Mercurial > repos > devteam > ccat
changeset 2:e0b378d6844f draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"
| author | devteam |
|---|---|
| date | Fri, 03 Dec 2021 16:27:17 +0000 |
| parents | bbfd1fbff28a |
| children | |
| files | ccat_wrapper.py ccat_wrapper.xml test-data/1.interval test-data/1.txt test-data/2.interval test-data/2.txt test-data/ES_CTCF_chr19.bed test-data/ES_CTCF_chr19.log test-data/ES_CTCF_chr19.significant.peak test-data/ES_CTCF_chr19.significant.region test-data/ES_CTCF_chr19.top100000.peak test-data/ES_GFP_chr19.bed test-data/a.tab test-data/ccat_configurations.loc test-data/chipseq_enriched.bed test-data/chipseq_enriched.bed.gz test-data/chipseq_input.bed test-data/chipseq_input.bed.gz test-data/config_TF.txt test-data/genome_length_mm8_chr19.txt test-data/hg18.len 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_table_conf.xml.test tool_dependencies.xml |
| diffstat | 31 files changed, 229182 insertions(+), 2902 deletions(-) [+] |
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--- a/ccat_wrapper.py Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -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()
--- a/ccat_wrapper.xml Tue Oct 13 12:14:19 2015 -0400 +++ b/ccat_wrapper.xml Fri Dec 03 16:27:17 2021 +0000 @@ -1,23 +1,49 @@ -<tool id="peakcalling_ccat" name="CCAT" version="0.0.1"> +<tool id="peakcalling_ccat" name="CCAT" version="0.0.2" profile="20.01"> <description>Control-based ChIP-seq Analysis Tool</description> <requirements> - <requirement type="package" version="3.0">CCAT</requirement> + <requirement type="package" version="3.0">ccat</requirement> </requirements> - <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' - #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': - '$input_advanced_config_file' - #else: - '${ options_type.input_config_file.fields.path }' - #end if - 'CCAT in Galaxy' - '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> + <stdio> + <regex match="Usage: <library 1 tag file name> <library 2 tag file name> <chromosome length file name> <config file name> <project name>" + source="both" + level="fatal" + description="CLI error" /> + <regex match="tag file error" source="both" level="fatal" description="tag file error" /> + </stdio> + <command detect_errors="aggressive"><![CDATA[ + echo $in_test_mode && CCAT '$input_tag_file' + '$input_control_file' + #if str($in_test_mode) == "no": + '$chromInfo' + #else: + '$__tool_directory__/test-data/genome_length_mm8_chr19.txt' + #end if + #if str($options_type['options_type_selector']) == 'advanced': + '$input_advanced_config_file' + #else: + '${options_type.input_config_file.fields.path}' + #end if + CCAT + | tee '$output_log_file' + ]]></command> + <configfiles> + <configfile name="input_advanced_config_file"><![CDATA[ +#if str($options_type['options_type_selector']) == 'advanced': +fragmentSize ${options_type['fragment_size']} +slidingWinSize ${options_type['sliding_window_size']} +movingStep ${options_type['moving_step']} +isStrandSensitiveMode ${options_type['is_strand_sensitive_mode']} +minCount ${options_type['min_count']} +outputNum ${options_type['output_num']} +randomSeed ${options_type['random_seed']} +minScore ${options_type['min_score']} +bootstrapPass ${options_type['bootstrap_pass']} +#end if + ]]></configfile> + </configfiles> <inputs> - <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > - <validator type="unspecified_build" /> - </param> - <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > - <validator type="unspecified_build" /> - </param> + <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File"/> + <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File"/> <conditional name="options_type"> <param name="options_type_selector" type="select" label="Advanced Options"> <option value="basic" selected="True">Hide Advanced Options</option> @@ -45,23 +71,24 @@ <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> </when> </conditional> + <param name="in_test_mode" type="hidden" value="no" /> </inputs> <outputs> - <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> + <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)" from_work_dir="CCAT.significant.peak"> <actions> <action type="metadata" name="chromCol" default="1"/> <action type="metadata" name="startCol" default="3"/> <action type="metadata" name="endCol" default="4"/> </actions> </data> - <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> + <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)" from_work_dir="CCAT.significant.region"> <actions> <action type="metadata" name="chromCol" default="1"/> <action type="metadata" name="startCol" default="3"/> <action type="metadata" name="endCol" default="4"/> </actions> </data> - <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> + <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)" from_work_dir="CCAT.top100000.peak"> <actions> <action type="metadata" name="chromCol" default="1"/> <action type="metadata" name="startCol" default="3"/> @@ -70,78 +97,44 @@ </data> <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> </outputs> - <configfiles> - <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': -fragmentSize ${options_type[ 'fragment_size' ]} -slidingWinSize ${options_type[ 'sliding_window_size' ]} -movingStep ${options_type[ 'moving_step' ]} -isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} -minCount ${options_type[ 'min_count' ]} -outputNum ${options_type[ 'output_num' ]} -randomSeed ${options_type[ 'random_seed' ]} -minScore ${options_type[ 'min_score' ]} -bootstrapPass ${options_type[ 'bootstrap_pass' ]} -#end if</configfile> - </configfiles> <tests> <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> + <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" /> + <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" /> <param name="options_type_selector" value="advanced" /> <param name="fragment_size" value="200" /> - <param name="sliding_window_size" value="500" /> - <param name="moving_step" value="50" /> - <param name="is_strand_sensitive_mode" value="0" /> - <param name="min_count" value="4" /> + <param name="sliding_window_size" value="300" /> + <param name="moving_step" value="10" /> + <param name="is_strand_sensitive_mode" value="1" /> + <param name="min_count" value="3" /> <param name="output_num" value="100000" /> <param name="random_seed" value="123456" /> <param name="min_score" value="5.0" /> <param name="bootstrap_pass" value="50" /> - <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> - <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> - <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" /> - <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> + <param name="in_test_mode" value="yes" /> + <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak"/> + <output name="output_region_file" file="ES_CTCF_chr19.significant.region" /> + <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" /> + <output name="output_log_file" file="ES_CTCF_chr19.log" /> </test> <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> + <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" /> + <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" /> <param name="options_type_selector" value="basic" /> - <param name="input_config_file" value="ccat_3.0_histone_config" /> - <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> - <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> - <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" /> - <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> + <param name="input_config_file" value="config_TF" /> + <param name="in_test_mode" value="yes" /> + <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak" /> + <output name="output_region_file" file="ES_CTCF_chr19.significant.region" /> + <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" /> + <output name="output_log_file" file="ES_CTCF_chr19.log" /> </test> - <!-- Test below gives different answers on different architectures, - 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 - slidingWinSize was fixed to be 1000, default as per readme.txt - --> - <!-- - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="basic" /> - <param name="input_config_file" value="ccat_3.0_histone_config_readme" /> - <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" /> - <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" /> - <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match" compare="re_match" sort="true" /> - <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" /> - </test> - --> </tests> <help> **What it does** This tool allows ChIP-seq peak/region calling using CCAT. -View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. - ------- - -**Citation** - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - +View the original CCAT documentation: https://www.comp.nus.edu.sg/~bioinfo/CCAT3.0/ </help> <citations> <citation type="doi">10.1093/bioinformatics/btq128</citation>
--- a/test-data/1.interval Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -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
--- a/test-data/1.txt Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -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
--- a/test-data/2.interval Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -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
--- a/test-data/2.txt Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ES_CTCF_chr19.bed Fri Dec 03 16:27:17 2021 +0000 @@ -0,0 +1,103146 @@ +chr19 35798438 35798462 0 0 - +chr19 9305251 9305275 0 0 - +chr19 46591732 46591756 0 0 - +chr19 4012842 4012866 0 0 + +chr19 16327499 16327523 0 0 + +chr19 56112992 56113016 0 0 - +chr19 46635313 46635337 0 0 + +chr19 17194923 17194947 0 0 - +chr19 27493695 27493719 0 0 + +chr19 12995495 12995519 0 0 + +chr19 3731679 3731703 0 0 - +chr19 48728456 48728480 0 0 + +chr19 33107756 33107780 0 0 - +chr19 6988322 6988346 0 0 + +chr19 37091346 37091370 0 0 + +chr19 46598474 46598498 0 0 + +chr19 58638548 58638572 0 0 - +chr19 56619598 56619622 0 0 - +chr19 41187429 41187453 0 0 - +chr19 28270125 28270149 0 0 + +chr19 29750291 29750315 0 0 - +chr19 43541043 43541067 0 0 - +chr19 33300508 33300532 0 0 + +chr19 31408339 31408363 0 0 - +chr19 13867675 13867699 0 0 + +chr19 11046457 11046481 0 0 - +chr19 21814723 21814747 0 0 - +chr19 4046129 4046153 0 0 - +chr19 51879925 51879949 0 0 + +chr19 47814862 47814886 0 0 + +chr19 41284424 41284448 0 0 + +chr19 44249489 44249513 0 0 - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ES_CTCF_chr19.log Fri Dec 03 16:27:17 2021 +0000 @@ -0,0 +1,53 @@ +chromosome length information read. chromNum = 1! +config file read. +fragmentSize = 200 +isStrandSensitiveMode = 1 +slidingWinSize = 300 +movingStep = 10 +outputNum = 100000 +minCount = 3 +minScore = 5.000000 +bootstrapPass = 50 +randSeed = 123456 +reading tag files...... +103146 tags in L1, 97149 tags in L2. +tag file read. +pre-processing...... +pre-processing finished. +estimating noise rate...... +iteration 0: nr=0.669578 +iteration 1: nr=0.613605 +iteration 2: nr=0.593059 +iteration 3: nr=0.586303 +iteration 4: nr=0.583061 +iteration 5: nr=0.583061 +iteration 6: nr=0.582451 +iteration 7: nr=0.586573 +iteration 8: nr=0.583271 +iteration 9: nr=0.581424 +iteration 10: nr=0.585253 +iteration 11: nr=0.583917 +iteration 12: nr=0.583446 +iteration 13: nr=0.581896 +iteration 14: nr=0.583084 +iteration 15: nr=0.581582 +iteration 16: nr=0.582966 +iteration 17: nr=0.583596 +iteration 18: nr=0.586691 +iteration 19: nr=0.584954 +noise rate = 0.583743 +peak-finding...... +chr19......2946 candidate peaks. +peak-finding finished. +Significance Analysis...... +estimating paramters...... +smoothing factor = 20.048787 +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...... +chr19......finished. +post-processing finished. +Significance analysis finished. +saving results....... +results saved. +CCAT process completed!
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--- a/test-data/a.tab Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ccat_configurations.loc Fri Dec 03 16:27:17 2021 +0000 @@ -0,0 +1,1 @@ +config_TF config_TF ${__HERE__}/config_TF.txt
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config_TF.txt Fri Dec 03 16:27:17 2021 +0000 @@ -0,0 +1,9 @@ +fragmentSize 200 +slidingWinSize 300 +movingStep 10 +isStrandSensitiveMode 1 +minCount 3 +outputNum 100000 +randomSeed 123456 +minScore 5.0 +bootstrapPass 50
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_length_mm8_chr19.txt Fri Dec 03 16:27:17 2021 +0000 @@ -0,0 +1,1 @@ +chr19 61321190 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg18.len Fri Dec 03 16:27:17 2021 +0000 @@ -0,0 +1,49 @@ +1 chr1 247249719 +2 chr2 242951149 +3 chr3 199501827 +4 chr4 191273063 +5 chr5 180857866 +6 chr6 170899992 +7 chr7 158821424 +8 chr8 146274826 +9 chr9 140273252 +10 chr10 135374737 +11 chr11 134452384 +12 chr12 132349534 +13 chr13 114142980 +14 chr14 106368585 +15 chr15 100338915 +16 chr16 88827254 +17 chr17 78774742 +18 chr18 76117153 +19 chr19 63811651 +20 chr20 62435964 +21 chr21 46944323 +22 chr22 49691432 +23 chrX 154913754 +24 chrY 57772954 + + + + + + + + + + + + + + + + + + + + + + + + +
--- a/test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ -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!
--- a/test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ -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!
--- a/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,382 +0,0 @@ -chr1 4760025 4756750 4762650 128 0 399\.\d+ 0\.133000 -chr1 4761475 4756750 4762650 74 0 230\.\d+ 0\.133000 -chr1 4771725 4768050 4778800 37 0 115\.\d+ 0\.133000 -chr1 5061925 5060800 5063500 15 0 46\.\d+ 0\.133000 -chr1 5174925 5172300 5175650 15 0 46\.\d+ 0\.133000 -chr1 5198225 5193500 5203550 13 0 40\.\d+ 0\.133000 -chr1 5094525 5090900 5098600 12 0 37\.\d+ 0\.133000 -chr1 5649775 5646050 5655200 12 0 37\.\d+ 0\.133000 -chr1 4764325 4763100 4767650 11 0 34\.\d+ 0\.189000 -chr1 5250175 5247500 5252250 11 0 34\.\d+ 0\.189000 -chr1 4861125 4856150 4863100 11 0 34\.\d+ 0\.189000 -chr1 5202075 5193500 5203550 11 0 34\.\d+ 0\.189000 -chr1 4961625 4952100 4964300 11 0 34\.\d+ 0\.189000 -chr1 4830175 4828350 4831300 11 0 34\.\d+ 0\.189000 -chr1 5177075 5175750 5180950 11 0 34\.\d+ 0\.189000 -chr1 4849575 4842300 4852000 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--- a/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,272 +0,0 @@ -chr1 4760225 4725450 4779800 139 0 507\.\d+ 0\.025000 -chr1 4761625 4725450 4779800 87 0 318\.\d+ 0\.025000 -chr1 4771925 4725450 4779800 48 0 175\.\d+ 0\.025000 -chr1 5061725 5053400 5068550 19 0 69\.\d+ 0\.025000 -chr1 5174775 5163300 5181450 19 0 69\.\d+ 0\.025000 -chr1 5094825 5080750 5101500 19 0 69\.\d+ 0\.025000 -chr1 5593825 5575300 5618600 17 0 62\.\d+ 0\.025000 -chr1 5198075 5193000 5227900 17 0 62\.\d+ 0\.025000 -chr1 5177325 5163300 5181450 17 0 62\.\d+ 0\.025000 -chr1 4740175 4725450 4779800 16 0 58\.\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 5201925 5193000 5227900 15 0 54\.\d+ 0\.025000 -chr1 5132075 5121600 5140300 14 0 51\.\d+ 0\.025000 -chr1 4820975 4818750 4863650 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--- a/test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,183 +0,0 @@ -chr1 4760025 4756750 4762650 128 0 399\.\d+ 0\.133000 -chr1 4771725 4768050 4778800 37 0 115\.\d+ 0\.133000 -chr1 5061925 5060800 5063500 15 0 46\.\d+ 0\.133000 -chr1 5174925 5172300 5175650 15 0 46\.\d+ 0\.133000 -chr1 5198225 5193500 5203550 13 0 40\.\d+ 0\.133000 -chr1 5094525 5090900 5098600 12 0 37\.\d+ 0\.133000 -chr1 5649775 5646050 5655200 12 0 37\.\d+ 0\.133000 -chr1 5250175 5247500 5252250 11 0 34\.\d+ 0\.189000 -chr1 4861125 4856150 4863100 11 0 34\.\d+ 0\.189000 -chr1 4830175 4828350 4831300 11 0 34\.\d+ 0\.189000 -chr1 4764325 4763100 4767650 11 0 34\.\d+ 0\.189000 -chr1 5177075 5175750 5180950 11 0 34\.\d+ 0\.189000 -chr1 4961625 4952100 4964300 11 0 34\.\d+ 0\.189000 -chr1 4849575 4842300 4852000 10 0 31\.\d+ 0\.189000 -chr1 4908575 4907850 4911250 10 0 31\.\d+ 0\.189000 -chr1 4792275 4789000 4793650 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--- a/test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -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
--- a/test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,884 +0,0 @@ -chr1 3002975 3002975 3002975 4 5 0\.\d+ 1\.000000 -chr1 3018775 3018775 3018775 4 7 0\.\d+ 1\.000000 -chr1 3021225 3021225 3021225 8 6 1\.\d+ 1\.000000 -chr1 3026925 3026925 3026925 4 2 1\.\d+ 1\.000000 -chr1 3035625 3035625 3035625 4 6 0\.\d+ 1\.000000 -chr1 3037175 3037175 3037175 4 5 0\.\d+ 1\.000000 -chr1 3038725 3038725 3038725 6 7 0\.\d+ 1\.000000 -chr1 3041075 3041075 3041075 4 2 1\.\d+ 1\.000000 -chr1 3054875 3054500 3055300 5 0 15\.\d+ 0\.193000 -chr1 3062525 3062250 3062900 4 0 12\.\d+ 0\.193000 -chr1 3063225 3063225 3063225 4 3 1\.\d+ 1\.000000 -chr1 3066125 3066125 3066125 4 6 0\.\d+ 1\.000000 -chr1 3071275 3071275 3071275 4 7 0\.\d+ 1\.000000 -chr1 3086425 3086425 3086425 11 15 0\.\d+ 1\.000000 -chr1 3089625 3089625 3089625 5 4 1\.\d+ 1\.000000 -chr1 3095475 3095475 3095475 7 8 0\.\d+ 1\.000000 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Dec 03 16:27:17 2021 +0000 @@ -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="${__HERE__}/test-data/ccat_configurations.loc" /> + </table> +</tables>
--- a/tool_dependencies.xml Tue Oct 13 12:14:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="CCAT" version="3.0"> - <repository changeset_revision="bf3346b28104" name="package_ccat_3_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>