| Next changeset 1:201d8e7dfc43 (2015-07-21) |
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Commit message:
Imported from capsule None |
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added:
ccat_wrapper.py ccat_wrapper.xml test-data/1.interval test-data/1.txt test-data/2.interval test-data/2.txt test-data/a.tab test-data/chipseq_enriched.bed.gz test-data/chipseq_input.bed.gz test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match test-data/peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match tool-data/ccat_configurations.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r a0c8dc671a23 ccat_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ccat_wrapper.py Mon Jan 27 09:27:03 2014 -0500 |
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| @@ -0,0 +1,41 @@ +import sys, subprocess, tempfile, shutil, os.path + +CCAT_BINARY = "CCAT" + +def get_top_count( filename ): + for line in open( filename ): + if line.startswith( 'outputNum' ): + return int( line.split()[-1].strip() ) + +def stop_err( tmp_dir, exception ): + print >> sys.stderr, "Error running CCAT." + shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory + raise exception + +def main(): + input_tag_file = sys.argv[1] + input_control_file = sys.argv[2] + chrom_info_file = sys.argv[3] + input_config_file = sys.argv[4] + project_name = sys.argv[5] + output_peak_file = sys.argv[6] + output_region_file = sys.argv[7] + output_top_file = sys.argv[8] + output_log_file = sys.argv[9] + + tmp_dir = tempfile.mkdtemp() + try: + assert os.path.exists( chrom_info_file ), "The required chromosome length file does not exist." + proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "'%s'" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir ) + proc.wait() + if proc.returncode: + raise Exception( "Error code: %i" % proc.returncode ) + output_num = get_top_count( input_config_file ) + shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file ) + shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file ) + shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file ) + except Exception, e: + return stop_err( tmp_dir, e ) + os.rmdir( tmp_dir ) #clean up empty temp working directory + +if __name__ == "__main__": main() |
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| diff -r 000000000000 -r a0c8dc671a23 ccat_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ccat_wrapper.xml Mon Jan 27 09:27:03 2014 -0500 |
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| b'@@ -0,0 +1,148 @@\n+<tool id="peakcalling_ccat" name="CCAT" version="0.0.1">\n+ <description>Control-based ChIP-seq Analysis Tool</description>\n+ <requirements>\n+ <requirement type="package" version="3.0">CCAT</requirement>\n+ </requirements>\n+ <command interpreter="python">ccat_wrapper.py \'$input_tag_file\' \'$input_control_file\' \'$chromInfo\' \n+ #if str( $options_type[ \'options_type_selector\' ] ) == \'advanced\':\n+ \'$input_advanced_config_file\' \n+ #else:\n+ \'${ options_type.input_config_file.fields.path }\'\n+ #end if\n+ \'CCAT in Galaxy\' \n+ \'$output_peak_file\' \'$output_region_file\' \'$output_top_file\' \'$output_log_file\'</command>\n+ <inputs>\n+ <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" >\n+ <validator type="unspecified_build" />\n+ </param>\n+ <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" >\n+ <validator type="unspecified_build" />\n+ </param>\n+ <conditional name="options_type">\n+ <param name="options_type_selector" type="select" label="Advanced Options">\n+ <option value="basic" selected="True">Hide Advanced Options</option>\n+ <option value="advanced">Show Advanced Options</option>\n+ </param>\n+ <when value="basic">\n+ <param name="input_config_file" type="select" label="Select a pre-defined configuration file">\n+ <options from_data_table="ccat_configurations">\n+ <validator type="no_options" message="No configurations are available"/>\n+ </options>\n+ </param>\n+ </when>\n+ <when value="advanced">\n+ <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>\n+ <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>\n+ <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>\n+ <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >\n+ <option value="1">Transition from sense strand to anti-sense strand</option>\n+ <option value="0" selected="True">Local maximum of read-enrichment profile</option>\n+ </param>\n+ <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>\n+ <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>\n+ <param name="random_seed" type="integer" label="Random Seed" value="123456"/>\n+ <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>\n+ <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">\n+ <actions>\n+ <action type="metadata" name="chromCol" default="1"/>\n+ <action type="metadata" name="startCol" default="3"/>\n+ <action type="metadata" name="endCol" default="4"/>\n+ </actions>\n+ </data>\n+ <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">\n+ <actions>\n+ <action type="metadata" name="chromCol" default="1"/>\n+ <action type="metadata" name="startCol" default="3"/>\n+ <action type="metadata" name="endCol" default="4"/>\n+ </actions>\n+ </data>\n+ <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">\n+ <actions>\n+ <action type="metadata" name="chromCol" default="1"/>\n+ <action type="metadata" name="startCol" default="3"/>\n+ <action type="metadata" name="endCol" default="4"/>\n+ </actions>\n+ </data>\n+ <data name="output_log_file" fo'..b' ]}\n+minScore\t${options_type[ \'min_score\' ]}\t\n+bootstrapPass\t${options_type[ \'bootstrap_pass\' ]}\n+#end if</configfile>\n+ </configfiles>\n+ <tests>\n+ <test>\n+ <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />\n+ <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />\n+ <param name="options_type_selector" value="advanced" />\n+ <param name="fragment_size" value="200" />\n+ <param name="sliding_window_size" value="500" />\n+ <param name="moving_step" value="50" />\n+ <param name="is_strand_sensitive_mode" value="0" />\n+ <param name="min_count" value="4" />\n+ <param name="output_num" value="100000" />\n+ <param name="random_seed" value="123456" />\n+ <param name="min_score" value="5.0" />\n+ <param name="bootstrap_pass" value="50" />\n+ <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />\n+ <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />\n+ <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" />\n+ <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />\n+ </test>\n+ <test>\n+ <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />\n+ <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />\n+ <param name="options_type_selector" value="basic" />\n+ <param name="input_config_file" value="ccat_3.0_histone_config" />\n+ <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />\n+ <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />\n+ <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />\n+ <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />\n+ </test>\n+ <!-- Test below gives different answers on different architectures, \n+ e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386 \n+ slidingWinSize was fixed to be 1000, default as per readme.txt\n+ -->\n+ <!--\n+ <test>\n+ <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />\n+ <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />\n+ <param name="options_type_selector" value="basic" />\n+ <param name="input_config_file" value="ccat_3.0_histone_config_readme" />\n+ <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" />\n+ <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" />\n+ <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match" compare="re_match" sort="true" />\n+ <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" />\n+ </test>\n+ -->\n+ </tests>\n+ <help>\n+**What it does**\n+\n+This tool allows ChIP-seq peak/region calling using CCAT.\n+\n+View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm.\n+\n+------\n+\n+**Citation**\n+\n+For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. <http://www.ncbi.nlm.nih.gov/pubmed/20371496>`_\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 a0c8dc671a23 test-data/1.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.interval Mon Jan 27 09:27:03 2014 -0500 |
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| @@ -0,0 +1,5 @@ +chr1 4348187 4348589 3.70 4.90 2.55 0.24 0.46 +chr1 4488177 4488442 4.03 5.77 1.92 -0.67 0.81 +chr1 4774091 4774440 8.07 8.33 7.82 0.85 -0.40 +chr1 4800122 4800409 6.40 7.35 5.44 1.19 -0.42 +chr1 4878925 4879277 2.18 0.28 4.93 -0.96 1.24 |
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| diff -r 000000000000 -r a0c8dc671a23 test-data/1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.txt Mon Jan 27 09:27:03 2014 -0500 |
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| @@ -0,0 +1,10 @@ +chr1 4225 19670 +chr10 6 8 +chr1 24417 24420 +chr6_hla_hap2 0 150 +chr2 1 5 +chr10 2 10 +chr1 30 55 +chrY 1 20 +chr1 1225979 42287290 +chr10 7 8 |
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| diff -r 000000000000 -r a0c8dc671a23 test-data/2.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.interval Mon Jan 27 09:27:03 2014 -0500 |
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| @@ -0,0 +1,14 @@ +chrX 151117436 151117437 + 0.14351 +chrX 151117437 151117438 + 0.139843 +chrX 151117438 151117439 + 0.132509 +chrX 151117439 151117440 + 0.139843 +chrX 151117440 151117441 + 0.169179 +chrX 151117441 151117442 + 0.257185 +chrX 151117442 151117443 + 0.319523 +chrX 151117443 151117444 + 0.367193 +chrX 151117444 151117445 + 0.400195 +chrX 151117445 151117446 + 0.425864 +chrX 151117446 151117447 + 0.444198 +chrX 151117447 151117448 + 0.455199 +chrX 151117448 151117449 + 0.462533 +chrX 151117449 151117450 + 0.4662 |
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| diff -r 000000000000 -r a0c8dc671a23 test-data/2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.txt Mon Jan 27 09:27:03 2014 -0500 |
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| @@ -0,0 +1,8 @@ +chr1 4225 19670 +chr10 6 8 +chr1 24417 24420 +chr6_hla_hap2 0 150 +chr2 1 5 +chr1 30 55 +chrY 1 20 +chr1 1225979 42287290 |
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| diff -r 000000000000 -r a0c8dc671a23 test-data/a.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.tab Mon Jan 27 09:27:03 2014 -0500 |
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| @@ -0,0 +1,15 @@ +CHR SNP BP A1 TEST NMISS BETA STAT P +1 rs1181876 3671541 T DOMDEV 958 -1.415 -3.326 0.0009161 +1 rs10492923 5092886 C ADD 1007 5.105 4.368 1.382e-05 +1 rs10492923 5092886 C DOMDEV 1007 -5.612 -4.249 2.35e-05 +1 rs10492923 5092886 C GENO_2DF 1007 NA 19.9 4.775e-05 +1 rs1801133 11778965 T ADD 1022 1.23 3.97 7.682e-05 +1 rs1801133 11778965 T GENO_2DF 1022 NA 16.07 0.0003233 +1 rs1361912 12663121 A ADD 1021 12.69 4.093 4.596e-05 +1 rs1361912 12663121 A DOMDEV 1021 -12.37 -3.945 8.533e-05 +1 rs1361912 12663121 A GENO_2DF 1021 NA 17.05 0.0001982 +1 rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826 +1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05 +1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339 +1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05 +1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05 |
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| diff -r 000000000000 -r a0c8dc671a23 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 a0c8dc671a23 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 a0c8dc671a23 test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt Mon Jan 27 09:27:03 2014 -0500 |
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| @@ -0,0 +1,131 @@ +chromosome length information read. chromNum = 49! +config file read. +fragmentSize = 200 +isStrandSensitiveMode = 0 +slidingWinSize = 500 +movingStep = 50 +outputNum = 100000 +minCount = 4 +minScore = 5.000000 +bootstrapPass = 50 +randSeed = 123456 +reading tag files...... +10000 tags in L1, 10000 tags in L2. +tag file read. +pre-processing...... +pre-processing finished. +estimating noise rate...... +not enough reads for noise rate estimation. +noise rate estimation failed. noise rate set to be 1.0 +noise rate = 1.000000 +peak-finding...... +chr1......884 candidate peaks. +chr1_random......0 candidate peaks. +chr10......0 candidate peaks. +chr10_random......0 candidate peaks. +chr11......0 candidate peaks. +chr11_random......0 candidate peaks. +chr12......0 candidate peaks. +chr13......0 candidate peaks. +chr13_random......0 candidate peaks. +chr14......0 candidate peaks. +chr15......0 candidate peaks. +chr15_random......0 candidate peaks. +chr16......0 candidate peaks. +chr16_random......0 candidate peaks. +chr17......0 candidate peaks. +chr17_random......0 candidate peaks. +chr18......0 candidate peaks. +chr18_random......0 candidate peaks. +chr19......0 candidate peaks. +chr19_random......0 candidate peaks. +chr2......0 candidate peaks. +chr2_random......0 candidate peaks. +chr20......0 candidate peaks. +chr21......0 candidate peaks. +chr21_random......0 candidate peaks. +chr22......0 candidate peaks. +chr22_random......0 candidate peaks. +chr22_h2_hap1......0 candidate peaks. +chr3......0 candidate peaks. +chr3_random......0 candidate peaks. +chr4......0 candidate peaks. +chr4_random......0 candidate peaks. +chr5......0 candidate peaks. +chr5_random......0 candidate peaks. +chr5_h2_hap1......0 candidate peaks. +chr6......0 candidate peaks. +chr6_random......0 candidate peaks. +chr6_cox_hap1......0 candidate peaks. +chr6_qbl_hap2......0 candidate peaks. +chr7......0 candidate peaks. +chr7_random......0 candidate peaks. +chr8......0 candidate peaks. +chr8_random......0 candidate peaks. +chr9......0 candidate peaks. +chr9_random......0 candidate peaks. +chrM......0 candidate peaks. +chrX......0 candidate peaks. +chrX_random......0 candidate peaks. +chrY......0 candidate peaks. +peak-finding finished. +Significance Analysis...... +estimating paramters...... +smoothing factor = 0.356298 +estimating local FDR..... +FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files. +post-processing...... +chr1......finished. +chr1_random......finished. +chr10......finished. +chr10_random......finished. +chr11......finished. +chr11_random......finished. +chr12......finished. +chr13......finished. +chr13_random......finished. +chr14......finished. +chr15......finished. +chr15_random......finished. +chr16......finished. +chr16_random......finished. +chr17......finished. +chr17_random......finished. +chr18......finished. +chr18_random......finished. +chr19......finished. +chr19_random......finished. +chr2......finished. +chr2_random......finished. +chr20......finished. +chr21......finished. +chr21_random......finished. +chr22......finished. +chr22_random......finished. +chr22_h2_hap1......finished. +chr3......finished. +chr3_random......finished. +chr4......finished. +chr4_random......finished. +chr5......finished. +chr5_random......finished. +chr5_h2_hap1......finished. +chr6......finished. +chr6_random......finished. +chr6_cox_hap1......finished. +chr6_qbl_hap2......finished. +chr7......finished. +chr7_random......finished. +chr8......finished. +chr8_random......finished. +chr9......finished. +chr9_random......finished. +chrM......finished. +chrX......finished. +chrX_random......finished. +chrY......finished. +post-processing finished. +Significance analysis finished. +saving results....... +results saved. +CCAT process completed! |
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| diff -r 000000000000 -r a0c8dc671a23 test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt Mon Jan 27 09:27:03 2014 -0500 |
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| @@ -0,0 +1,131 @@ +chromosome length information read. chromNum = 49! +config file read. +fragmentSize = 200 +isStrandSensitiveMode = 0 +slidingWinSize = 1000 +movingStep = 50 +outputNum = 100000 +minCount = 4 +minScore = 5.000000 +bootstrapPass = 50 +randSeed = 123456 +reading tag files...... +10000 tags in L1, 10000 tags in L2. +tag file read. +pre-processing...... +pre-processing finished. +estimating noise rate...... +not enough reads for noise rate estimation. +noise rate estimation failed. noise rate set to be 1.0 +noise rate = 1.000000 +peak-finding...... +chr1......673 candidate peaks. +chr1_random......0 candidate peaks. +chr10......0 candidate peaks. +chr10_random......0 candidate peaks. +chr11......0 candidate peaks. +chr11_random......0 candidate peaks. +chr12......0 candidate peaks. +chr13......0 candidate peaks. +chr13_random......0 candidate peaks. +chr14......0 candidate peaks. +chr15......0 candidate peaks. +chr15_random......0 candidate peaks. +chr16......0 candidate peaks. +chr16_random......0 candidate peaks. +chr17......0 candidate peaks. +chr17_random......0 candidate peaks. +chr18......0 candidate peaks. +chr18_random......0 candidate peaks. +chr19......0 candidate peaks. +chr19_random......0 candidate peaks. +chr2......0 candidate peaks. +chr2_random......0 candidate peaks. +chr20......0 candidate peaks. +chr21......0 candidate peaks. +chr21_random......0 candidate peaks. +chr22......0 candidate peaks. +chr22_random......0 candidate peaks. +chr22_h2_hap1......0 candidate peaks. +chr3......0 candidate peaks. +chr3_random......0 candidate peaks. +chr4......0 candidate peaks. +chr4_random......0 candidate peaks. +chr5......0 candidate peaks. +chr5_random......0 candidate peaks. +chr5_h2_hap1......0 candidate peaks. +chr6......0 candidate peaks. +chr6_random......0 candidate peaks. +chr6_cox_hap1......0 candidate peaks. +chr6_qbl_hap2......0 candidate peaks. +chr7......0 candidate peaks. +chr7_random......0 candidate peaks. +chr8......0 candidate peaks. +chr8_random......0 candidate peaks. +chr9......0 candidate peaks. +chr9_random......0 candidate peaks. +chrM......0 candidate peaks. +chrX......0 candidate peaks. +chrX_random......0 candidate peaks. +chrY......0 candidate peaks. +peak-finding finished. +Significance Analysis...... +estimating paramters...... +smoothing factor = 0.287387 +estimating local FDR..... +FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files. +post-processing...... +chr1......finished. +chr1_random......finished. +chr10......finished. +chr10_random......finished. +chr11......finished. +chr11_random......finished. +chr12......finished. +chr13......finished. +chr13_random......finished. +chr14......finished. +chr15......finished. +chr15_random......finished. +chr16......finished. +chr16_random......finished. +chr17......finished. +chr17_random......finished. +chr18......finished. +chr18_random......finished. +chr19......finished. +chr19_random......finished. +chr2......finished. +chr2_random......finished. +chr20......finished. +chr21......finished. +chr21_random......finished. +chr22......finished. +chr22_random......finished. +chr22_h2_hap1......finished. +chr3......finished. +chr3_random......finished. +chr4......finished. +chr4_random......finished. +chr5......finished. +chr5_random......finished. +chr5_h2_hap1......finished. +chr6......finished. +chr6_random......finished. +chr6_cox_hap1......finished. +chr6_qbl_hap2......finished. +chr7......finished. +chr7_random......finished. +chr8......finished. +chr8_random......finished. +chr9......finished. +chr9_random......finished. +chrM......finished. +chrX......finished. +chrX_random......finished. +chrY......finished. +post-processing finished. +Significance analysis finished. +saving results....... +results saved. +CCAT process completed! |
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| diff -r 000000000000 -r a0c8dc671a23 test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match Mon Jan 27 09:27:03 2014 -0500 |
| b |
| b'@@ -0,0 +1,382 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|
| b |
| diff -r 000000000000 -r a0c8dc671a23 test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match Mon Jan 27 09:27:03 2014 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r a0c8dc671a23 test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match Mon Jan 27 09:27:03 2014 -0500 |
| b |
| b'@@ -0,0 +1,183 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|
| b |
| diff -r 000000000000 -r a0c8dc671a23 test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match Mon Jan 27 09:27:03 2014 -0500 |
| b |
| @@ -0,0 +1,74 @@ +chr1 4760225 4725450 4779800 139 0 507\.\d+ 0\.025000 +chr1 5061725 5053400 5068550 19 0 69\.\d+ 0\.025000 +chr1 5094825 5080750 5101500 19 0 69\.\d+ 0\.025000 +chr1 5174775 5163300 5181450 19 0 69\.\d+ 0\.025000 +chr1 5198075 5193000 5227900 17 0 62\.\d+ 0\.025000 +chr1 5593825 5575300 5618600 17 0 62\.\d+ 0\.025000 +chr1 4716275 4707550 4722700 16 0 58\.\d+ 0\.025000 +chr1 4961575 4951600 4964800 15 0 54\.\d+ 0\.025000 +chr1 4996075 4990250 5026600 15 0 54\.\d+ 0\.025000 +chr1 4792775 4788500 4798400 14 0 51\.\d+ 0\.025000 +chr1 4820975 4818750 4863650 14 0 51\.\d+ 0\.025000 +chr1 4892125 4888750 4938450 14 0 51\.\d+ 0\.025000 +chr1 4811575 4798500 4818650 14 0 51\.\d+ 0\.025000 +chr1 5132075 5121600 5140300 14 0 51\.\d+ 0\.025000 +chr1 5078525 5073200 5080700 13 0 47\.\d+ 0\.025000 +chr1 5249925 5247000 5258700 13 0 47\.\d+ 0\.025000 +chr1 4666375 4662050 4671350 13 0 47\.\d+ 0\.025000 +chr1 5649475 5645550 5668850 13 0 47\.\d+ 0\.025000 +chr1 4872625 4871150 4888250 12 0 43\.\d+ 0\.025000 +chr1 5510825 5501200 5517200 12 0 43\.\d+ 0\.025000 +chr1 4967025 4965050 4970850 12 0 43\.\d+ 0\.025000 +chr1 5306825 5300700 5319250 12 0 43\.\d+ 0\.025000 +chr1 5270275 5269300 5281550 11 0 40\.\d+ 0\.034000 +chr1 5570325 5567450 5573850 11 0 40\.\d+ 0\.034000 +chr1 5106525 5105050 5117450 11 0 40\.\d+ 0\.034000 +chr1 5045675 5044200 5048700 11 0 40\.\d+ 0\.034000 +chr1 5532875 5521900 5536850 11 0 40\.\d+ 0\.034000 +chr1 5429475 5427200 5435250 11 0 40\.\d+ 0\.034000 +chr1 5726025 5720500 5731000 11 0 40\.\d+ 0\.034000 +chr1 5386675 5368500 5389350 11 0 40\.\d+ 0\.034000 +chr1 4692075 4673000 4701600 11 0 40\.\d+ 0\.034000 +chr1 5286125 5282250 5299950 11 0 40\.\d+ 0\.034000 +chr1 5412475 5406500 5414000 11 0 40\.\d+ 0\.034000 +chr1 5151825 5140350 5157200 10 0 36\.\d+ 0\.034000 +chr1 4945325 4943900 4949650 10 0 36\.\d+ 0\.034000 +chr1 5267725 5263750 5268900 10 0 36\.\d+ 0\.034000 +chr1 5442625 5438750 5445150 10 0 36\.\d+ 0\.034000 +chr1 4981425 4978900 4987150 10 0 36\.\d+ 0\.034000 +chr1 5746175 5741000 5748200 9 0 32\.\d+ 0\.034000 +chr1 4865425 4863900 4870300 9 0 32\.\d+ 0\.034000 +chr1 5448375 5445350 5450050 9 0 32\.\d+ 0\.034000 +chr1 5706725 5703650 5710750 8 0 29\.\d+ 0\.034000 +chr1 5679325 5675600 5681850 8 0 29\.\d+ 0\.034000 +chr1 5229925 5228750 5242150 8 0 29\.\d+ 0\.034000 +chr1 5364775 5357550 5366350 8 0 29\.\d+ 0\.034000 +chr1 5401025 5390850 5406350 8 0 29\.\d+ 0\.034000 +chr1 5324575 5322550 5334750 8 0 29\.\d+ 0\.034000 +chr1 5355975 5352900 5357500 7 0 25\.\d+ 0\.135000 +chr1 5548775 5547250 5552250 7 0 25\.\d+ 0\.135000 +chr1 5716025 5711700 5719950 7 0 25\.\d+ 0\.135000 +chr1 5496625 5495200 5499750 7 0 25\.\d+ 0\.135000 +chr1 5695175 5693900 5701400 7 0 25\.\d+ 0\.135000 +chr1 4787225 4783350 4788300 7 0 25\.\d+ 0\.135000 +chr1 5751925 5749150 5753500 7 0 25\.\d+ 0\.135000 +chr1 5453625 5450900 5458700 7 0 25\.\d+ 0\.135000 +chr1 5688775 5687300 5691900 6 0 21\.\d+ 0\.135000 +chr1 5632975 5631350 5638100 6 0 21\.\d+ 0\.135000 +chr1 4975525 4974200 4976900 6 0 21\.\d+ 0\.135000 +chr1 5487825 5482700 5489150 6 0 21\.\d+ 0\.135000 +chr1 5539925 5538950 5542250 6 0 21\.\d+ 0\.135000 +chr1 5348875 5347750 5349950 6 0 21\.\d+ 0\.135000 +chr1 5621625 5618950 5622950 6 0 21\.\d+ 0\.135000 +chr1 5119225 5117850 5121550 6 0 21\.\d+ 0\.135000 +chr1 4507925 4507250 4509100 44 2 20\.\d+ 0\.199000 +chr1 5161725 5159000 5163250 5 0 18\.\d+ 0\.199000 +chr1 4781325 4780250 4782350 5 0 18\.\d+ 0\.199000 +chr1 5475625 5474600 5479600 5 0 18\.\d+ 0\.199000 +chr1 5039275 5037850 5040800 5 0 18\.\d+ 0\.199000 +chr1 4337875 4336700 4338600 60 4 14\.\d+ 0\.199000 +chr1 3023575 3022750 3024750 4 0 14\.\d+ 1\.000000 +chr1 5033175 5032000 5036100 4 0 14\.\d+ 1\.000000 +chr1 5564125 5562650 5566050 4 0 14\.\d+ 1\.000000 +chr1 4408525 4407200 4409200 88 13 6\.\d+ 1\.000000 +chr1 4324025 4322650 4324900 48 7 6\.\d+ 1\.000000 |
| b |
| diff -r 000000000000 -r a0c8dc671a23 test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match Mon Jan 27 09:27:03 2014 -0500 |
| b |
| b'@@ -0,0 +1,884 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|
| b |
| diff -r 000000000000 -r a0c8dc671a23 test-data/peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match Mon Jan 27 09:27:03 2014 -0500 |
| b |
| b'@@ -0,0 +1,673 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|
| b |
| diff -r 000000000000 -r a0c8dc671a23 tool-data/ccat_configurations.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ccat_configurations.loc.sample Mon Jan 27 09:27:03 2014 -0500 |
| b |
| @@ -0,0 +1,5 @@ +#Provide Pre-compiled CCAT peak/region caller configuration files +#UID Description path_to_config_file +#ccat_3.0_tf_config CCAT 3.0 provided Transcription Factor Binding /path_to/ccat/configs/3.0/config_TF.txt +#ccat_3.0_histone_config CCAT 3.0 provided Histone Modification /path_to/ccat/configs/3.0/config_histone.txt +#ccat_3.0_histone_config_fixed CCAT 3.0 Histone Factor Binding (readme.txt defaults: slidingWinSize=1000) /path_to/ccat/configs/3.0/config_histone_readme.txt \ No newline at end of file |
| b |
| diff -r 000000000000 -r a0c8dc671a23 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Jan 27 09:27:03 2014 -0500 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of configurations in the CCAT peak/region caller format --> + <table name="ccat_configurations" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/ccat_configurations.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r a0c8dc671a23 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:27:03 2014 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="CCAT" version="3.0"> + <repository changeset_revision="b65b1bab9226" name="package_ccat_3_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |