| Next changeset 1:6e5fcffb68c9 (2015-07-21) |
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Commit message:
Imported from capsule None |
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added:
macs_wrapper.py macs_wrapper.xml test-data/chipseq_enriched.bed.gz test-data/chipseq_input.bed.gz test-data/peakcalling_macs/macs_test_1_out.bed test-data/peakcalling_macs/macs_test_1_out.html test-data/peakcalling_macs/macs_test_2_neg_peaks_out.interval test-data/peakcalling_macs/macs_test_2_peaks_out.interval test-data/peakcalling_macs/macs_test_3_control_out.wig test-data/peakcalling_macs/macs_test_3_out.html test-data/peakcalling_macs/macs_test_3_treatment_out.wig test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.pdf test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.r test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.r.log test-data/peakcalling_macs/test2/Galaxy_Test_Run_negative_peaks.xls test-data/peakcalling_macs/test2/Galaxy_Test_Run_peaks.xls tool_dependencies.xml |
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| diff -r 000000000000 -r ae2ec275332a macs_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs_wrapper.py Mon Jan 27 09:28:45 2014 -0500 |
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| @@ -0,0 +1,139 @@ +import glob +import gzip +import json +import os +import os.path +import shutil +import subprocess +import sys +import tempfile + +CHUNK_SIZE = 1024 + +def gunzip_cat_glob_path( glob_path, target_filename, delete = False ): + out = open( target_filename, 'wb' ) + for filename in glob.glob( glob_path ): + fh = gzip.open( filename, 'rb' ) + while True: + data = fh.read( CHUNK_SIZE ) + if data: + out.write( data ) + else: + break + fh.close() + if delete: + os.unlink( filename ) + out.close() + +def xls_to_interval( xls_file, interval_file, header = None ): + out = open( interval_file, 'wb' ) + if header: + out.write( '#%s\n' % header ) + wrote_header = False + #From macs readme: Coordinates in XLS is 1-based which is different with BED format. + for line in open( xls_file ): + #keep all existing comment lines + if line.startswith( '#' ): + out.write( line ) + elif not wrote_header: + out.write( '#%s' % line ) + wrote_header = True + else: + fields = line.split( '\t' ) + if len( fields ) > 1: + fields[1] = str( int( fields[1] ) - 1 ) + out.write( '\t'.join( fields ) ) + out.close() + +def main(): + options = json.load( open( sys.argv[1] ) ) + output_bed = sys.argv[2] + output_extra_html = sys.argv[3] + output_extra_path = sys.argv[4] + + experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name here, it will be used by macs for filenames (gzip of wig files will fail with spaces - macs doesn't properly escape them)..need to replace all whitespace, split makes this easier + cmdline = "macs -t %s" % ",".join( options['input_chipseq'] ) + if options['input_control']: + cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] ) + if 'wig' in options: + wigextend = int( options['wig']['wigextend'] ) + if wigextend >= 0: + wigextend = "--wigextend='%s'" % wigextend + else: + wigextend = '' + cmdline = "%s --wig %s --space='%s'" % ( cmdline, wigextend, options['wig']['space'] ) + if 'nomodel' in options: + cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] ) + if 'diag' in options: + cmdline = "%s --diag --fe-min='%s' --fe-max='%s' --fe-step='%s'" % ( cmdline, options['diag']['fe-min'], options['diag']['fe-max'], options['diag']['fe-step'] ) + + tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user + stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report + proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) + proc.wait() + #We don't want to set tool run to error state if only warnings or info, e.g. mfold could be decreased to improve model, but let user view macs log + #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup + if proc.returncode: + stderr_f = open( stderr_name ) + while True: + chunk = stderr_f.read( CHUNK_SIZE ) + if not chunk: + stderr_f.close() + break + sys.stderr.write( chunk ) + + #run R to create pdf from model script + if os.path.exists( os.path.join( tmp_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=tmp_dir ) + proc.wait() + + + #move bed out to proper output file + created_bed_name = os.path.join( tmp_dir, "%s_peaks.bed" % experiment_name ) + if os.path.exists( created_bed_name ): + shutil.move( created_bed_name, output_bed ) + + #parse xls files to interval files as needed + if options['xls_to_interval']: + create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name ) + if os.path.exists( create_peak_xls_file ): + xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) + create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name ) + if os.path.exists( create_peak_xls_file ): + xls_to_interval( create_peak_xls_file, options['xls_to_interval']['negative_peaks_file'], header = 'negative peaks file' ) + + #merge and move wig files as needed, delete gz'd files and remove emptied dirs + if 'wig' in options: + wig_base_dir = os.path.join( tmp_dir, "%s_MACS_wiggle" % experiment_name ) + if os.path.exists( wig_base_dir ): + #treatment + treatment_dir = os.path.join( wig_base_dir, "treat" ) + if os.path.exists( treatment_dir ): + gunzip_cat_glob_path( os.path.join( treatment_dir, "*.wig.gz" ), options['wig']['output_treatment_file'], delete = True ) + os.rmdir( treatment_dir ) + #control + if options['input_control']: + control_dir = os.path.join( wig_base_dir, "control" ) + if os.path.exists( control_dir ): + gunzip_cat_glob_path( os.path.join( control_dir, "*.wig.gz" ), options['wig']['output_control_file'], delete = True ) + os.rmdir( control_dir ) + os.rmdir( wig_base_dir ) + + #move all remaining files to extra files path of html file output to allow user download + out_html = open( output_extra_html, 'wb' ) + out_html.write( '<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name ) + os.mkdir( output_extra_path ) + for filename in sorted( os.listdir( tmp_dir ) ): + shutil.move( os.path.join( tmp_dir, filename ), os.path.join( output_extra_path, filename ) ) + out_html.write( '<li><a href="%s">%s</a></li>\n' % ( filename, filename ) ) + out_html.write( '</ul></p>\n' ) + out_html.write( '<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % open( stderr_name, 'rb' ).read() ) + out_html.write( '</body></html>\n' ) + out_html.close() + + os.unlink( stderr_name ) + os.rmdir( tmp_dir ) + +if __name__ == "__main__": main() |
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| diff -r 000000000000 -r ae2ec275332a macs_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs_wrapper.xml Mon Jan 27 09:28:45 2014 -0500 |
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| b'@@ -0,0 +1,239 @@\n+<tool id="peakcalling_macs" name="MACS" version="1.0.1">\n+ <description>Model-based Analysis of ChIP-Seq</description>\n+ <command interpreter="python">macs_wrapper.py $options_file $output_bed_file $output_extra_files $output_extra_files.files_path</command>\n+ <requirements>\n+ <requirement type="package" version="1.3.7.1">macs</requirement>\n+ <requirement type="package" version="2.15.0">R</requirement>\n+ </requirements>\n+ <inputs>\n+ <param name="experiment_name" type="text" value="MACS in Galaxy" size="50" label="Experiment Name"/>\n+ <conditional name="input_type">\n+ <param name="input_type_selector" type="select" label="Paired End Sequencing">\n+ <option value="paired_end">Paired End (requires elandmulti format)</option>\n+ <option value="single_end" selected="true">Single End</option>\n+ </param>\n+ <when value="paired_end">\n+ <param name="input_chipseq_file1" type="data" format="elandmulti" label="ChIP-Seq Tag File 1" />\n+ <param name="input_chipseq_file2" type="data" format="elandmulti" label="ChIP-Seq Tag File 2" />\n+ <param name="input_control_file1" type="data" format="elandmulti" optional="True" label="ChIP-Seq Control File 1" />\n+ <param name="input_control_file2" type="data" format="elandmulti" optional="True" label="ChIP-Seq Control File 2" />\n+ <param name="petdist" type="integer" label="Best distance between Pair-End Tags" value="200"/>\n+ </when>\n+ <when value="single_end">\n+ <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n+ <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" optional="True" label="ChIP-Seq Control File" />\n+ </when>\n+ </conditional>\n+ <param name="gsize" type="float" label="Effective genome size" value="2.7e+9" help="default: 2.7e+9"/>\n+ <param name="tsize" type="integer" label="Tag size" value="25"/>\n+ <param name="bw" type="integer" label="Band width" value="300"/>\n+ <param name="pvalue" type="float" label="Pvalue cutoff for peak detection" value="1e-5" help="default: 1e-5"/>\n+ <param name="mfold" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="32"/>\n+ <param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="create" falsevalue="do_not_create" checked="False"/>\n+ <conditional name="wig_type">\n+ <param name="wig_type_selector" type="select" label="Save shifted raw tag count at every bp into a wiggle file">\n+ <option value="wig">Save</option>\n+ <option value="no_wig" selected="true">Do not create wig file (faster)</option>\n+ </param>\n+ <when value="wig">\n+ <param name="wigextend" type="integer" label="Extend tag from its middle point to a wigextend size fragment." value="-1" help="Use value less than 0 for default (modeled d)"/>\n+ <param name="space" type="integer" label="Resolution for saving wiggle files" value="10"/>\n+ </when>\n+ <when value="no_wig">\n+ <!-- do nothing here -->\n+ </when>\n+ </conditional>\n+ <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"/>\n+ <param name="lambdaset" type="text" label="3 levels of regions around the peak region to calculate the maximum lambda as local lambda" value="1000,5000,10000" size="50"/>\n+ <conditional name="nomodel_type">\n+ <param name="nomodel_type_selector" type="select" label="Build Model">\n+ <option value="nomodel">Do not build the shifting model</option>\n+ <option value="create_model" selected="true">Build the shifting model</option>\n+ </param>\n+ <when value="nomodel">\n+ <param name="shiftsize" type="integer" label='..b'e1" value="chipseq_enriched.bed.gz" ftype="bed" />\n+ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" />\n+ <param name="experiment_name" value="Galaxy Test Run" />\n+ <param name="tsize" value="36" />\n+ <param name="mfold" value="13" />\n+ <param name="gsize" value="2.7e+9" />\n+ <param name="bw" value="300" />\n+ <param name="pvalue" value="1e-5" />\n+ <param name="xls_to_interval" value="true" />\n+ <param name="wig_type_selector" value="no_wig" />\n+ <param name="nolambda"/>\n+ <param name="lambdaset" value="1000,5000,10000"/>\n+ <param name="nomodel_type_selector" value="create_model" />\n+ <param name="diag_type_selector" value="no_diag" />\n+ <param name="futurefdr"/>\n+ <output name="output_bed_file" file="peakcalling_macs/macs_test_1_out.bed" />\n+ <output name="output_xls_to_interval_peaks_file" file="peakcalling_macs/macs_test_2_peaks_out.interval" lines_diff="4" />\n+ <output name="output_xls_to_interval_negative_peaks_file" file="peakcalling_macs/macs_test_2_neg_peaks_out.interval" />\n+ <output name="output_html_file" file="peakcalling_macs/macs_test_1_out.html" compare="re_match" >\n+ <extra_files type="directory" value="peakcalling_macs/test2/" compare="re_match"/>\n+ </output>\n+ </test>\n+ <!-- <test>\n+ <param name="input_type_selector" value="single_end" />\n+ <param name="input_chipseq_file1" value="chipseq_enriched.bed.gz" ftype="bed" />\n+ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" />\n+ <param name="experiment_name" value="Galaxy Test Run" />\n+ <param name="tsize" value="36" />\n+ <param name="mfold" value="13" />\n+ <param name="gsize" value="2.7e+9" />\n+ <param name="bw" value="300" />\n+ <param name="pvalue" value="1e-5" />\n+ <param name="xls_to_interval" value="true" />\n+ <param name="wig_type_selector" value="wig" />\n+ <param name="wigextend" value="-1" />\n+ <param name="space" value="10" />\n+ <param name="nolambda"/>\n+ <param name="lambdaset" value="1000,5000,10000"/>\n+ <param name="nomodel_type_selector" value="create_model" />\n+ <param name="diag_type_selector" value="no_diag" />\n+ <param name="futurefdr"/>\n+ <output name="output_bed_file" file="peakcalling_macs/macs_test_1_out.bed" />\n+ <output name="output_xls_to_interval_peaks_file" file="peakcalling_macs/macs_test_2_peaks_out.interval" lines_diff="4" />\n+ <output name="output_xls_to_interval_negative_peaks_file" file="macs_test_2_neg_peaks_out.interval" />\n+ <output name="output_treatment_wig_file" file="peakcalling_macs/macs_test_3_treatment_out.wig" />\n+ <output name="output_control_wig_file" file="peakcalling_macs/macs_test_3_control_out.wig" />\n+ <output name="output_html_file" file="peakcalling_macs/macs_test_3_out.html" compare="re_match" >\n+ <extra_files type="directory" value="peakcalling_macs/test2/" compare="re_match"/>\n+ </output>\n+ </test> -->\n+ </tests>\n+ <help>\n+**What it does**\n+\n+This tool allows ChIP-seq peak calling using MACS.\n+\n+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.\n+\n+View the original MACS documentation: http://liulab.dfci.harvard.edu/MACS/00README.html.\n+\n+------\n+\n+**Citation**\n+\n+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>`_\n+\n+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r ae2ec275332a test-data/chipseq_enriched.bed.gz |
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| Binary file test-data/chipseq_enriched.bed.gz has changed |
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| diff -r 000000000000 -r ae2ec275332a test-data/chipseq_input.bed.gz |
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| Binary file test-data/chipseq_input.bed.gz has changed |
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| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/macs_test_1_out.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/macs_test_1_out.bed Mon Jan 27 09:28:45 2014 -0500 |
| b |
| b'@@ -0,0 +1,1271 @@\n+track name="MACS peaks for Galaxy_Test_Run"\n+chr1\t3138857\t3139271\tMACS_peak_1\t53.08\n+chr1\t4133899\t4134700\tMACS_peak_2\t51.91\n+chr1\t4323670\t4324367\tMACS_peak_3\t272.01\n+chr1\t4336486\t4337946\tMACS_peak_4\t228.35\n+chr1\t4407086\t4409120\tMACS_peak_5\t300.46\n+chr1\t4507832\t4508710\tMACS_peak_6\t161.74\n+chr1\t4657704\t4658572\tMACS_peak_7\t280.37\n+chr1\t4658705\t4659021\tMACS_peak_8\t131.25\n+chr1\t4659147\t4660581\tMACS_peak_9\t463.08\n+chr1\t4661156\t4661317\tMACS_peak_10\t174.88\n+chr1\t4661505\t4661617\tMACS_peak_11\t100.24\n+chr1\t4661790\t4662463\tMACS_peak_12\t219.58\n+chr1\t4662710\t4663434\tMACS_peak_13\t395.94\n+chr1\t4664135\t4664430\tMACS_peak_14\t169.10\n+chr1\t4665001\t4665113\tMACS_peak_15\t100.24\n+chr1\t4665839\t4666425\tMACS_peak_16\t332.40\n+chr1\t4666581\t4666693\tMACS_peak_17\t100.24\n+chr1\t4666840\t4666981\tMACS_peak_18\t174.88\n+chr1\t4667600\t4667712\tMACS_peak_19\t100.24\n+chr1\t4668711\t4669005\tMACS_peak_20\t169.17\n+chr1\t4669126\t4669238\tMACS_peak_21\t100.24\n+chr1\t4669537\t4669752\tMACS_peak_22\t174.88\n+chr1\t4669936\t4670048\tMACS_peak_23\t100.24\n+chr1\t4670216\t4670449\tMACS_peak_24\t212.68\n+chr1\t4673856\t4674051\tMACS_peak_25\t137.07\n+chr1\t4674349\t4674478\tMACS_peak_26\t137.07\n+chr1\t4675027\t4675152\tMACS_peak_27\t137.07\n+chr1\t4676227\t4676339\tMACS_peak_28\t100.24\n+chr1\t4676511\t4676623\tMACS_peak_29\t100.24\n+chr1\t4676954\t4677151\tMACS_peak_30\t100.24\n+chr1\t4677646\t4677758\tMACS_peak_31\t100.24\n+chr1\t4678360\t4678472\tMACS_peak_32\t100.24\n+chr1\t4678659\t4679136\tMACS_peak_33\t230.04\n+chr1\t4679439\t4679551\tMACS_peak_34\t100.24\n+chr1\t4680106\t4680523\tMACS_peak_35\t126.43\n+chr1\t4680822\t4680934\tMACS_peak_36\t100.24\n+chr1\t4681075\t4682050\tMACS_peak_37\t241.81\n+chr1\t4682229\t4682387\tMACS_peak_38\t100.24\n+chr1\t4682594\t4682706\tMACS_peak_39\t100.24\n+chr1\t4683158\t4683270\tMACS_peak_40\t100.24\n+chr1\t4683473\t4683585\tMACS_peak_41\t100.24\n+chr1\t4683832\t4683944\tMACS_peak_42\t100.24\n+chr1\t4684591\t4684775\tMACS_peak_43\t100.24\n+chr1\t4685292\t4685404\tMACS_peak_44\t100.24\n+chr1\t4685810\t4686198\tMACS_peak_45\t127.69\n+chr1\t4686493\t4686605\tMACS_peak_46\t100.24\n+chr1\t4686818\t4686930\tMACS_peak_47\t100.24\n+chr1\t4687387\t4687499\tMACS_peak_48\t100.24\n+chr1\t4687692\t4687902\tMACS_peak_49\t174.88\n+chr1\t4688181\t4688790\tMACS_peak_50\t258.16\n+chr1\t4689101\t4689557\tMACS_peak_51\t231.41\n+chr1\t4690039\t4690151\tMACS_peak_52\t100.24\n+chr1\t4690290\t4690402\tMACS_peak_53\t100.24\n+chr1\t4690780\t4690907\tMACS_peak_54\t137.07\n+chr1\t4691478\t4692335\tMACS_peak_55\t315.89\n+chr1\t4692464\t4692768\tMACS_peak_56\t131.92\n+chr1\t4693243\t4693751\tMACS_peak_57\t228.13\n+chr1\t4694306\t4694418\tMACS_peak_58\t100.24\n+chr1\t4694738\t4695016\tMACS_peak_59\t170.38\n+chr1\t4695207\t4695378\tMACS_peak_60\t100.24\n+chr1\t4695503\t4696600\tMACS_peak_61\t374.29\n+chr1\t4696903\t4697015\tMACS_peak_62\t100.24\n+chr1\t4697569\t4697912\tMACS_peak_63\t240.07\n+chr1\t4698224\t4698395\tMACS_peak_64\t100.24\n+chr1\t4698790\t4698904\tMACS_peak_65\t137.07\n+chr1\t4699223\t4699430\tMACS_peak_66\t137.07\n+chr1\t4699642\t4699754\tMACS_peak_67\t100.24\n+chr1\t4700457\t4700569\tMACS_peak_68\t100.24\n+chr1\t4700853\t4700965\tMACS_peak_69\t100.24\n+chr1\t4708474\t4708898\tMACS_peak_70\t126.15\n+chr1\t4709426\t4709741\tMACS_peak_71\t167.67\n+chr1\t4709925\t4710127\tMACS_peak_72\t137.07\n+chr1\t4710465\t4710577\tMACS_peak_73\t100.24\n+chr1\t4710812\t4711277\tMACS_peak_74\t194.68\n+chr1\t4711462\t4711762\tMACS_peak_75\t132.15\n+chr1\t4712202\t4712479\tMACS_peak_76\t97.58\n+chr1\t4712673\t4713163\tMACS_peak_77\t340.17\n+chr1\t4713659\t4714656\tMACS_peak_78\t414.78\n+chr1\t4714840\t4715470\tMACS_peak_79\t221.59\n+chr1\t4715671\t4715783\tMACS_peak_80\t100.24\n+chr1\t4715908\t4716811\tMACS_peak_81\t530.04\n+chr1\t4717318\t4717430\tMACS_peak_82\t100.24\n+chr1\t4717789\t4718230\tMACS_peak_83\t232.43\n+chr1\t4718990\t4719236\tMACS_peak_84\t99.13\n+chr1\t4719718\t4719830\tMACS_peak_85\t100.24\n+chr1\t4720276\t4720388\tMACS_peak_86\t100.24\n+chr1\t4721061\t4721173\tMACS_peak_87\t100.24\n+chr1\t4721620\t4721782\tMACS_peak_88\t100.24\n+chr1\t4722229\t4722341\tMACS_peak_89\t100.24\n+chr1\t4723262\t4723374\tMACS_peak_90\t100.24\n+chr1\t4724496\t4724608\tMACS_peak_91\t100.24\n+chr1\t4726179\t4726291\tMACS_peak_92\t100.24\n+chr1\t4726472\t4727091\tMACS_peak_93\t187.23\n+chr1\t4727268\t4727705\tMACS_peak_94\t196.30\n'..b'chr1\t5659194\t5659308\tMACS_peak_1180\t137.07\n+chr1\t5660375\t5660575\tMACS_peak_1181\t137.07\n+chr1\t5660781\t5660893\tMACS_peak_1182\t100.24\n+chr1\t5661327\t5661439\tMACS_peak_1183\t100.24\n+chr1\t5662504\t5662697\tMACS_peak_1184\t137.07\n+chr1\t5663691\t5663885\tMACS_peak_1185\t137.07\n+chr1\t5664582\t5664750\tMACS_peak_1186\t100.24\n+chr1\t5665076\t5665188\tMACS_peak_1187\t100.24\n+chr1\t5665895\t5666007\tMACS_peak_1188\t100.24\n+chr1\t5666448\t5666930\tMACS_peak_1189\t193.75\n+chr1\t5667751\t5667934\tMACS_peak_1190\t100.24\n+chr1\t5674057\t5674169\tMACS_peak_1191\t100.24\n+chr1\t5675063\t5675175\tMACS_peak_1192\t100.24\n+chr1\t5676274\t5676386\tMACS_peak_1193\t100.24\n+chr1\t5676599\t5676711\tMACS_peak_1194\t100.24\n+chr1\t5677228\t5677340\tMACS_peak_1195\t100.24\n+chr1\t5677740\t5677852\tMACS_peak_1196\t100.24\n+chr1\t5679022\t5679667\tMACS_peak_1197\t291.97\n+chr1\t5680026\t5681034\tMACS_peak_1198\t240.66\n+chr1\t5682911\t5683023\tMACS_peak_1199\t100.24\n+chr1\t5688032\t5688144\tMACS_peak_1200\t100.24\n+chr1\t5688335\t5688657\tMACS_peak_1201\t130.92\n+chr1\t5688801\t5688913\tMACS_peak_1202\t100.24\n+chr1\t5689087\t5689348\tMACS_peak_1203\t98.36\n+chr1\t5689475\t5689587\tMACS_peak_1204\t100.24\n+chr1\t5689771\t5689883\tMACS_peak_1205\t100.24\n+chr1\t5690261\t5690373\tMACS_peak_1206\t100.24\n+chr1\t5690750\t5690873\tMACS_peak_1207\t137.07\n+chr1\t5694742\t5695180\tMACS_peak_1208\t160.51\n+chr1\t5695333\t5695675\tMACS_peak_1209\t129.88\n+chr1\t5696080\t5696192\tMACS_peak_1210\t100.24\n+chr1\t5696612\t5697345\tMACS_peak_1211\t251.72\n+chr1\t5697961\t5698073\tMACS_peak_1212\t100.24\n+chr1\t5698235\t5698383\tMACS_peak_1213\t137.07\n+chr1\t5698832\t5699021\tMACS_peak_1214\t100.24\n+chr1\t5699479\t5699591\tMACS_peak_1215\t100.24\n+chr1\t5700029\t5700141\tMACS_peak_1216\t100.24\n+chr1\t5700387\t5700503\tMACS_peak_1217\t137.07\n+chr1\t5703736\t5703848\tMACS_peak_1218\t100.24\n+chr1\t5704571\t5704683\tMACS_peak_1219\t100.24\n+chr1\t5704979\t5705219\tMACS_peak_1220\t136.03\n+chr1\t5705728\t5705840\tMACS_peak_1221\t100.24\n+chr1\t5706213\t5706482\tMACS_peak_1222\t247.45\n+chr1\t5706879\t5706991\tMACS_peak_1223\t100.24\n+chr1\t5707211\t5707414\tMACS_peak_1224\t100.24\n+chr1\t5707733\t5707955\tMACS_peak_1225\t100.24\n+chr1\t5708418\t5708530\tMACS_peak_1226\t100.24\n+chr1\t5708711\t5708823\tMACS_peak_1227\t100.24\n+chr1\t5709009\t5709168\tMACS_peak_1228\t100.24\n+chr1\t5709626\t5709738\tMACS_peak_1229\t100.24\n+chr1\t5710175\t5710287\tMACS_peak_1230\t100.24\n+chr1\t5711491\t5711603\tMACS_peak_1231\t100.24\n+chr1\t5712452\t5712913\tMACS_peak_1232\t159.40\n+chr1\t5713590\t5713702\tMACS_peak_1233\t100.24\n+chr1\t5714277\t5714835\tMACS_peak_1234\t189.93\n+chr1\t5715628\t5715793\tMACS_peak_1235\t100.24\n+chr1\t5715919\t5716031\tMACS_peak_1236\t100.24\n+chr1\t5716150\t5716384\tMACS_peak_1237\t174.12\n+chr1\t5717000\t5717112\tMACS_peak_1238\t100.24\n+chr1\t5717383\t5717774\tMACS_peak_1239\t127.55\n+chr1\t5718298\t5718531\tMACS_peak_1240\t136.54\n+chr1\t5718754\t5719002\tMACS_peak_1241\t172.86\n+chr1\t5719627\t5719739\tMACS_peak_1242\t100.24\n+chr1\t5720578\t5720690\tMACS_peak_1243\t100.24\n+chr1\t5721523\t5721843\tMACS_peak_1244\t95.71\n+chr1\t5722221\t5722388\tMACS_peak_1245\t100.24\n+chr1\t5722739\t5722851\tMACS_peak_1246\t100.24\n+chr1\t5723148\t5723403\tMACS_peak_1247\t134.98\n+chr1\t5724342\t5724566\tMACS_peak_1248\t100.24\n+chr1\t5725453\t5725597\tMACS_peak_1249\t137.07\n+chr1\t5725942\t5726075\tMACS_peak_1250\t137.07\n+chr1\t5726202\t5726647\tMACS_peak_1251\t306.48\n+chr1\t5726801\t5726913\tMACS_peak_1252\t100.24\n+chr1\t5727303\t5727415\tMACS_peak_1253\t100.24\n+chr1\t5727541\t5727720\tMACS_peak_1254\t213.48\n+chr1\t5728015\t5728127\tMACS_peak_1255\t100.24\n+chr1\t5728661\t5728922\tMACS_peak_1256\t98.36\n+chr1\t5729591\t5729703\tMACS_peak_1257\t100.24\n+chr1\t5729971\t5730118\tMACS_peak_1258\t137.07\n+chr1\t5735097\t5735209\tMACS_peak_1259\t100.24\n+chr1\t5738165\t5738277\tMACS_peak_1260\t100.24\n+chr1\t5741886\t5742013\tMACS_peak_1261\t137.07\n+chr1\t5742222\t5742493\tMACS_peak_1262\t133.92\n+chr1\t5742624\t5742892\tMACS_peak_1263\t98.02\n+chr1\t5743479\t5743591\tMACS_peak_1264\t100.24\n+chr1\t5743802\t5743943\tMACS_peak_1265\t137.07\n+chr1\t5744327\t5745001\tMACS_peak_1266\t185.01\n+chr1\t5745544\t5746174\tMACS_peak_1267\t221.59\n+chr1\t5746482\t5747182\tMACS_peak_1268\t218.38\n+chr1\t5747751\t5747863\tMACS_peak_1269\t100.24\n+chr1\t5749480\t5749592\tMACS_peak_1270\t100.24\n' |
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/macs_test_1_out.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/macs_test_1_out.html Mon Jan 27 09:28:45 2014 -0500 |
| b |
| @@ -0,0 +1,48 @@ +\<html\>\<head\>\<title\>Additional\ output\ created\ by\ MACS\ \(Galaxy\_Test\_Run\)\<\/title\>\<\/head\>\<body\>\<h3\>Additional\ Files\:\<\/h3\>\<p\>\<ul\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.pdf\"\>Galaxy\_Test\_Run\_model\.pdf\<\/a\>\<\/li\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\"\>Galaxy\_Test\_Run\_model\.r\<\/a\>\<\/li\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\.log\"\>Galaxy\_Test\_Run\_model\.r\.log\<\/a\>\<\/li\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_negative\_peaks\.xls\"\>Galaxy\_Test\_Run\_negative\_peaks\.xls\<\/a\>\<\/li\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_peaks\.xls\"\>Galaxy\_Test\_Run\_peaks\.xls\<\/a\>\<\/li\> +\<\/ul\>\<\/p\> +\<h3\>Messages\ from\ MACS\:\<\/h3\> +\<p\>\<pre\>INFO\ \ \@\ .*\:\ +\#\ ARGUMENTS\ LIST\: +\#\ name\ \=\ Galaxy\_Test\_Run +\#\ format\ \=\ BED +\#\ ChIP\-seq\ file\ \=\ .*.dat +\#\ control\ file\ \=\ .*.dat +\#\ effective\ genome\ size\ \=\ 2\.70e\+09 +\#\ tag\ size\ \=\ 36 +\#\ band\ width\ \=\ 300 +\#\ model\ fold\ \=\ 13 +\#\ pvalue\ cutoff\ \=\ 1\.00e\-05 +\#\ Ranges\ for\ calculating\ regional\ lambda\ are\ \:\ peak\_region\,1000\,5000\,10000\ +INFO\ \ \@\ .*\:\ \#1\ read\ tag\ files\.\.\.\ +INFO\ \ \@\ .*\:\ \#1\ read\ treatment\ tags\.\.\.\ +INFO\ \ \@\ .*\:\ \#1\.2\ read\ input\ tags\.\.\.\ +INFO\ \ \@\ .*\:\ \#1\ \ Background\ Redundant\ rate\:\ 1\.00\ +INFO\ \ \@\ .*\:\ \#1\ finished\!\ +INFO\ \ \@\ .*\:\ \#2\ Build\ Peak\ Model\.\.\.\ +INFO\ \ \@\ .*\:\ \#2\ number\ of\ paired\ peaks\:\ 549\ +WARNING\ \@\ .*\:\ Fewer\ paired\ peaks\ \(549\)\ than\ 1000\!\ Model\ may\ not\ be\ build\ well\!\ Lower\ your\ MFOLD\ parameter\ may\ erase\ this\ warning\.\ Now\ I\ will\ use\ 549\ pairs\ to\ build\ model\!\ +INFO\ \ \@\ .*\:\ \#2\ finished\!\ +INFO\ \ \@\ .*\:\ \#2\.2\ Generate\ R\ script\ for\ model\ \:\ Galaxy\_Test\_Run\_model\.r\ +INFO\ \ \@\ .*\:\ \#3\ Call\ peaks\.\.\.\ +INFO\ \ \@\ .*\:\ \#3\ shift\ treatment\ data\ +INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ treatment\ data\ +INFO\ \ \@\ .*\:\ \#3\ call\ peak\ candidates\ +INFO\ \ \@\ .*\:\ \#3\ shift\ control\ data\ +INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ control\ data\ +INFO\ \ \@\ .*\:\ \#3\ call\ negative\ peak\ candidates\ +INFO\ \ \@\ .*\:\ \#3\ use\ control\ data\ to\ filter\ peak\ candidates\.\.\.\ +INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 1270\ peaks\ are\ called\!\ +INFO\ \ \@\ .*\:\ \#3\ find\ negative\ peaks\ by\ reversing\ treat\ and\ control\ +INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 57\ peaks\ are\ called\!\ +INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.xls\ +INFO\ \ \@\ .*\:\ \#4\ Write\ output\ bed\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.bed\ +INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\ for\ negative\ peaks\.\.\.\ Galaxy\_Test\_Run\_negative\_peaks\.xls\ +INFO\ \ \@\ .*\:\ \#5\ Done\!\ Check\ the\ output\ files\! +\ +\<\/pre\>\<\/p\> +\<\/body\>\<\/html\> |
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/macs_test_2_neg_peaks_out.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/macs_test_2_neg_peaks_out.interval Mon Jan 27 09:28:45 2014 -0500 |
| b |
| @@ -0,0 +1,59 @@ +#negative peaks file +#chr start end length summit tags -10*log10(pvalue) fold_enrichment +chr1 3012338 3012474 136 69 3 79.72 265.54 +chr1 3012631 3012751 120 61 3 79.72 265.54 +chr1 3055826 3056120 294 96 9 59.49 18.22 +chr1 3066934 3067568 634 101 10 53.35 18.44 +chr1 3076059 3076339 280 112 6 58.24 29.50 +chr1 3092687 3093270 583 344 11 50.81 10.32 +chr1 3114123 3114523 400 107 10 51.47 11.06 +chr1 3125324 3126255 931 573 13 65.69 12.07 +chr1 3126473 3127174 701 249 11 65.43 13.28 +chr1 3127353 3127879 526 265 14 110.59 22.13 +chr1 3195224 3195844 620 395 13 56.61 13.28 +chr1 3228283 3228748 465 388 6 50.25 26.55 +chr1 3275975 3276467 492 404 9 55.17 15.39 +chr1 3285007 3286005 998 891 18 66.19 11.06 +chr1 3312699 3313743 1044 204 21 60.12 11.06 +chr1 3446632 3447508 876 176 14 61.26 14.75 +chr1 3468402 3469436 1034 109 18 50.75 7.08 +chr1 3474772 3476374 1602 960 22 66.92 12.29 +chr1 3514508 3515086 578 110 13 59.90 11.06 +chr1 3517009 3518094 1085 84 14 50.75 11.80 +chr1 3599829 3601141 1312 109 19 65.77 10.41 +chr1 3605828 3605951 123 62 4 52.20 18.63 +chr1 3606596 3607433 837 548 10 66.22 27.23 +chr1 3613851 3614116 265 103 6 57.63 34.04 +chr1 3614432 3615882 1450 85 15 63.55 13.28 +chr1 3617465 3617784 319 211 9 51.03 11.06 +chr1 3640315 3641949 1634 273 32 81.39 10.68 +chr1 3647349 3648562 1213 411 19 67.14 9.83 +chr1 3735801 3736852 1051 878 17 73.61 14.75 +chr1 3796005 3796544 539 65 5 54.89 44.26 +chr1 3797371 3797763 392 70 6 54.44 26.55 +chr1 3835421 3835673 252 171 6 53.74 22.13 +chr1 3856581 3857561 980 110 19 52.84 9.48 +chr1 3968246 3968621 375 85 7 60.72 34.04 +chr1 3970428 3970718 290 69 5 56.15 50.58 +chr1 4034953 4036094 1141 465 15 66.64 18.44 +chr1 4051823 4055268 3445 669 46 119.08 9.32 +chr1 4099917 4100882 965 256 18 84.48 11.39 +chr1 4112353 4113269 916 72 15 53.99 9.32 +chr1 4139620 4140296 676 399 14 71.23 11.06 +chr1 4191034 4191488 454 386 9 51.16 15.81 +chr1 4191774 4192345 571 102 10 51.50 12.64 +chr1 4201259 4202176 917 651 13 64.28 19.24 +chr1 4218597 4219458 861 460 16 53.64 5.77 +chr1 4223608 4224231 623 472 14 78.93 14.75 +chr1 4238528 4239382 854 90 14 54.69 15.12 +chr1 4283406 4284196 790 400 11 60.42 22.13 +chr1 4368609 4369824 1215 504 19 72.89 10.75 +chr1 4382657 4385390 2733 1297 36 97.80 12.10 +chr1 4439048 4440167 1119 927 19 80.31 13.83 +chr1 4447108 4448669 1561 1375 31 62.31 7.54 +chr1 4462162 4466719 4557 4366 75 90.49 8.30 +chr1 4479282 4480091 809 700 19 60.40 10.33 +chr1 4568704 4569556 852 319 25 69.71 8.62 +chr1 4596926 4597745 819 449 17 51.74 9.48 +chr1 4636007 4637827 1820 110 30 51.27 8.57 +chr1 4646136 4647867 1731 101 28 53.47 7.38 |
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/macs_test_2_peaks_out.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/macs_test_2_peaks_out.interval Mon Jan 27 09:28:45 2014 -0500 |
| b |
| b'@@ -0,0 +1,1289 @@\n+#peaks file\n+# This file is generated by MACS\n+# ARGUMENTS LIST:\n+# name = Galaxy_Test_Run\n+# format = BED\n+# ChIP-seq file = /galaxy/home/dan/central/database/files/000/dataset_404.dat\n+# control file = /galaxy/home/dan/central/database/files/000/dataset_405.dat\n+# effective genome size = 2.70e+09\n+# tag size = 36\n+# band width = 300\n+# model fold = 13\n+# pvalue cutoff = 1.00e-05\n+# Ranges for calculating regional lambda are : peak_region,1000,5000,10000\n+# unique tags in treatment: 9898\n+# total tags in treatment: 10000\n+# unique tags in control: 9896\n+# total tags in control: 10000\n+# d = 113\n+#chr\tstart\tend\tlength\tsummit\ttags\t-10*log10(pvalue)\tfold_enrichment\tFDR(%)\n+chr1\t3138857\t3139271\t414\t95\t6\t53.08\t35.39\t3.55\n+chr1\t4133899\t4134700\t801\t157\t27\t51.91\t9.92\t3.70\n+chr1\t4323670\t4324367\t697\t306\t49\t272.01\t29.81\t0.00\n+chr1\t4336486\t4337946\t1460\t1216\t65\t228.35\t32.00\t0.00\n+chr1\t4407086\t4409120\t2034\t1133\t105\t300.46\t29.27\t0.00\n+chr1\t4507832\t4508710\t878\t245\t44\t161.74\t18.90\t0.00\n+chr1\t4657704\t4658572\t868\t775\t9\t280.37\t7242.01\t0.00\n+chr1\t4658705\t4659021\t316\t110\t4\t131.25\t4828.01\t0.00\n+chr1\t4659147\t4660581\t1434\t844\t15\t463.08\t7242.01\t0.00\n+chr1\t4661156\t4661317\t161\t81\t4\t174.88\t9656.01\t0.00\n+chr1\t4661505\t4661617\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4661790\t4662463\t673\t287\t7\t219.58\t4828.01\t0.00\n+chr1\t4662710\t4663434\t724\t623\t12\t395.94\t9656.01\t0.00\n+chr1\t4664135\t4664430\t295\t64\t5\t169.10\t7242.01\t0.00\n+chr1\t4665001\t4665113\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4665839\t4666425\t586\t475\t10\t332.40\t12070.02\t0.00\n+chr1\t4666581\t4666693\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4666840\t4666981\t141\t71\t4\t174.88\t9656.01\t0.00\n+chr1\t4667600\t4667712\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4668711\t4669005\t294\t75\t5\t169.17\t7242.01\t0.00\n+chr1\t4669126\t4669238\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4669537\t4669752\t215\t108\t5\t174.88\t12070.02\t0.00\n+chr1\t4669936\t4670048\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4670216\t4670449\t233\t97\t6\t212.68\t12070.02\t0.00\n+chr1\t4673856\t4674051\t195\t98\t4\t137.07\t9656.01\t0.00\n+chr1\t4674349\t4674478\t129\t65\t3\t137.07\t7242.01\t0.00\n+chr1\t4675027\t4675152\t125\t63\t3\t137.07\t7242.01\t0.00\n+chr1\t4676227\t4676339\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4676511\t4676623\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4676954\t4677151\t197\t99\t3\t100.24\t7242.01\t0.17\n+chr1\t4677646\t4677758\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4678360\t4678472\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4678659\t4679136\t477\t307\t7\t230.04\t7242.01\t0.00\n+chr1\t4679439\t4679551\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4680106\t4680523\t417\t103\t5\t126.43\t4828.01\t0.00\n+chr1\t4680822\t4680934\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4681075\t4682050\t975\t104\t8\t241.81\t4828.01\t0.00\n+chr1\t4682229\t4682387\t158\t80\t3\t100.24\t7242.01\t0.17\n+chr1\t4682594\t4682706\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4683158\t4683270\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4683473\t4683585\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4683832\t4683944\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4684591\t4684775\t184\t93\t3\t100.24\t7242.01\t0.17\n+chr1\t4685292\t4685404\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4685810\t4686198\t388\t75\t4\t127.69\t4828.01\t0.00\n+chr1\t4686493\t4686605\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4686818\t4686930\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4687387\t4687499\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4687692\t4687902\t210\t106\t5\t174.88\t12070.02\t0.00\n+chr1\t4688181\t4688790\t609\t96\t8\t258.16\t9656.01\t0.00\n+chr1\t4689101\t4689557\t456\t250\t7\t231.41\t9656.01\t0.00\n+chr1\t4690039\t4690151\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4690290\t4690402\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4690780\t4690907\t127\t64\t3\t137.07\t7242.01\t0.00\n+chr1\t4691478\t4692335\t857\t509\t10\t315.89\t7242.01\t0.00\n+chr1\t4692464\t4692768\t304\t67\t4\t131.92\t7242.01\t0.00\n+chr1\t4693243\t4693751\t508\t307\t7\t228.13\t9656.01\t0.00\n+chr1\t4694306\t4694418\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4694738\t4695016\t278\t75\t5\t170.38\t9656.01\t0.00\n+chr1\t4695207\t4695378\t171\t86\t3\t100.24\t7242.01\t0.17\n+chr1\t4695503\t4696600\t1097\t535\t12\t374.29\t7242.01\t0.00\n+chr1\t4696903\t4697015\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t4697569\t4697912\t343\t106\t7\t240.07\t12070.02\t0.00\n+chr1\t4698224\t4698395\t171\t86\t3\t100.24\t7242.01\t0.17\n+chr1\t46'..b'01\t0.17\n+chr1\t5676274\t5676386\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5676599\t5676711\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5677228\t5677340\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5677740\t5677852\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5679022\t5679667\t645\t364\t9\t291.97\t9656.01\t0.00\n+chr1\t5680026\t5681034\t1008\t230\t8\t240.66\t4828.01\t0.00\n+chr1\t5682911\t5683023\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5688032\t5688144\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5688335\t5688657\t322\t88\t4\t130.92\t4828.01\t0.00\n+chr1\t5688801\t5688913\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5689087\t5689348\t261\t57\t3\t98.36\t4828.01\t0.16\n+chr1\t5689475\t5689587\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5689771\t5689883\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5690261\t5690373\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5690750\t5690873\t123\t62\t3\t137.07\t7242.01\t0.00\n+chr1\t5694742\t5695180\t438\t98\t5\t160.51\t4828.01\t0.00\n+chr1\t5695333\t5695675\t342\t102\t4\t129.88\t7242.01\t0.00\n+chr1\t5696080\t5696192\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5696612\t5697345\t733\t264\t8\t251.72\t7242.01\t0.00\n+chr1\t5697961\t5698073\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5698235\t5698383\t148\t75\t3\t137.07\t7242.01\t0.00\n+chr1\t5698832\t5699021\t189\t95\t3\t100.24\t7242.01\t0.17\n+chr1\t5699479\t5699591\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5700029\t5700141\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5700387\t5700503\t116\t59\t3\t137.07\t7242.01\t0.00\n+chr1\t5703736\t5703848\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5704571\t5704683\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5704979\t5705219\t240\t82\t4\t136.03\t7242.01\t0.00\n+chr1\t5705728\t5705840\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5706213\t5706482\t269\t112\t7\t247.45\t14484.02\t0.00\n+chr1\t5706879\t5706991\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5707211\t5707414\t203\t102\t3\t100.24\t7242.01\t0.17\n+chr1\t5707733\t5707955\t222\t112\t3\t100.24\t7242.01\t0.17\n+chr1\t5708418\t5708530\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5708711\t5708823\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5709009\t5709168\t159\t80\t3\t100.24\t7242.01\t0.17\n+chr1\t5709626\t5709738\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5710175\t5710287\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5711491\t5711603\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5712452\t5712913\t461\t84\t5\t159.40\t4828.01\t0.00\n+chr1\t5713590\t5713702\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5714277\t5714835\t558\t448\t6\t189.93\t7242.01\t0.00\n+chr1\t5715628\t5715793\t165\t83\t3\t100.24\t7242.01\t0.17\n+chr1\t5715919\t5716031\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5716150\t5716384\t234\t111\t5\t174.12\t9656.01\t0.00\n+chr1\t5717000\t5717112\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5717383\t5717774\t391\t111\t4\t127.55\t7242.01\t0.00\n+chr1\t5718298\t5718531\t233\t88\t4\t136.54\t7242.01\t0.00\n+chr1\t5718754\t5719002\t248\t96\t5\t172.86\t9656.01\t0.00\n+chr1\t5719627\t5719739\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5720578\t5720690\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5721523\t5721843\t320\t57\t3\t95.71\t4828.01\t0.24\n+chr1\t5722221\t5722388\t167\t84\t3\t100.24\t7242.01\t0.17\n+chr1\t5722739\t5722851\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5723148\t5723403\t255\t105\t4\t134.98\t4828.01\t0.00\n+chr1\t5724342\t5724566\t224\t57\t3\t100.24\t4828.01\t0.17\n+chr1\t5725453\t5725597\t144\t73\t3\t137.07\t7242.01\t0.00\n+chr1\t5725942\t5726075\t133\t67\t3\t137.07\t7242.01\t0.00\n+chr1\t5726202\t5726647\t445\t349\t9\t306.48\t12070.02\t0.00\n+chr1\t5726801\t5726913\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5727303\t5727415\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5727541\t5727720\t179\t90\t5\t213.48\t12070.02\t0.00\n+chr1\t5728015\t5728127\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5728661\t5728922\t261\t57\t3\t98.36\t4828.01\t0.16\n+chr1\t5729591\t5729703\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5729971\t5730118\t147\t74\t3\t137.07\t7242.01\t0.00\n+chr1\t5735097\t5735209\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5738165\t5738277\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5741886\t5742013\t127\t64\t3\t137.07\t7242.01\t0.00\n+chr1\t5742222\t5742493\t271\t85\t4\t133.92\t7242.01\t0.00\n+chr1\t5742624\t5742892\t268\t57\t3\t98.02\t4828.01\t0.16\n+chr1\t5743479\t5743591\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5743802\t5743943\t141\t71\t3\t137.07\t7242.01\t0.00\n+chr1\t5744327\t5745001\t674\t99\t6\t185.01\t4828.01\t0.00\n+chr1\t5745544\t5746174\t630\t291\t7\t221.59\t4828.01\t0.00\n+chr1\t5746482\t5747182\t700\t89\t7\t218.38\t9656.01\t0.00\n+chr1\t5747751\t5747863\t112\t57\t2\t100.24\t4828.01\t0.17\n+chr1\t5749480\t5749592\t112\t57\t2\t100.24\t4828.01\t0.17\n' |
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/macs_test_3_control_out.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/macs_test_3_control_out.wig Mon Jan 27 09:28:45 2014 -0500 |
| b |
| b'@@ -0,0 +1,69418 @@\n+track type=wiggle_0 name="MACS_in_Galaxy_control_chr1" description="Shifted Merged MACS tag counts for every 10 bp"\n+variableStep chrom=chr1 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|
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/macs_test_3_out.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/macs_test_3_out.html Mon Jan 27 09:28:45 2014 -0500 |
| b |
| @@ -0,0 +1,54 @@ +\<html\>\<head\>\<title\>Additional\ output\ created\ by\ MACS\ \(Galaxy\_Test\_Run\)\<\/title\>\<\/head\>\<body\>\<h3\>Additional\ Files\:\<\/h3\>\<p\>\<ul\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.pdf\"\>Galaxy\_Test\_Run\_model\.pdf\<\/a\>\<\/li\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\"\>Galaxy\_Test\_Run\_model\.r\<\/a\>\<\/li\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\.log\"\>Galaxy\_Test\_Run\_model\.r\.log\<\/a\>\<\/li\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_negative\_peaks\.xls\"\>Galaxy\_Test\_Run\_negative\_peaks\.xls\<\/a\>\<\/li\> +\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_peaks\.xls\"\>Galaxy\_Test\_Run\_peaks\.xls\<\/a\>\<\/li\> +\<\/ul\>\<\/p\> +\<h3\>Messages\ from\ MACS\:\<\/h3\> +\<p\>\<pre\>INFO\ \ \@\ .*\:\ +\#\ ARGUMENTS\ LIST\: +\#\ name\ \=\ Galaxy\_Test\_Run +\#\ format\ \=\ BED +\#\ ChIP\-seq\ file\ \=\ .*\.dat +\#\ control\ file\ \=\ .*\.dat +\#\ effective\ genome\ size\ \=\ 2\.70e\+09 +\#\ tag\ size\ \=\ 36 +\#\ band\ width\ \=\ 300 +\#\ model\ fold\ \=\ 13 +\#\ pvalue\ cutoff\ \=\ 1\.00e\-05 +\#\ Ranges\ for\ calculating\ regional\ lambda\ are\ \:\ peak\_region\,1000\,5000\,10000\ +INFO\ \ \@\ .*\:\ \#1\ read\ tag\ files\.\.\.\ +INFO\ \ \@\ .*\:\ \#1\ read\ treatment\ tags\.\.\.\ +INFO\ \ \@\ .*\:\ \#1\.2\ read\ input\ tags\.\.\.\ +INFO\ \ \@\ .*\:\ \#1\ \ Background\ Redundant\ rate\:\ 1\.00\ +INFO\ \ \@\ .*\:\ \#1\ finished\!\ +INFO\ \ \@\ .*\:\ \#2\ Build\ Peak\ Model\.\.\.\ +INFO\ \ \@\ .*\:\ \#2\ number\ of\ paired\ peaks\:\ 549\ +WARNING\ \@\ .*\:\ Fewer\ paired\ peaks\ \(549\)\ than\ 1000\!\ Model\ may\ not\ be\ build\ well\!\ Lower\ your\ MFOLD\ parameter\ may\ erase\ this\ warning\.\ Now\ I\ will\ use\ 549\ pairs\ to\ build\ model\!\ +INFO\ \ \@\ .*\:\ \#2\ finished\!\ +INFO\ \ \@\ .*\:\ \#2\.2\ Generate\ R\ script\ for\ model\ \:\ Galaxy\_Test\_Run\_model\.r\ +INFO\ \ \@\ .*\:\ \#3\ Call\ peaks\.\.\.\ +INFO\ \ \@\ .*\:\ \#3\ shift\ treatment\ data\ +INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ treatment\ data\ +INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\ +INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/treat\/Galaxy\_Test\_Run\_treat\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\ +INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\ +INFO\ \ \@\ .*\:\ \#3\ call\ peak\ candidates\ +INFO\ \ \@\ .*\:\ \#3\ shift\ control\ data\ +INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ control\ data\ +INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\ +INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/control\/Galaxy\_Test\_Run\_control\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\ +INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\ +INFO\ \ \@\ .*\:\ \#3\ call\ negative\ peak\ candidates\ +INFO\ \ \@\ .*\:\ \#3\ use\ control\ data\ to\ filter\ peak\ candidates\.\.\.\ +INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 1270\ peaks\ are\ called\!\ +INFO\ \ \@\ .*\:\ \#3\ find\ negative\ peaks\ by\ reversing\ treat\ and\ control\ +INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 57\ peaks\ are\ called\!\ +INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.xls\ +INFO\ \ \@\ .*\:\ \#4\ Write\ output\ bed\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.bed\ +INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\ for\ negative\ peaks\.\.\.\ Galaxy\_Test\_Run\_negative\_peaks\.xls\ +INFO\ \ \@\ .*\:\ \#5\ Done\!\ Check\ the\ output\ files\! +\ +\<\/pre\>\<\/p\> +\<\/body\>\<\/html\> |
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/macs_test_3_treatment_out.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/macs_test_3_treatment_out.wig Mon Jan 27 09:28:45 2014 -0500 |
| b |
| b'@@ -0,0 +1,77293 @@\n+track type=wiggle_0 name="MACS_in_Galaxy_treat_chr1" description="Shifted Merged MACS tag counts for every 10 bp"\n+variableStep chrom=chr1 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|
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.pdf Mon Jan 27 09:28:45 2014 -0500 |
| [ |
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| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.r Mon Jan 27 09:28:45 2014 -0500 |
| [ |
| b'@@ -0,0 +1,16 @@\n+\\#\\ R\\ script\\ for\\ Peak\\ Model\n+\\#\\ \\ \\-\\-\\ generated\\ by\\ MACS\n+p\\ \\<\\-\\ 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\\<\\-\\ seq\\.int\\(\\(length\\(p\\)\\-1\\)\\/2\\*\\-1\\,\\(length\\(p\\)\\-1\\)\\/2\\)\n+pdf\\(\\"Galaxy\\_Test\\_Run\\_model\\.pdf\\"\\,height\\=6\\,width\\=6\\)\n+plot\\(x\\,p\\,type\\=\\"l\\"\\,col\\=c\\(\\"red\\"\\)\\,main\\=\\"Peak\\ Model\\"\\,xlab\\=\\"Distance\\ to\\ the\\ middle\\"\\,ylab\\=\\"Percentage\\"\\)\n+lines\\(x\\,m\\,col\\=c\\(\\"blue\\"\\)\\)\n+lines\\(x\\,s\\,col\\=c\\(\\"black\\"\\)\\)\n+abline\\(v\\=median\\(x\\[p\\=\\=max\\(p\\)\\]\\)\\,lty\\=2\\,col\\=c\\(\\"red\\"\\)\\)\n+abline\\(v\\=median\\(x\\[m\\=\\=max\\(m\\)\\]\\)\\,lty\\=2\\,col\\=c\\(\\"blue\\"\\)\\)\n+abline\\(v\\=median\\(x\\[s\\=\\=max\\(s\\)\\]\\)\\,lty\\=2\\,col\\=c\\(\\"black\\"\\)\\)\n+legend\\(\\"topleft\\"\\,c\\(\\"forward\\ tags\\"\\,\\"reverse\\ tags\\"\\,\\"shifted\\ tags\\"\\)\\,lty\\=c\\(1\\,1\\,1\\)\\,col\\=c\\(\\"red\\"\\,\\"blue\\"\\,\\"black\\"\\)\\)\n+legend\\(\\"right\\"\\,c\\(\\"d\\=113\\"\\)\\,bty\\=\\"n\\"\\)\n+dev\\.off\\(\\)\n' |
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.r.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.r.log Mon Jan 27 09:28:45 2014 -0500 |
| b |
| @@ -0,0 +1,2 @@ +null device + 1 |
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/test2/Galaxy_Test_Run_negative_peaks.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/test2/Galaxy_Test_Run_negative_peaks.xls Mon Jan 27 09:28:45 2014 -0500 |
| b |
| @@ -0,0 +1,58 @@ +chr\ start\ end\ length\ summit\ tags\ \-10\*log10\(pvalue\)\ fold\_enrichment +chr1\ 3012339\ 3012474\ 136\ 69\ 3\ 79\.72\ 265\.54 +chr1\ 3012632\ 3012751\ 120\ 61\ 3\ 79\.72\ 265\.54 +chr1\ 3055827\ 3056120\ 294\ 96\ 9\ 59\.49\ 18\.22 +chr1\ 3066935\ 3067568\ 634\ 101\ 10\ 53\.35\ 18\.44 +chr1\ 3076060\ 3076339\ 280\ 112\ 6\ 58\.24\ 29\.50 +chr1\ 3092688\ 3093270\ 583\ 344\ 11\ 50\.81\ 10\.32 +chr1\ 3114124\ 3114523\ 400\ 107\ 10\ 51\.47\ 11\.06 +chr1\ 3125325\ 3126255\ 931\ 573\ 13\ 65\.69\ 12\.07 +chr1\ 3126474\ 3127174\ 701\ 249\ 11\ 65\.43\ 13\.28 +chr1\ 3127354\ 3127879\ 526\ 265\ 14\ 110\.59\ 22\.13 +chr1\ 3195225\ 3195844\ 620\ 395\ 13\ 56\.61\ 13\.28 +chr1\ 3228284\ 3228748\ 465\ 388\ 6\ 50\.25\ 26\.55 +chr1\ 3275976\ 3276467\ 492\ 404\ 9\ 55\.17\ 15\.39 +chr1\ 3285008\ 3286005\ 998\ 891\ 18\ 66\.19\ 11\.06 +chr1\ 3312700\ 3313743\ 1044\ 204\ 21\ 60\.12\ 11\.06 +chr1\ 3446633\ 3447508\ 876\ 176\ 14\ 61\.26\ 14\.75 +chr1\ 3468403\ 3469436\ 1034\ 109\ 18\ 50\.75\ 7\.08 +chr1\ 3474773\ 3476374\ 1602\ 960\ 22\ 66\.92\ 12\.29 +chr1\ 3514509\ 3515086\ 578\ 110\ 13\ 59\.90\ 11\.06 +chr1\ 3517010\ 3518094\ 1085\ 84\ 14\ 50\.75\ 11\.80 +chr1\ 3599830\ 3601141\ 1312\ 109\ 19\ 65\.77\ 10\.41 +chr1\ 3605829\ 3605951\ 123\ 62\ 4\ 52\.20\ 18\.63 +chr1\ 3606597\ 3607433\ 837\ 548\ 10\ 66\.22\ 27\.23 +chr1\ 3613852\ 3614116\ 265\ 103\ 6\ 57\.63\ 34\.04 +chr1\ 3614433\ 3615882\ 1450\ 85\ 15\ 63\.55\ 13\.28 +chr1\ 3617466\ 3617784\ 319\ 211\ 9\ 51\.03\ 11\.06 +chr1\ 3640316\ 3641949\ 1634\ 273\ 32\ 81\.39\ 10\.68 +chr1\ 3647350\ 3648562\ 1213\ 411\ 19\ 67\.14\ 9\.83 +chr1\ 3735802\ 3736852\ 1051\ 878\ 17\ 73\.61\ 14\.75 +chr1\ 3796006\ 3796544\ 539\ 65\ 5\ 54\.89\ 44\.26 +chr1\ 3797372\ 3797763\ 392\ 70\ 6\ 54\.44\ 26\.55 +chr1\ 3835422\ 3835673\ 252\ 171\ 6\ 53\.74\ 22\.13 +chr1\ 3856582\ 3857561\ 980\ 110\ 19\ 52\.84\ 9\.48 +chr1\ 3968247\ 3968621\ 375\ 85\ 7\ 60\.72\ 34\.04 +chr1\ 3970429\ 3970718\ 290\ 69\ 5\ 56\.15\ 50\.58 +chr1\ 4034954\ 4036094\ 1141\ 465\ 15\ 66\.64\ 18\.44 +chr1\ 4051824\ 4055268\ 3445\ 669\ 46\ 119\.08\ 9\.32 +chr1\ 4099918\ 4100882\ 965\ 256\ 18\ 84\.48\ 11\.39 +chr1\ 4112354\ 4113269\ 916\ 72\ 15\ 53\.99\ 9\.32 +chr1\ 4139621\ 4140296\ 676\ 399\ 14\ 71\.23\ 11\.06 +chr1\ 4191035\ 4191488\ 454\ 386\ 9\ 51\.16\ 15\.81 +chr1\ 4191775\ 4192345\ 571\ 102\ 10\ 51\.50\ 12\.64 +chr1\ 4201260\ 4202176\ 917\ 651\ 13\ 64\.28\ 19\.24 +chr1\ 4218598\ 4219458\ 861\ 460\ 16\ 53\.64\ 5\.77 +chr1\ 4223609\ 4224231\ 623\ 472\ 14\ 78\.93\ 14\.75 +chr1\ 4238529\ 4239382\ 854\ 90\ 14\ 54\.69\ 15\.12 +chr1\ 4283407\ 4284196\ 790\ 400\ 11\ 60\.42\ 22\.13 +chr1\ 4368610\ 4369824\ 1215\ 504\ 19\ 72\.89\ 10\.75 +chr1\ 4382658\ 4385390\ 2733\ 1297\ 36\ 97\.80\ 12\.10 +chr1\ 4439049\ 4440167\ 1119\ 927\ 19\ 80\.31\ 13\.83 +chr1\ 4447109\ 4448669\ 1561\ 1375\ 31\ 62\.31\ 7\.54 +chr1\ 4462163\ 4466719\ 4557\ 4366\ 75\ 90\.49\ 8\.30 +chr1\ 4479283\ 4480091\ 809\ 700\ 19\ 60\.40\ 10\.33 +chr1\ 4568705\ 4569556\ 852\ 319\ 25\ 69\.71\ 8\.62 +chr1\ 4596927\ 4597745\ 819\ 449\ 17\ 51\.74\ 9\.48 +chr1\ 4636008\ 4637827\ 1820\ 110\ 30\ 51\.27\ 8\.57 +chr1\ 4646137\ 4647867\ 1731\ 101\ 28\ 53\.47\ 7\.38 |
| b |
| diff -r 000000000000 -r ae2ec275332a test-data/peakcalling_macs/test2/Galaxy_Test_Run_peaks.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/test2/Galaxy_Test_Run_peaks.xls Mon Jan 27 09:28:45 2014 -0500 |
| b |
| b'@@ -0,0 +1,1288 @@\n+\\#\\ This\\ file\\ is\\ generated\\ by\\ MACS\n+\\#\\ ARGUMENTS\\ LIST\\:\n+\\#\\ name\\ \\=\\ Galaxy\\_Test\\_Run\n+\\#\\ format\\ \\=\\ BED\n+\\#\\ ChIP\\-seq\\ file\\ \\=\\ .*\\.dat\n+\\#\\ control\\ file\\ \\=\\ .*\\.dat\n+\\#\\ effective\\ genome\\ size\\ \\=\\ 2\\.70e\\+09\n+\\#\\ tag\\ size\\ \\=\\ 36\n+\\#\\ band\\ width\\ \\=\\ 300\n+\\#\\ model\\ fold\\ \\=\\ 13\n+\\#\\ pvalue\\ cutoff\\ \\=\\ 1\\.00e\\-05\n+\\#\\ Ranges\\ for\\ calculating\\ regional\\ lambda\\ are\\ \\:\\ peak\\_region\\,1000\\,5000\\,10000\n+\\#\\ unique\\ tags\\ in\\ treatment\\:\\ 9898\n+\\#\\ total\\ tags\\ in\\ treatment\\:\\ 10000\n+\\#\\ unique\\ tags\\ in\\ control\\:\\ 9896\n+\\#\\ total\\ tags\\ in\\ control\\:\\ 10000\n+\\#\\ d\\ \\=\\ 113\n+chr\\\tstart\\\tend\\\tlength\\\tsummit\\\ttags\\\t\\-10\\*log10\\(pvalue\\)\\\tfold\\_enrichment\\\tFDR\\(\\%\\)\n+chr1\\\t3138858\\\t3139271\\\t414\\\t95\\\t6\\\t53\\.08\\\t35\\.39\\\t3\\.55\n+chr1\\\t4133900\\\t4134700\\\t801\\\t157\\\t27\\\t51\\.91\\\t9\\.92\\\t3\\.70\n+chr1\\\t4323671\\\t4324367\\\t697\\\t306\\\t49\\\t272\\.01\\\t29\\.81\\\t0\\.00\n+chr1\\\t4336487\\\t4337946\\\t1460\\\t1216\\\t65\\\t228\\.35\\\t32\\.00\\\t0\\.00\n+chr1\\\t4407087\\\t4409120\\\t2034\\\t1133\\\t105\\\t300\\.46\\\t29\\.27\\\t0\\.00\n+chr1\\\t4507833\\\t4508710\\\t878\\\t245\\\t44\\\t161\\.74\\\t18\\.90\\\t0\\.00\n+chr1\\\t4657705\\\t4658572\\\t868\\\t775\\\t9\\\t280\\.37\\\t7242\\.01\\\t0\\.00\n+chr1\\\t4658706\\\t4659021\\\t316\\\t110\\\t4\\\t131\\.25\\\t4828\\.01\\\t0\\.00\n+chr1\\\t4659148\\\t4660581\\\t1434\\\t844\\\t15\\\t463\\.08\\\t7242\\.01\\\t0\\.00\n+chr1\\\t4661157\\\t4661317\\\t161\\\t81\\\t4\\\t174\\.88\\\t9656\\.01\\\t0\\.00\n+chr1\\\t4661506\\\t4661617\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4661791\\\t4662463\\\t673\\\t287\\\t7\\\t219\\.58\\\t4828\\.01\\\t0\\.00\n+chr1\\\t4662711\\\t4663434\\\t724\\\t623\\\t12\\\t395\\.94\\\t9656\\.01\\\t0\\.00\n+chr1\\\t4664136\\\t4664430\\\t295\\\t64\\\t5\\\t169\\.10\\\t7242\\.01\\\t0\\.00\n+chr1\\\t4665002\\\t4665113\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4665840\\\t4666425\\\t586\\\t475\\\t10\\\t332\\.40\\\t12070\\.02\\\t0\\.00\n+chr1\\\t4666582\\\t4666693\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4666841\\\t4666981\\\t141\\\t71\\\t4\\\t174\\.88\\\t9656\\.01\\\t0\\.00\n+chr1\\\t4667601\\\t4667712\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4668712\\\t4669005\\\t294\\\t75\\\t5\\\t169\\.17\\\t7242\\.01\\\t0\\.00\n+chr1\\\t4669127\\\t4669238\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4669538\\\t4669752\\\t215\\\t108\\\t5\\\t174\\.88\\\t12070\\.02\\\t0\\.00\n+chr1\\\t4669937\\\t4670048\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4670217\\\t4670449\\\t233\\\t97\\\t6\\\t212\\.68\\\t12070\\.02\\\t0\\.00\n+chr1\\\t4673857\\\t4674051\\\t195\\\t98\\\t4\\\t137\\.07\\\t9656\\.01\\\t0\\.00\n+chr1\\\t4674350\\\t4674478\\\t129\\\t65\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t4675028\\\t4675152\\\t125\\\t63\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t4676228\\\t4676339\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4676512\\\t4676623\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4676955\\\t4677151\\\t197\\\t99\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t4677647\\\t4677758\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4678361\\\t4678472\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4678660\\\t4679136\\\t477\\\t307\\\t7\\\t230\\.04\\\t7242\\.01\\\t0\\.00\n+chr1\\\t4679440\\\t4679551\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4680107\\\t4680523\\\t417\\\t103\\\t5\\\t126\\.43\\\t4828\\.01\\\t0\\.00\n+chr1\\\t4680823\\\t4680934\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4681076\\\t4682050\\\t975\\\t104\\\t8\\\t241\\.81\\\t4828\\.01\\\t0\\.00\n+chr1\\\t4682230\\\t4682387\\\t158\\\t80\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t4682595\\\t4682706\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4683159\\\t4683270\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4683474\\\t4683585\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4683833\\\t4683944\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4684592\\\t4684775\\\t184\\\t93\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t4685293\\\t4685404\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4685811\\\t4686198\\\t388\\\t75\\\t4\\\t127\\.69\\\t4828\\.01\\\t0\\.00\n+chr1\\\t4686494\\\t4686605\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4686819\\\t4686930\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4687388\\\t4687499\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4687693\\\t4687902\\\t210\\\t106\\\t5\\\t174\\.88\\\t12070\\.02\\\t0\\.00\n+chr1\\\t4688182\\\t4688790\\\t609\\\t96\\\t8\\\t258\\.16\\\t9656\\.01\\\t0\\.00\n+chr1\\\t4689102\\\t4689557\\\t456\\\t250\\\t7\\\t231\\.41\\\t9656\\.01\\\t0\\.00\n+chr1\\\t4690040\\\t4690151\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t4690291\\\t4690402\\\t112\\\t57\\\t2\\\t100'..b'24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5690751\\\t5690873\\\t123\\\t62\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5694743\\\t5695180\\\t438\\\t98\\\t5\\\t160\\.51\\\t4828\\.01\\\t0\\.00\n+chr1\\\t5695334\\\t5695675\\\t342\\\t102\\\t4\\\t129\\.88\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5696081\\\t5696192\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5696613\\\t5697345\\\t733\\\t264\\\t8\\\t251\\.72\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5697962\\\t5698073\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5698236\\\t5698383\\\t148\\\t75\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5698833\\\t5699021\\\t189\\\t95\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t5699480\\\t5699591\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5700030\\\t5700141\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5700388\\\t5700503\\\t116\\\t59\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5703737\\\t5703848\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5704572\\\t5704683\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5704980\\\t5705219\\\t240\\\t82\\\t4\\\t136\\.03\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5705729\\\t5705840\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5706214\\\t5706482\\\t269\\\t112\\\t7\\\t247\\.45\\\t14484\\.02\\\t0\\.00\n+chr1\\\t5706880\\\t5706991\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5707212\\\t5707414\\\t203\\\t102\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t5707734\\\t5707955\\\t222\\\t112\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t5708419\\\t5708530\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5708712\\\t5708823\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5709010\\\t5709168\\\t159\\\t80\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t5709627\\\t5709738\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5710176\\\t5710287\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5711492\\\t5711603\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5712453\\\t5712913\\\t461\\\t84\\\t5\\\t159\\.40\\\t4828\\.01\\\t0\\.00\n+chr1\\\t5713591\\\t5713702\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5714278\\\t5714835\\\t558\\\t448\\\t6\\\t189\\.93\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5715629\\\t5715793\\\t165\\\t83\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t5715920\\\t5716031\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5716151\\\t5716384\\\t234\\\t111\\\t5\\\t174\\.12\\\t9656\\.01\\\t0\\.00\n+chr1\\\t5717001\\\t5717112\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5717384\\\t5717774\\\t391\\\t111\\\t4\\\t127\\.55\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5718299\\\t5718531\\\t233\\\t88\\\t4\\\t136\\.54\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5718755\\\t5719002\\\t248\\\t96\\\t5\\\t172\\.86\\\t9656\\.01\\\t0\\.00\n+chr1\\\t5719628\\\t5719739\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5720579\\\t5720690\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5721524\\\t5721843\\\t320\\\t57\\\t3\\\t95\\.71\\\t4828\\.01\\\t0\\.24\n+chr1\\\t5722222\\\t5722388\\\t167\\\t84\\\t3\\\t100\\.24\\\t7242\\.01\\\t0\\.17\n+chr1\\\t5722740\\\t5722851\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5723149\\\t5723403\\\t255\\\t105\\\t4\\\t134\\.98\\\t4828\\.01\\\t0\\.00\n+chr1\\\t5724343\\\t5724566\\\t224\\\t57\\\t3\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5725454\\\t5725597\\\t144\\\t73\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5725943\\\t5726075\\\t133\\\t67\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5726203\\\t5726647\\\t445\\\t349\\\t9\\\t306\\.48\\\t12070\\.02\\\t0\\.00\n+chr1\\\t5726802\\\t5726913\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5727304\\\t5727415\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5727542\\\t5727720\\\t179\\\t90\\\t5\\\t213\\.48\\\t12070\\.02\\\t0\\.00\n+chr1\\\t5728016\\\t5728127\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5728662\\\t5728922\\\t261\\\t57\\\t3\\\t98\\.36\\\t4828\\.01\\\t0\\.16\n+chr1\\\t5729592\\\t5729703\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5729972\\\t5730118\\\t147\\\t74\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5735098\\\t5735209\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5738166\\\t5738277\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5741887\\\t5742013\\\t127\\\t64\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5742223\\\t5742493\\\t271\\\t85\\\t4\\\t133\\.92\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5742625\\\t5742892\\\t268\\\t57\\\t3\\\t98\\.02\\\t4828\\.01\\\t0\\.16\n+chr1\\\t5743480\\\t5743591\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5743803\\\t5743943\\\t141\\\t71\\\t3\\\t137\\.07\\\t7242\\.01\\\t0\\.00\n+chr1\\\t5744328\\\t5745001\\\t674\\\t99\\\t6\\\t185\\.01\\\t4828\\.01\\\t0\\.00\n+chr1\\\t5745545\\\t5746174\\\t630\\\t291\\\t7\\\t221\\.59\\\t4828\\.01\\\t0\\.00\n+chr1\\\t5746483\\\t5747182\\\t700\\\t89\\\t7\\\t218\\.38\\\t9656\\.01\\\t0\\.00\n+chr1\\\t5747752\\\t5747863\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n+chr1\\\t5749481\\\t5749592\\\t112\\\t57\\\t2\\\t100\\.24\\\t4828\\.01\\\t0\\.17\n' |
| b |
| diff -r 000000000000 -r ae2ec275332a tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:28:45 2014 -0500 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="macs" version="1.3.7.1"> + <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="2.15.0"> + <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |