling +================================================================== + +Galaxy tool wrapper for the peak calling function of MACS 2.1.0. MACS has been +developed by Tao Lui +https://github.com/taoliu/MACS/ + +The reference for MACS is: + +- 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 + +Automated installation +====================== + +Installation via the Galaxy Tool Shed will take of installing the tool wrapper and +the MACS 2.1.0 program. + +Manual Installation +=================== + +There are two files to install: + +- ``macs21_wrapper.xml`` (the Galaxy tool definition) +- ``macs21_wrapper.py.sh`` (the Python script wrapper) + +The suggested location is in a ``tools/macs21/`` folder. You will then +need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool +by adding the line: + + <tool file="macs21/macs21_wrapper.xml" /> + +You will also need to install MACS 2.1.0 and its dependencies: + +- https://pypi.python.org/pypi/MACS2 + +and ensure that it's on your Galaxy user's ``PATH`` when running the tool. + +If you want to run the functional tests, copy the sample test files under +sample test files under Galaxy's ``test-data/`` directory. Then: + + ./run_tests.sh -id macs2_wrapper + + +History +======= + +This tool was originally based on the ``modencode-dcc`` MACS2 tool developed +by Ziru Zhou (ziruzhou@gmail.com), specifically the ``16:14f378e35191`` +revision of the tool available via + +- http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 + +This version has been substantially modified both to adapt it to MACS 2.1.0, and +to re-implement the internal workings of the tool to conform with current +practices in invoking commands from Galaxy, and to add new functionality. + +========== ====================================================================== +Version Changes +---------- ---------------------------------------------------------------------- +2.1.0-4 - Remove 'bdgcmp' functionality. +2.1.0-3 - Add tool tests +2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with -B + option; make --mfold defaults consistent. +2.1.0-1 - Initial version +========== ====================================================================== + + +Developers +========== + +This tool is developed on the following GitHub repository: +https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/macs21 + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the ``package_macs21_wrapper.sh`` script. + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs21_wrapper.py Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,262 @@ +#!/bin/env python +# +# Galaxy wrapper to run MACS 2.1 +# +# Completely rewritten from the original macs2 wrapped by Ziru Zhou +# taken from http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 + +import sys +import os +import subprocess +import tempfile +import shutil + +def move_file(working_dir,name,destination): + """Move a file 'name' from 'working_dir' to 'destination' + + """ + if destination is None: + # Nothing to do + return + source = os.path.join(working_dir,name) + if os.path.exists(source): + shutil.move(source,destination) + +def convert_xls_to_interval(xls_file,interval_file,header=None): + """Convert MACS XLS file to interval + + From the MACS readme: "Coordinates in XLS is 1-based which is different with + BED format." + + However this function no longer performs any coordinate conversions, it + simply ensures that any blank or non-data lines are commented out + + """ + fp = open(interval_file,'wb') + if header: + fp.write('#%s\n' % header) + for line in open(xls_file): + # Keep all existing comment lines + if line.startswith('#'): + fp.write(line) + else: + # Split line into fields and test to see if + # the 'start' field is actually an integer + fields = line.split('\t') + if len(fields) > 1: + try: + int(fields[1]) + except ValueError: + # Integer conversion failed so comment out + # "bad" line instead + fields[0] = "#%s" % fields[0] + fp.write( '\t'.join( fields ) ) + fp.close() + +def make_bigwig_from_bedgraph(bedgraph_file,bigwig_file, + chrom_sizes,working_dir=None): + """Make bigWig file from a bedGraph + + The protocol is: + + $ fetchChromSizes.sh mm9 > mm9.chrom.sizes + $ bedClip treat.bedgraph mm9.chrom.sizes treat.clipped + $ bedGraphToBigWig treat.clipped mm9.chrom.sizes treat.bw + + Get the binaries from + http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ + + We skip the fetchChromSizes step if the 'chrom_sizes' + argument supplied a valid file with the chromosome sizes + for the genome build in question. + + """ + print "Generating bigWig from bedGraph..." + # Check for chromosome sizes + if not os.path.exists(chrom_sizes): + # Determine genome build + chrom_sizes = os.path.basename(chrom_sizes) + genome_build = chrom_sizes.split('.')[0] + if genome_build == '?': + # No genome build set + sys.stderr.write("ERROR genome build not set, cannot get sizes for '?'\n") + sys.stderr.write("Assign a genome build to your input dataset and rerun\n") + sys.exit(1) + print "Missing chrom sizes file, attempting to fetch for '%s'" % genome_build + # Run fetchChromSizes + chrom_sizes = os.path.join(working_dir,chrom_sizes) + stderr_file = os.path.join(working_dir,"fetchChromSizes.stderr") + cmd = "fetchChromSizes %s" % genome_build + print "Running %s" % cmd + proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir, + stdout=open(chrom_sizes,'wb'), + stderr=open(stderr_file,'wb')) + proc.wait() + # Copy stderr from fetchChromSizes for information only + for line in open(stderr_file,'r'): + print line.strip() + os.remove(stderr_file) + # Check that the sizes file was downloaded + if not os.path.exists(chrom_sizes): + sys.stderr.write("Failed to download chrom sizes for '%s'\n" % genome_build) + sys.exit(1) + # Run bedClip + treat_clipped = "%s.clipped" % os.path.basename(bedgraph_file) + cmd = "bedClip %s %s %s" % (bedgraph_file,chrom_sizes,treat_clipped) + print "Running %s" % cmd + proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir) + proc.wait() + # Check that clipped file exists + treat_clipped = os.path.join(working_dir,treat_clipped) + if not os.path.exists(treat_clipped): + sys.stderr.write("Failed to create clipped bed file\n") + sys.exit(1) + # Run bedGraphToBigWig + cmd = "bedGraphToBigWig %s %s %s" % (treat_clipped,chrom_sizes, + bigwig_file) + print "Running %s" % cmd + proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir) + proc.wait() + # Clean up temporary chrom length file + if os.path.dirname(chrom_sizes) == working_dir: + print "Removing temporary chrom sizes file" + os.remove(chrom_sizes) + +if __name__ == "__main__": + + # Echo the command line + print ' '.join(sys.argv) + + # Initialise output files - values are set by reading from + # the command line supplied by the Galaxy wrapper + output_extra_html = None + output_extra_path = None + output_broadpeaks = None + output_gappedpeaks = None + output_narrowpeaks = None + output_treat_pileup = None + output_lambda_bedgraph = None + output_bigwig = None + output_xls_to_interval_peaks_file = None + output_peaks = None + output_bdgcmp = None + + # Other initialisations + chrom_sizes_file = None + + # Build the MACS 2.1 command line + # Initial arguments are always the same: command & input ChIP-seq file name + cmdline = ["macs2 %s -t %s" % (sys.argv[1],sys.argv[2])] + + # Process remaining args + for arg in sys.argv[3:]: + if arg.startswith('--format='): + # Convert format to uppercase + format_ = arg.split('=')[1].upper() + cmdline.append("--format=%s" % format_) + elif arg.startswith('--name='): + # Replace whitespace in name with underscores + experiment_name = '_'.join(arg.split('=')[1].split()) + cmdline.append("--name=%s" % experiment_name) + elif arg.startswith('--length='): + # Extract chromosome size file + chrom_sizes_file = arg.split('=')[1] + elif arg.startswith('--output-'): + # Handle destinations for output files + arg0,filen = arg.split('=') + if arg0 == '--output-summits': + output_summits = filen + elif arg0 == '--output-extra-files': + output_extra_html = filen + elif arg0 == '--output-extra-files-path': + output_extra_path = filen + elif arg0 == '--output-broadpeaks': + output_broadpeaks = filen + elif arg0 == '--output-gappedpeaks': + output_gappedpeaks = filen + elif arg0 == '--output-narrowpeaks': + output_narrowpeaks = filen + elif arg0 == '--output-pileup': + output_treat_pileup = filen + elif arg0 == '--output-lambda-bedgraph': + output_lambda_bedgraph = filen + elif arg0 == '--output-bigwig': + output_bigwig = filen + elif arg0 == '--output-xls-to-interval': + output_xls_to_interval_peaks_file = filen + elif arg0 == '--output-peaks': + output_peaks = filen + else: + # Pass remaining args directly to MACS + # command line + cmdline.append(arg) + + cmdline = ' '.join(cmdline) + print "Generated command line:\n%s" % cmdline + + # Execute MACS2 + # + # Make a working directory + working_dir = tempfile.mkdtemp() + # + # Collect stderr in a file for reporting later + stderr_filen = tempfile.NamedTemporaryFile().name + # + # Run MACS2 + proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir, + stderr=open(stderr_filen,'wb')) + proc.wait() + + # Run R script to create PDF from model script + if os.path.exists(os.path.join(working_dir,"%s_model.r" % experiment_name)): + cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % \ + (experiment_name, experiment_name) + proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir) + proc.wait() + + # Convert XLS to interval, if requested + if output_xls_to_interval_peaks_file is not None: + peaks_xls_file = os.path.join(working_dir,'%s_peaks.xls' % experiment_name ) + if os.path.exists(peaks_xls_file): + convert_xls_to_interval(peaks_xls_file,output_xls_to_interval_peaks_file, + header='peaks file') + + # Create bigWig from bedGraph, if requested + if output_bigwig is not None: + treat_bedgraph_file = os.path.join(working_dir,'%s_treat_pileup.bdg' % experiment_name) + if os.path.exists(treat_bedgraph_file): + make_bigwig_from_bedgraph(treat_bedgraph_file,output_bigwig, + chrom_sizes_file,working_dir) + + # Move MACS2 output files from working dir to their final destinations + move_file(working_dir,"%s_summits.bed" % experiment_name,output_summits) + move_file(working_dir,"%s_peaks.xls" % experiment_name,output_peaks) + move_file(working_dir,"%s_peaks.narrowPeak" % experiment_name,output_narrowpeaks) + move_file(working_dir,"%s_peaks.broadPeak" % experiment_name,output_broadpeaks) + move_file(working_dir,"%s_peaks.gappedPeak" % experiment_name,output_gappedpeaks) + move_file(working_dir,"%s_treat_pileup.bdg" % experiment_name,output_treat_pileup) + move_file(working_dir,"%s_control_lambda.bdg" % experiment_name,output_lambda_bedgraph) + move_file(working_dir,"bdgcmp_out.bdg",output_bdgcmp) + + # Move remaining file to the 'extra files' path and link from the HTML + # file to allow user to access them from within Galaxy + html_file = open(output_extra_html,'wb') + html_file.write('<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name) + # Make the 'extra files' directory + os.mkdir(output_extra_path) + # Move the files + for filen in sorted(os.listdir(working_dir)): + shutil.move(os.path.join(working_dir,filen), + os.path.join(output_extra_path,filen)) + html_file.write( '<li><a href="%s">%s</a></li>\n' % (filen,filen)) + # All files moved, close out HTML + html_file.write( '</ul></p>\n' ) + # Append any stderr output + html_file.write('<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % + open(stderr_filen,'rb').read()) + html_file.write('</body></html>\n') + html_file.close() + + # Clean up the working directory and files + os.unlink(stderr_filen) + os.rmdir(working_dir)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs21_wrapper.xml Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,398 @@ +<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-4"> + <description>Model-based Analysis of ChIP-Seq: peak calling</description> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.9">numpy</requirement> + <requirement type="package" version="2.1.0.20140616">macs2</requirement> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="1.0">ucsc_tools_for_macs21</requirement> + </requirements> + <version_command>macs2 --version</version_command> + <command interpreter="python"> + macs21_wrapper.py callpeak + ## + ## ChIP-seq input + $input_chipseq_file1 + ## + ## ChIP-seq control + #if str($input_control_file1) != 'None' + -c $input_control_file1 + #end if + ## + --format=$input_chipseq_file1.extension + --name="$experiment_name" + --bw=$bw + ## + ## Genome size + #if str($genome_size.gsize) == '' + --gsize=$genome_size.user_defined_gsize + #else: + --gsize=$genome_size.gsize + #end if + ## + ## Broad peaks + #if str($broad_options.broad_regions) == 'broad' + --broad --broad-cutoff=$broad_options.broad_cutoff + #end if + ## + ## (no)model options + #if str($nomodel_type.nomodel_type_selector) == 'nomodel' + --nomodel --extsize=$nomodel_type.extsize + #end if + ## + ## pq value select options + #if str($pq_options.pq_options_selector) == 'qvalue' + --qvalue=$pq_options.qvalue + #else + --pvalue=$pq_options.pvalue + #end if + ## + ## Bedgraph options + #if $bdg_options.bdg + -B $bdg_options.spmr + #end if + ## + ## Advanced options + #if $advanced_options.advanced_options_selector + --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi + $advanced_options.nolambda + $advanced_options.call_summits + #if str($advanced_options.keep_duplicates.keep_dup) == '' + --keep-dup $advanced_options.keep_duplicates.maximum_tags + #else + --keep-dup $advanced_options.keep_duplicates.keep_dup + #end if + #else + ## Defaults if advanced options not set + --mfold 10 30 --keep-dup 1 + #end if + ## + ## Output files + --output-summits=$output_summits_bed_file + --output-extra-files=$output_extra_files + --output-extra-files-path=$output_extra_files.files_path + ## + ## Narrow/broad peak outputs + #if str($broad_options.broad_regions) == 'broad' + --output-broadpeaks=$output_broadpeaks_file + --output-gappedpeaks=$output_gappedpeaks_file + #else + --output-narrowpeaks=$output_narrowpeaks_file + #end if + ## + ## Bedgraph outputs + #if $bdg_options.bdg + --output-pileup=$output_treat_pileup_file + --output-lambda-bedgraph=$output_lambda_bedgraph_file + #if $bdg_options.make_bigwig + --output-bigwig=$output_bigwig_file + --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${input_chipseq_file1.dbkey}.len + #end if + #end if + ## + ## XLS/interval output + #if str($xls_to_interval) == 'True' + --output-xls-to-interval=$output_xls_to_interval_peaks_file + #else + --output-peaks=$output_peaks_file + #end if + </command> + <inputs> + <!--experiment name used as base for output file names --> + <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50" + label="Experiment Name"/> + <!--choose 'broad' or 'narrow' regions--> + <conditional name="broad_options"> + <param name="broad_regions" type="select" label="Type of region to call" + help="Broad regions are formed by linking nearby enriched regions"> + <option value="" selected="true">Narrow regions</option> + <option value="broad">Broad regions</option> + </param> + <when value="broad"> + <param name="broad_cutoff" type="float" + label="Cutoff for broad regions" + value="0.1" help="default: 0.1 (--broad-cutoff)"/> + </when> + </conditional> + <param name="input_chipseq_file1" type="data" format="bed,sam,bam" + label="ChIP-seq read file" /> + <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" + label="ChIP-seq control read file" /> + <conditional name="genome_size"> + <param name="gsize" type="select" label="Effective genome size" + help="Either pre-defined (for common organisms), or user-defined (--gsize)"> + <option value="hs" selected="true">Human (2.7e9)</option> + <option value="mm">Mouse (1.87e9)</option> + <option value="ce">C. elegans (9e7)</option> + <option value="dm">Fruitfly (1.2e8)</option> + <option value="">User-defined</option> + </param> + <when value=""> + <!-- User-defined effective genome size --> + <param name="user_defined_gsize" type="float" value="" + label="Enter effective genome size (number of bases)" + help="e.g. '1.0e+9' or '1000000000'" /> + </when> + </conditional> + <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> + <param name="xls_to_interval" label="Include XLS file from MACS" + type="boolean" truevalue="True" falsevalue="False" checked="True" + 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."/> + + <conditional name="bdg_options"> + <param name="bdg" + label="Save treatment and control lambda pileups in bedGraph" + type="boolean" truevalue="-B" falsevalue="" checked="False" /> + <when value="-B"> + <param name="spmr" + type="boolean" truevalue="--SPMR" falsevalue="" checked="False" + label="Save signal per million reads for fragment pileup profiles" + help="(--SPMR)" /> + <param name="make_bigwig" type="boolean" checked="True" + truevalue="True" falsevalue="" + label="Also generate bigWig file from bedGraph" + help="bigWig file can used in subsequent analyses e.g. CEAS" /> + </when> + <when value=""> + <!-- Display nothing --> + </when> + </conditional> + + <conditional name="pq_options"> + <param name="pq_options_selector" type="select" + label="Select p-value or q-value" help="default uses q-value"> + <option value="qvalue">q-value</option> + <option value="pvalue">p-value</option> + </param> + <when value="pvalue"> + <param name="pvalue" type="float" + label="p-value cutoff for binding region detection" + value="1e-2" help="default: 1e-2 (--pvalue)"/> + </when> + <when value="qvalue"> + <param name="qvalue" type="float" + label="q-value cutoff for binding region detection" + value="0.01" help="default: 0.01 (--qvalue)"/> + </when> + </conditional> + <conditional name="advanced_options"> + <param name="advanced_options_selector" + type="boolean" truevalue="on" falsevalue="off" checked="False" + label="Use advanced options?" /> + <when value="on"> + <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)"/> + <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)"/> + <param name="nolambda" + label="Use fixed background lambda as local lambda for every binding region" + type="boolean" truevalue="--nolambda" falsevalue="" checked="False" + help="(--nolambda)"/> + <param name="call_summits" + label="Detect subpeaks within binding region" + type="boolean" truevalue="--call-summits" falsevalue="" checked="False" + help="(--call-summits)"/> + <conditional name="keep_duplicates"> + <param name="keep_dup" type="select" + label="Use of duplicate reads"> + <option value="auto">Automatically calculate maximum number of duplicates to keep (auto)</option> + <option value="all">Use all duplicates (all)</option> + <option value="" selected="true">Manually specify maxium number of duplicates</option> + </param> + <when value=""> + <param name="maximum_tags" type="integer" value="1" + label="Maxium number of duplicated tags to keep at each location"/> + </when> + </conditional> + </when> + <when value="off"> + <!--display nothing--> + </when> + </conditional> + <conditional name="nomodel_type"> + <param name="nomodel_type_selector" type="select" label="Build Model"> + <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option> + <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option> + </param> + <when value="nomodel"> + <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)"/> + </when> + </conditional> + </inputs> + + <outputs> + <!--callpeaks output--> + <data name="output_extra_files" format="html" + label="${tool.name}: callpeak on ${on_string} (html report)"> + </data> + <data name="output_summits_bed_file" format="bed" + label="${tool.name}: callpeak on ${on_string} (summits: bed)"> + </data> + <data name="output_peaks_file" format="xls" + label="${tool.name}: callpeak on ${on_string} (peaks: xls)"> + <filter>xls_to_interval is False</filter> + </data> + <data name="output_narrowpeaks_file" format="interval" + label="${tool.name}: callpeak on ${on_string} (peaks: narrowPeak)"> + <filter>broad_options['broad_regions'] == ''</filter> + </data> + <data name="output_broadpeaks_file" format="interval" + label="${tool.name}: callpeak on ${on_string} (peaks: broadPeak)"> + <filter>broad_options['broad_regions'] == 'broad'</filter> + </data> + <data name="output_gappedpeaks_file" format="interval" + label="${tool.name}: callpeak on ${on_string} (peaks: gappedPeak)"> + <filter>broad_options['broad_regions'] == 'broad'</filter> + </data> + <data name="output_xls_to_interval_peaks_file" format="interval" + label="${tool.name}: callpeak on ${on_string} (peaks: interval)"> + <filter>xls_to_interval is True</filter> + </data> + <data name="output_treat_pileup_file" format="bedgraph" + label="${tool.name}: callpeak on ${on_string} (treat pileup: bedGraph)"> + <filter>bdg_options['bdg'] is True</filter> + </data> + <data name="output_lambda_bedgraph_file" format="bedgraph" + label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)"> + <filter>bdg_options['bdg'] is True</filter> + </data> + <data name="output_bigwig_file" format="bigwig" + label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)"> + <filter>bdg_options['bdg'] is True</filter> + <filter>bdg_options['make_bigwig'] is True</filter> + </data> + </outputs> + <tests> + <!-- Peak calling without bigwig output --> + <test> + <!-- Inputs --> + <param name="experiment_name" value="test_MACS2.1.0" /> + <param name="broad_regions" value="" /> + <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" + ftype="bed" /> + <param name="input_control_file1" value="test_region_Input.bed" + ftype="bed" /> + <param name="gsize" value="" /> + <param name="user_defined_gsize" value="775000000.0" /> + <param name="bw" value="300" /> + <param name="xls_to_interval" value="true" /> + <param name="bdg_options|bdg" value="-B" /> + <param name="bdg_options|spmr" value="--SPMR" /> + <param name="bdg_options|make_bigwig" value="false" /> + <param name="pq_options_selector" value="qvalue" /> + <param name="qvalue" value="0.05" /> + <param name="advanced_options_selector" value="true" /> + <param name="advanced_options|mfoldlo" value="5" /> + <param name="advanced_options|mfoldhi" value="50" /> + <param name="advanced_options|nolambda" value="" /> + <param name="advanced_options|call_summits" value="" /> + <param name="advanced_options|keep_duplicates" value="" /> + <param name="advanced_options|maximum_tags" value="1" /> + <param name="nomodel_type_selector" value="nomodel" /> + <param name="nomodel_type|extsize" value="243" /> + <!-- Outputs --> + <output name="output_extra_files" file="test_MACS2.1.0_html_report.zip" + compare="sim_size" delta="1500" /> + <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" /> + <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" /> + <output name="output_xls_to_interval_peaks_file" + file="test_MACS2.1.0_peaks.xls.re_match" + compare="re_match" lines_diff="1" /> + <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" /> + <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" /> + </test> + <!-- Peak calling with bigwig output --> + <test> + <!-- Inputs --> + <param name="experiment_name" value="test_MACS2.1.0" /> + <param name="broad_regions" value="" /> + <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" + ftype="bed" /> + <param name="input_control_file1" value="test_region_Input.bed" + ftype="bed" /> + <param name="gsize" value="" /> + <param name="user_defined_gsize" value="775000000.0" /> + <param name="bw" value="300" /> + <param name="xls_to_interval" value="true" /> + <param name="bdg_options|bdg" value="-B" /> + <param name="bdg_options|spmr" value="--SPMR" /> + <param name="bdg_options|make_bigwig" value="true" /> + <param name="pq_options_selector" value="qvalue" /> + <param name="qvalue" value="0.05" /> + <param name="advanced_options_selector" value="true" /> + <param name="advanced_options|mfoldlo" value="5" /> + <param name="advanced_options|mfoldhi" value="50" /> + <param name="advanced_options|nolambda" value="" /> + <param name="advanced_options|call_summits" value="" /> + <param name="advanced_options|keep_duplicates" value="" /> + <param name="advanced_options|maximum_tags" value="1" /> + <param name="nomodel_type_selector" value="nomodel" /> + <param name="nomodel_type|extsize" value="243" /> + <!-- Outputs --> + <output name="output_extra_files" file="test_MACS2.1.0_bw_html_report.zip" + compare="sim_size" delta="2500" /> + <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" /> + <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" /> + <output name="output_xls_to_interval_peaks_file" + file="test_MACS2.1.0_peaks.xls.re_match" + compare="re_match" lines_diff="1" /> + <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" /> + <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" /> + <output name="output_bigwig_file" file="test_MACS2.1.0_treat_pileup.bw" + compare="sim_size" /> + </test> + </tests> + <help> +**What it does** + +MACS (Model-based Analysis of ChIP-seq) 2.1.0 provides algorithms for identifying +transcript factor binding sites. The program can be used either for ChIP-Seq data alone, +or with control sample data to improve specificity. + +View the MACS2 documentation at: +https://github.com/taoliu/MACS/blob/master/README.rst + +------ + +**Usage** + +The tool interfaces with the **callpeak** function in MACS, which calls peaks from +alignment results. + +------ + +**Credits** + +This Galaxy tool was based on the MACS2 tool hosted in the Galaxy toolshed at + + * http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 + +(specifically the 16:14f378e35191 revision of the tool) which is credited to Ziru +Zhou. This version is a reimplemented version developed within the Bioinformatics +Core Facility at the University of Manchester, which uses more up-to-date Galaxy +syntax and adds some extra features. + +The tool runs Tao Liu's MACS2 software: + + * https://github.com/taoliu/MACS + +The reference for MACS is: + + * 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. + +Please kindly acknowledge both this Galaxy tool and the MACS2 package if you +use it. + </help> + <citations> + <!-- + See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set + Can be either DOI or Bibtex + Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex + --> + <citation type="doi">10.1186/gb-2008-9-9-r137</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_control_lambda.bdg Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,153 @@ +chr26 0 4102915 0.31355 +chr26 4102915 4103978 486.00000 +chr26 4103978 4103998 972.00000 +chr26 4103998 4104449 1458.00000 +chr26 4104449 4105233 1944.00000 +chr26 4105233 4105326 2430.00000 +chr26 4105326 4105398 2916.00000 +chr26 4105398 4105644 3402.00024 +chr26 4105644 4105855 3888.00000 +chr26 4105855 4105980 4374.00000 +chr26 4105980 4106825 4860.00000 +chr26 4106825 4107471 5346.00049 +chr26 4107471 4107794 5832.00000 +chr26 4107794 4108037 20000.00000 +chr26 4108037 4108498 6804.00049 +chr26 4108498 4108857 9720.00000 +chr26 4108857 4108877 20000.00000 +chr26 4108877 4109100 40000.00000 +chr26 4109100 4109120 20000.00000 +chr26 4109120 4109327 14580.00000 +chr26 4109327 4109570 20000.00000 +chr26 4109570 4109733 8262.00000 +chr26 4109733 4109826 9720.00000 +chr26 4109826 4109898 14580.00000 +chr26 4109898 4109949 19440.00000 +chr26 4109949 4110111 14580.00000 +chr26 4110111 4110204 20000.00000 +chr26 4110204 4110276 40000.00000 +chr26 4110276 4110354 60000.00000 +chr26 4110354 4110447 40000.00000 +chr26 4110447 4110480 24300.00195 +chr26 4110480 4110733 29160.00000 +chr26 4110733 4110765 40000.00000 +chr26 4110765 4110826 24300.00195 +chr26 4110826 4110859 20000.00000 +chr26 4110859 4110976 40000.00000 +chr26 4110976 4111102 20000.00000 +chr26 4111102 4111144 14580.00000 +chr26 4111144 4111325 12150.00098 +chr26 4111325 4111355 14580.00000 +chr26 4111355 4111704 12636.00000 +chr26 4111704 4111947 20000.00000 +chr26 4111947 4112349 13608.00098 +chr26 4112349 4112592 20000.00000 +chr26 4112592 4112706 14580.00000 +chr26 4112706 4112862 20000.00000 +chr26 4112862 4112949 40000.00000 +chr26 4112949 4113105 20000.00000 +chr26 4113105 4113145 13608.00098 +chr26 4113145 4113327 14580.00000 +chr26 4113327 4113524 13608.00098 +chr26 4113524 4113767 20000.00000 +chr26 4113767 4113775 13608.00098 +chr26 4113775 4114145 14580.00000 +chr26 4114145 4114146 12636.00000 +chr26 4114146 4114154 20000.00000 +chr26 4114154 4114389 40000.00000 +chr26 4114389 4114686 24300.00195 +chr26 4114686 4114732 40000.00000 +chr26 4114732 4114855 60000.00000 +chr26 4114855 4114929 40000.00000 +chr26 4114929 4114975 20000.00000 +chr26 4114975 4115116 14580.00000 +chr26 4115116 4115234 19440.00000 +chr26 4115234 4115308 14580.00000 +chr26 4115308 4115326 12150.00098 +chr26 4115326 4115398 11664.00000 +chr26 4115398 4115495 11178.00000 +chr26 4115495 4115635 20000.00000 +chr26 4115635 4115837 24300.00195 +chr26 4115837 4115891 29160.00000 +chr26 4115891 4115990 40000.00000 +chr26 4115990 4116014 60000.00000 +chr26 4116014 4116072 80000.00000 +chr26 4116072 4116134 60000.00000 +chr26 4116134 4116215 40000.00000 +chr26 4116215 4116233 60000.00000 +chr26 4116233 4116257 40000.00000 +chr26 4116257 4116366 29160.00000 +chr26 4116366 4116450 34020.00000 +chr26 4116450 4116512 29160.00000 +chr26 4116512 4116611 24300.00195 +chr26 4116611 4116745 20000.00000 +chr26 4116745 4116831 40000.00000 +chr26 4116831 4116988 20000.00000 +chr26 4116988 4117136 11664.00000 +chr26 4117136 4117471 12150.00098 +chr26 4117471 4117730 11664.00000 +chr26 4117730 4117973 20000.00000 +chr26 4117973 4117983 11178.00000 +chr26 4117983 4118141 10692.00098 +chr26 4118141 4118645 11178.00000 +chr26 4118645 4118886 10692.00098 +chr26 4118886 4118904 11178.00000 +chr26 4118904 4119267 11664.00000 +chr26 4119267 4119275 11178.00000 +chr26 4119275 4119282 10692.00098 +chr26 4119282 4119525 20000.00000 +chr26 4119525 4119734 11178.00000 +chr26 4119734 4119808 10692.00098 +chr26 4119808 4119854 10206.00000 +chr26 4119854 4120286 9720.00000 +chr26 4120286 4120399 10206.00000 +chr26 4120399 4120642 20000.00000 +chr26 4120642 4120714 9720.00000 +chr26 4120714 4120957 20000.00000 +chr26 4120957 4120959 14580.00000 +chr26 4120959 4121021 19440.00000 +chr26 4121021 4121066 14580.00000 +chr26 4121066 4121216 19440.00000 +chr26 4121216 4121338 20000.00000 +chr26 4121338 4121445 40000.00000 +chr26 4121445 4121459 60000.00000 +chr26 4121459 4121581 40000.00000 +chr26 4121581 4121688 20000.00000 +chr26 4121688 4121837 19440.00000 +chr26 4121837 4121959 14580.00000 +chr26 4121959 4122015 9720.00000 +chr26 4122015 4122258 20000.00000 +chr26 4122258 4122851 8262.00000 +chr26 4122851 4123020 7776.00000 +chr26 4123020 4123263 20000.00000 +chr26 4123263 4123386 7776.00000 +chr26 4123386 4123404 9720.00000 +chr26 4123404 4123641 14580.00000 +chr26 4123641 4123764 9720.00000 +chr26 4123764 4123783 20000.00000 +chr26 4123783 4124007 40000.00000 +chr26 4124007 4124026 20000.00000 +chr26 4124026 4124386 14580.00000 +chr26 4124386 4124396 9720.00000 +chr26 4124396 4124639 20000.00000 +chr26 4124639 4124786 9234.00000 +chr26 4124786 4125017 9720.00000 +chr26 4125017 4125164 9234.00000 +chr26 4125164 4125407 20000.00000 +chr26 4125407 4125836 9234.00000 +chr26 4125836 4126337 8748.00000 +chr26 4126337 4126363 8262.00000 +chr26 4126363 4126459 9720.00000 +chr26 4126459 4126509 14580.00000 +chr26 4126509 4126699 19440.00000 +chr26 4126699 4126742 20000.00000 +chr26 4126742 4126837 40000.00000 +chr26 4126837 4126887 60000.00000 +chr26 4126887 4126942 80000.00000 +chr26 4126942 4126985 60000.00000 +chr26 4126985 4127080 40000.00000 +chr26 4127080 4127130 20000.00000 +chr26 4127130 4127320 19440.00000 +chr26 4127320 4127363 14580.00000 +chr26 4127363 4127459 9720.00000 +chr26 4127459 4127761 6804.00049
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_peaks.xls Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,29 @@ +#peaks file +# This file is generated by MACS version 2.1.0.20140616 +# Command line: callpeak -t /home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_46.dat -c /home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_45.dat --format=BED --name=test_MACS2.1.0 --bw=300 --gsize=775000000.0 --nomodel --extsize=243 --qvalue=0.05 -B --SPMR --mfold 5 50 --keep-dup 1 +# ARGUMENTS LIST: +# name = test_MACS2.1.0 +# format = BED +# ChIP-seq file = ['/home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_46.dat'] +# control file = ['/home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_45.dat'] +# effective genome size = 7.75e+08 +# band width = 300 +# model fold = [5, 50] +# qvalue cutoff = 5.00e-02 +# Larger dataset will be scaled towards smaller dataset. +# Range for calculating regional lambda is: 1000 bps and 10000 bps +# Broad region calling is off +# MACS will save fragment pileup signal per million reads + +# tag size is determined as 50 bps +# total tags in treatment: 50 +# tags after filtering in treatment: 50 +# maximum duplicate tags at the same position in treatment = 1 +# Redundant rate in treatment: 0.00 +# total tags in control: 50 +# tags after filtering in control: 50 +# maximum duplicate tags at the same position in control = 1 +# Redundant rate in control: 0.00 +# d = 243 +#chr start end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name +chr26 4118914 4119282 369 4119130 9.00 9.13132 6.31632 2.51561 test_MACS2.1.0_peak_1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_peaks.xls.re_match Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,29 @@ +\#peaks\ file +\#\ This\ file\ is\ generated\ by\ MACS\ version\ 2\.1\.0\.20140616 +\#\ Command\ line\:\ callpeak\ \-t\ .* \-c\ .* \-\-format\=BED\ \-\-name\=test\_MACS2\.1\.0\ \-\-bw\=300\ \-\-gsize\=775000000\.0\ \-\-nomodel\ \-\-extsize\=243\ \-\-qvalue\=0\.05\ \-B\ \-\-SPMR\ \-\-mfold\ 5\ 50\ \-\-keep\-dup\ 1 +\#\ ARGUMENTS\ LIST\: +\#\ name\ \=\ test\_MACS2\.1\.0 +\#\ format\ \=\ BED +\#\ ChIP\-seq\ file\ \=\ \[\'.*\'\] +\#\ control\ file\ \=\ \[\'.*\'\] +\#\ effective\ genome\ size\ \=\ 7\.75e\+08 +\#\ band\ width\ \=\ 300 +\#\ model\ fold\ \=\ \[5\,\ 50\] +\#\ qvalue\ cutoff\ \=\ 5\.00e\-02 +\#\ Larger\ dataset\ will\ be\ scaled\ towards\ smaller\ dataset\. +\#\ Range\ for\ calculating\ regional\ lambda\ is\:\ 1000\ bps\ and\ 10000\ bps +\#\ Broad\ region\ calling\ is\ off +\#\ MACS\ will\ save\ fragment\ pileup\ signal\ per\ million\ reads + +\#\ tag\ size\ is\ determined\ as\ 50\ bps +\#\ total\ tags\ in\ treatment\:\ 50 +\#\ tags\ after\ filtering\ in\ treatment\:\ 50 +\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ treatment\ \=\ 1 +\#\ Redundant\ rate\ in\ treatment\:\ 0\.00 +\#\ total\ tags\ in\ control\:\ 50 +\#\ tags\ after\ filtering\ in\ control\:\ 50 +\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ control\ \=\ 1 +\#\ Redundant\ rate\ in\ control\:\ 0\.00 +\#\ d\ \=\ 243 +\#chr\ start\ end\ length\ abs\_summit\ pileup\ \-log10\(pvalue\)\ fold\_enrichment\ \-log10\(qvalue\)\ name +chr26\ 4118914\ 4119282\ 369\ 4119130\ 9\.00\ 9\.13132\ 6\.31632\ 2\.51561\ test\_MACS2\.1\.0\_peak\_1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_peaks_narrowPeak.interval Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,1 @@ +chr26 4118913 4119282 test_MACS2.1.0_peak_1 25 . 6.31632 9.13132 2.51561 216
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_summits.bed Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,1 @@ +chr26 4119129 4119130 test_MACS2.1.0_peak_1 2.51561
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_treat_pileup.bdg Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,100 @@ +chr26 0 4107561 0.00000 +chr26 4107561 4107804 20000.00000 +chr26 4107804 4108165 0.00000 +chr26 4108165 4108408 20000.00000 +chr26 4108408 4108531 0.00000 +chr26 4108531 4108774 20000.00000 +chr26 4108774 4109009 0.00000 +chr26 4109009 4109252 20000.00000 +chr26 4109252 4109506 0.00000 +chr26 4109506 4109749 20000.00000 +chr26 4109749 4109782 0.00000 +chr26 4109782 4110025 20000.00000 +chr26 4110025 4110080 0.00000 +chr26 4110080 4110323 20000.00000 +chr26 4110323 4111276 0.00000 +chr26 4111276 4111519 20000.00000 +chr26 4111519 4112110 0.00000 +chr26 4112110 4112353 20000.00000 +chr26 4112353 4112762 0.00000 +chr26 4112762 4113005 20000.00000 +chr26 4113005 4113579 0.00000 +chr26 4113579 4113822 20000.00000 +chr26 4113822 4113899 0.00000 +chr26 4113899 4114142 20000.00000 +chr26 4114142 4115021 0.00000 +chr26 4115021 4115264 20000.00000 +chr26 4115264 4115555 0.00000 +chr26 4115555 4115792 20000.00000 +chr26 4115792 4115798 40000.00000 +chr26 4115798 4116035 20000.00000 +chr26 4116035 4116615 0.00000 +chr26 4116615 4116858 20000.00000 +chr26 4116858 4116931 0.00000 +chr26 4116931 4116988 20000.00000 +chr26 4116988 4117174 40000.00000 +chr26 4117174 4117231 20000.00000 +chr26 4117231 4117308 0.00000 +chr26 4117308 4117551 20000.00000 +chr26 4117551 4117615 0.00000 +chr26 4117615 4117642 20000.00000 +chr26 4117642 4117737 40000.00000 +chr26 4117737 4117858 60000.00000 +chr26 4117858 4117885 40000.00000 +chr26 4117885 4117905 20000.00000 +chr26 4117905 4117980 40000.00000 +chr26 4117980 4118037 20000.00000 +chr26 4118037 4118122 40000.00000 +chr26 4118122 4118148 60000.00000 +chr26 4118148 4118280 40000.00000 +chr26 4118280 4118365 20000.00000 +chr26 4118365 4118516 0.00000 +chr26 4118516 4118531 20000.00000 +chr26 4118531 4118561 40000.00000 +chr26 4118561 4118753 60000.00000 +chr26 4118753 4118759 80000.00000 +chr26 4118759 4118774 60000.00000 +chr26 4118774 4118804 40000.00000 +chr26 4118804 4118812 20000.00000 +chr26 4118812 4118827 40000.00000 +chr26 4118827 4118852 60000.00000 +chr26 4118852 4118898 80000.00000 +chr26 4118898 4118913 100000.00000 +chr26 4118913 4118963 120000.00000 +chr26 4118963 4118967 140000.00000 +chr26 4118967 4118996 160000.00000 +chr26 4118996 4119022 140000.00000 +chr26 4119022 4119047 160000.00000 +chr26 4119047 4119055 180000.00000 +chr26 4119055 4119070 160000.00000 +chr26 4119070 4119077 140000.00000 +chr26 4119077 4119095 160000.00000 +chr26 4119095 4119103 140000.00000 +chr26 4119103 4119118 160000.00000 +chr26 4119118 4119141 180000.00000 +chr26 4119141 4119156 160000.00000 +chr26 4119156 4119163 140000.00000 +chr26 4119163 4119168 160000.00000 +chr26 4119168 4119206 180000.00000 +chr26 4119206 4119210 160000.00000 +chr26 4119210 4119265 140000.00000 +chr26 4119265 4119290 120000.00000 +chr26 4119290 4119320 100000.00000 +chr26 4119320 4119346 80000.00000 +chr26 4119346 4119361 60000.00000 +chr26 4119361 4119406 40000.00000 +chr26 4119406 4119411 20000.00000 +chr26 4119411 4122292 0.00000 +chr26 4122292 4122535 20000.00000 +chr26 4122535 4124351 0.00000 +chr26 4124351 4124452 20000.00000 +chr26 4124452 4124594 40000.00000 +chr26 4124594 4124695 20000.00000 +chr26 4124695 4125766 0.00000 +chr26 4125766 4125809 20000.00000 +chr26 4125809 4126009 40000.00000 +chr26 4126009 4126052 20000.00000 +chr26 4126052 4126452 0.00000 +chr26 4126452 4126695 20000.00000 +chr26 4126695 4127518 0.00000 +chr26 4127518 4127761 20000.00000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_region_IP.bed Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,50 @@ +chr26 4107754 4107804 D3YGT8Q1:279:C6ND0ACXX:1:2307:11522:80910 255 - +chr26 4108358 4108408 D3YGT8Q1:279:C6ND0ACXX:1:1205:12295:24447 255 - +chr26 4108724 4108774 D3YGT8Q1:279:C6ND0ACXX:1:1212:7461:43211 255 - +chr26 4109009 4109059 D3YGT8Q1:279:C6ND0ACXX:1:2306:13509:41113 255 + +chr26 4109506 4109556 D3YGT8Q1:279:C6ND0ACXX:1:1316:8894:99440 255 + +chr26 4109975 4110025 D3YGT8Q1:279:C6ND0ACXX:1:1314:13929:4230 255 - +chr26 4110080 4110130 D3YGT8Q1:279:C6ND0ACXX:1:2116:20242:70310 255 + +chr26 4111276 4111326 D3YGT8Q1:279:C6ND0ACXX:1:1113:7893:68431 255 + +chr26 4112303 4112353 D3YGT8Q1:279:C6ND0ACXX:1:1312:10267:49823 255 - +chr26 4112955 4113005 D3YGT8Q1:279:C6ND0ACXX:1:1306:15218:93662 255 - +chr26 4113579 4113629 D3YGT8Q1:279:C6ND0ACXX:1:2101:12665:18403 255 + +chr26 4114092 4114142 D3YGT8Q1:279:C6ND0ACXX:1:2210:5952:64144 255 - +chr26 4115214 4115264 D3YGT8Q1:279:C6ND0ACXX:1:1214:9389:76439 255 - +chr26 4115748 4115798 D3YGT8Q1:279:C6ND0ACXX:1:1102:9329:33447 255 - +chr26 4115792 4115842 D3YGT8Q1:279:C6ND0ACXX:1:1209:7255:23188 255 + +chr26 4116615 4116665 D3YGT8Q1:279:C6ND0ACXX:1:2203:17446:35897 255 + +chr26 4116988 4117038 D3YGT8Q1:279:C6ND0ACXX:1:2203:8076:21265 255 + +chr26 4117124 4117174 D3YGT8Q1:279:C6ND0ACXX:1:1210:4683:41907 255 - +chr26 4117501 4117551 D3YGT8Q1:279:C6ND0ACXX:1:1112:18900:56439 255 - +chr26 4117615 4117665 D3YGT8Q1:279:C6ND0ACXX:1:2313:2299:78456 255 + +chr26 4117835 4117885 D3YGT8Q1:279:C6ND0ACXX:1:2107:13997:60524 255 - +chr26 4117905 4117955 D3YGT8Q1:279:C6ND0ACXX:1:2201:10479:92578 255 + +chr26 4117930 4117980 D3YGT8Q1:279:C6ND0ACXX:1:2110:14632:99394 255 - +chr26 4118037 4118087 D3YGT8Q1:279:C6ND0ACXX:1:1104:14470:25800 255 + +chr26 4118122 4118172 D3YGT8Q1:279:C6ND0ACXX:1:2115:11588:70088 255 + +chr26 4118709 4118759 D3YGT8Q1:279:C6ND0ACXX:1:1216:4958:48081 255 - +chr26 4118724 4118774 D3YGT8Q1:279:C6ND0ACXX:1:1103:19280:11053 255 - +chr26 4118753 4118803 D3YGT8Q1:279:C6ND0ACXX:1:1109:5242:36011 255 + +chr26 4118754 4118804 D3YGT8Q1:279:C6ND0ACXX:1:2115:21104:40586 255 - +chr26 4118852 4118902 D3YGT8Q1:279:C6ND0ACXX:1:2106:20411:76655 255 + +chr26 4118963 4119013 D3YGT8Q1:279:C6ND0ACXX:1:1115:12391:82672 255 + +chr26 4118967 4119017 D3YGT8Q1:279:C6ND0ACXX:1:1316:6521:21414 255 + +chr26 4119005 4119055 D3YGT8Q1:279:C6ND0ACXX:1:2304:6533:74899 255 - +chr26 4119020 4119070 D3YGT8Q1:279:C6ND0ACXX:1:2305:4205:52717 255 - +chr26 4119022 4119072 D3YGT8Q1:279:C6ND0ACXX:1:2209:3941:33541 255 + +chr26 4119047 4119097 D3YGT8Q1:279:C6ND0ACXX:1:1311:20210:42351 255 + +chr26 4119091 4119141 D3YGT8Q1:279:C6ND0ACXX:1:2106:1249:92735 255 - +chr26 4119106 4119156 D3YGT8Q1:279:C6ND0ACXX:1:2214:19237:88451 255 - +chr26 4119168 4119218 D3YGT8Q1:279:C6ND0ACXX:1:1205:5997:59335 255 + +chr26 4119270 4119320 D3YGT8Q1:279:C6ND0ACXX:1:1203:19488:98141 255 - +chr26 4119296 4119346 D3YGT8Q1:279:C6ND0ACXX:1:1215:19021:97547 255 - +chr26 4119311 4119361 D3YGT8Q1:279:C6ND0ACXX:1:1106:19108:19961 255 - +chr26 4119356 4119406 D3YGT8Q1:279:C6ND0ACXX:1:2108:17061:18071 255 - +chr26 4122292 4122342 D3YGT8Q1:279:C6ND0ACXX:1:2105:6803:72755 255 + +chr26 4124452 4124502 D3YGT8Q1:279:C6ND0ACXX:1:2303:8935:84202 255 + +chr26 4124544 4124594 D3YGT8Q1:279:C6ND0ACXX:1:1115:5982:45995 255 - +chr26 4125766 4125816 D3YGT8Q1:279:C6ND0ACXX:1:1214:15854:88292 255 + +chr26 4126002 4126052 D3YGT8Q1:279:C6ND0ACXX:1:1106:12069:84969 255 - +chr26 4126452 4126502 D3YGT8Q1:279:C6ND0ACXX:1:1301:4389:93421 255 + +chr26 4127711 4127761 D3YGT8Q1:279:C6ND0ACXX:1:1314:2721:99427 255 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_region_Input.bed Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,50 @@ +chr26 4107915 4107965 D3YGT8Q1:279:C6ND0ACXX:1:2205:7723:65712 255 + +chr26 4108978 4109028 D3YGT8Q1:279:C6ND0ACXX:1:2111:18182:78807 255 + +chr26 4108998 4109048 D3YGT8Q1:279:C6ND0ACXX:1:1102:16043:23843 255 + +chr26 4109399 4109449 D3YGT8Q1:279:C6ND0ACXX:1:2215:2801:57221 255 - +chr26 4110183 4110233 D3YGT8Q1:279:C6ND0ACXX:1:1315:19316:26775 255 - +chr26 4110276 4110326 D3YGT8Q1:279:C6ND0ACXX:1:1314:1280:77850 255 - +chr26 4110348 4110398 D3YGT8Q1:279:C6ND0ACXX:1:1216:4159:61939 255 - +chr26 4110594 4110644 D3YGT8Q1:279:C6ND0ACXX:1:1312:5546:70647 255 - +chr26 4110805 4110855 D3YGT8Q1:279:C6ND0ACXX:1:2210:12809:70996 255 - +chr26 4110980 4111030 D3YGT8Q1:279:C6ND0ACXX:1:2215:3014:41883 255 + +chr26 4111825 4111875 D3YGT8Q1:279:C6ND0ACXX:1:2314:17556:68202 255 + +chr26 4112421 4112471 D3YGT8Q1:279:C6ND0ACXX:1:1204:13331:57729 255 - +chr26 4112827 4112877 D3YGT8Q1:279:C6ND0ACXX:1:2309:11398:71181 255 + +chr26 4112983 4113033 D3YGT8Q1:279:C6ND0ACXX:1:1104:16671:54740 255 + +chr26 4113645 4113695 D3YGT8Q1:279:C6ND0ACXX:1:2212:20179:47885 255 + +chr26 4114267 4114317 D3YGT8Q1:279:C6ND0ACXX:1:2314:3773:63068 255 + +chr26 4114275 4114325 D3YGT8Q1:279:C6ND0ACXX:1:1116:18465:6326 255 + +chr26 4114684 4114734 D3YGT8Q1:279:C6ND0ACXX:1:1114:17981:44317 255 - +chr26 4114758 4114808 D3YGT8Q1:279:C6ND0ACXX:1:1103:15929:31123 255 - +chr26 4114804 4114854 D3YGT8Q1:279:C6ND0ACXX:1:1208:10693:22578 255 - +chr26 4115616 4115666 D3YGT8Q1:279:C6ND0ACXX:1:1101:1142:17054 255 + +chr26 4115950 4116000 D3YGT8Q1:279:C6ND0ACXX:1:1316:13040:39630 255 + +chr26 4116012 4116062 D3YGT8Q1:279:C6ND0ACXX:1:2107:20439:44058 255 + +chr26 4116111 4116161 D3YGT8Q1:279:C6ND0ACXX:1:2307:1504:41529 255 + +chr26 4116135 4116185 D3YGT8Q1:279:C6ND0ACXX:1:2210:2837:7759 255 + +chr26 4116287 4116337 D3YGT8Q1:279:C6ND0ACXX:1:2313:15422:100876 255 - +chr26 4116709 4116759 D3YGT8Q1:279:C6ND0ACXX:1:2301:13318:45125 255 + +chr26 4116866 4116916 D3YGT8Q1:279:C6ND0ACXX:1:1113:1326:96268 255 + +chr26 4117851 4117901 D3YGT8Q1:279:C6ND0ACXX:1:1310:2843:93758 255 + +chr26 4119403 4119453 D3YGT8Q1:279:C6ND0ACXX:1:1304:17211:28405 255 + +chr26 4120471 4120521 D3YGT8Q1:279:C6ND0ACXX:1:2116:18127:100146 255 - +chr26 4120786 4120836 D3YGT8Q1:279:C6ND0ACXX:1:1207:2164:6021 255 - +chr26 4121337 4121387 D3YGT8Q1:279:C6ND0ACXX:1:2215:9085:93015 255 + +chr26 4121459 4121509 D3YGT8Q1:279:C6ND0ACXX:1:2311:16000:27081 255 + +chr26 4121566 4121616 D3YGT8Q1:279:C6ND0ACXX:1:1216:18410:44768 255 + +chr26 4122136 4122186 D3YGT8Q1:279:C6ND0ACXX:1:2316:17558:30500 255 + +chr26 4123141 4123191 D3YGT8Q1:279:C6ND0ACXX:1:2203:15835:86872 255 + +chr26 4123836 4123886 D3YGT8Q1:279:C6ND0ACXX:1:2212:16650:8391 255 - +chr26 4123904 4123954 D3YGT8Q1:279:C6ND0ACXX:1:1307:7349:80960 255 + +chr26 4124517 4124567 D3YGT8Q1:279:C6ND0ACXX:1:1213:6010:82097 255 + +chr26 4125236 4125286 D3YGT8Q1:279:C6ND0ACXX:1:2216:1172:30684 255 - +chr26 4126820 4126870 D3YGT8Q1:279:C6ND0ACXX:1:2107:12500:48771 255 + +chr26 4126863 4126913 D3YGT8Q1:279:C6ND0ACXX:1:2105:1028:78112 255 + +chr26 4126909 4126959 D3YGT8Q1:279:C6ND0ACXX:1:1302:19618:57506 255 - +chr26 4126959 4127009 D3YGT8Q1:279:C6ND0ACXX:1:1204:9666:55269 255 - +chr26 4128534 4128584 D3YGT8Q1:279:C6ND0ACXX:1:2312:9851:2880 255 + +chr26 4129060 4129110 D3YGT8Q1:279:C6ND0ACXX:1:2104:4039:10225 255 + +chr26 4129077 4129127 D3YGT8Q1:279:C6ND0ACXX:1:1306:15379:11481 255 + +chr26 4129446 4129496 D3YGT8Q1:279:C6ND0ACXX:1:1303:9852:6188 255 + +chr26 4130521 4130571 D3YGT8Q1:279:C6ND0ACXX:1:1201:20815:69132 255 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 30 08:16:18 2015 -0400 @@ -0,0 +1,65 @@ +<?xml version="1.0"?> +<tool_dependency> + <!-- Dependencies from main/test toolsheds --> + <package name="numpy" version="1.9"> + <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="3.1.2"> + <repository changeset_revision="6e0eee4ea4e1" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <!-- Subset of UCSC tools --> + <package name="ucsc_tools_for_macs21" version="1.0"> + <install version="1.0"> + <actions> + <!-- fetchChromSizes --> + <action type="download_binary"> + <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template> + </action> + <action type="chmod"> + <file mode="755">$INSTALL_DIR/fetchChromSizes</file> + </action> + <!-- bedClip --> + <action type="download_binary"> + <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template> + </action> + <action type="chmod"> + <file mode="755">$INSTALL_DIR/bedClip</file> + </action> + <!-- bedGraphToBigWig --> + <action type="download_binary"> + <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template> + </action> + <action type="chmod"> + <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> + <!-- MACS 2.1.0 --> + <package name="macs2" version="2.1.0.20140616"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action> + <!-- Install environment for main & test toolsheds --> + <action type="set_environment_for_install"> + <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.9" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Macs2.1 depends on having python2.7 and numpy 1.8 installed on all nodes of the work cluster</readme> + </package> +</tool_dependency>