changeset 2:1a6979fbd544 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 16:27:57 +0000
parents 201d8e7dfc43
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(-) [+]
line wrap: on
line diff
--- a/ccat_wrapper.py	Tue Jul 21 14:13:34 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 Jul 21 14:13:34 2015 -0400
+++ b/ccat_wrapper.xml	Fri Dec 03 16:27:57 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: &lt;library 1 tag file name&gt; &lt;library 2 tag file name&gt; &lt;chromosome length file name&gt; &lt;config file name&gt; &lt;project name&gt;"
+           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 Jul 21 14:13:34 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 Jul 21 14:13:34 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 Jul 21 14:13:34 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 Jul 21 14:13:34 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 16:27:57 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	-
+chr19	35848016	35848040	0	0	-
+chr19	46692944	46692968	0	0	-
+chr19	56097680	56097704	0	0	+
+chr19	45297766	45297790	0	0	-
+chr19	15586680	15586704	0	0	+
+chr19	11895281	11895305	0	0	+
+chr19	3765662	3765686	0	0	-
+chr19	34979932	34979956	0	0	-
+chr19	45920415	45920439	0	0	+
+chr19	6663414	6663438	0	0	-
+chr19	38430163	38430187	0	0	-
+chr19	3729013	3729037	0	0	+
+chr19	6030124	6030148	0	0	+
+chr19	38884441	38884465	0	0	+
+chr19	46307719	46307743	0	0	-
+chr19	29455303	29455327	0	0	-
+chr19	47380673	47380697	0	0	+
+chr19	16823118	16823142	0	0	+
+chr19	6401555	6401579	0	0	+
+chr19	38019469	38019493	0	0	-
+chr19	41312299	41312323	0	0	-
+chr19	11678779	11678803	0	0	-
+chr19	27949067	27949091	0	0	-
+chr19	13886083	13886107	0	0	-
+chr19	56531064	56531088	0	0	-
+chr19	32897836	32897860	0	0	-
+chr19	36453545	36453569	0	0	+
+chr19	27940737	27940761	0	0	-
+chr19	57456695	57456719	0	0	+
+chr19	8852028	8852052	0	0	-
+chr19	4125331	4125355	0	0	+
+chr19	28143626	28143650	0	0	+
+chr19	3724937	3724961	0	0	+
+chr19	45101841	45101865	0	0	+
+chr19	42313867	42313891	0	0	+
+chr19	40807701	40807725	0	0	+
+chr19	17854244	17854268	0	0	+
+chr19	43624619	43624643	0	0	-
+chr19	40696929	40696953	0	0	-
+chr19	10142954	10142978	0	0	+
+chr19	44948840	44948864	0	0	-
+chr19	59054736	59054760	0	0	-
+chr19	57084820	57084844	0	0	+
+chr19	23843623	23843647	0	0	+
+chr19	41583364	41583388	0	0	-
+chr19	24363043	24363067	0	0	-
+chr19	36253597	36253621	0	0	+
+chr19	12081980	12082004	0	0	-
+chr19	42642697	42642721	0	0	+
+chr19	55075572	55075596	0	0	+
+chr19	4533566	4533590	0	0	+
+chr19	60610314	60610338	0	0	+
+chr19	45036737	45036761	0	0	-
+chr19	44793718	44793742	0	0	+
+chr19	46188636	46188660	0	0	+
+chr19	41700252	41700276	0	0	+
+chr19	52353480	52353504	0	0	+
+chr19	42093767	42093791	0	0	+
+chr19	56722636	56722660	0	0	-
+chr19	47313311	47313335	0	0	+
+chr19	33857341	33857365	0	0	-
+chr19	30619944	30619968	0	0	+
+chr19	29711010	29711034	0	0	-
+chr19	52814286	52814310	0	0	+
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+chr19	37667796	37667820	0	0	-
+chr19	59009963	59009987	0	0	-
+chr19	15734906	15734930	0	0	+
+chr19	46087296	46087320	0	0	-
+chr19	43532425	43532449	0	0	-
+chr19	35685220	35685244	0	0	-
+chr19	11043590	11043614	0	0	+
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+chr19	27462279	27462303	0	0	-
+chr19	57450818	57450842	0	0	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.log	Fri Dec 03 16:27:57 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!
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.significant.peak	Fri Dec 03 16:27:57 2021 +0000
@@ -0,0 +1,2946 @@
+chr19	44636155	44635690	44637010	138	2	281.402772	0.001000
+chr19	44416985	44416460	44417390	101	1	211.604907	0.001000
+chr19	59292915	59292150	59293510	85	1	177.560301	0.001000
+chr19	47936055	47935520	47936450	74	0	159.742535	0.001000
+chr19	40399185	40398760	40399610	74	0	159.742535	0.001000
+chr19	8645395	8645010	8646090	73	0	157.583853	0.001000
+chr19	24368185	24367620	24369230	75	1	157.286191	0.001000
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+chr19	45297825	45297050	45298220	70	0	151.107804	0.001000
+chr19	41125035	41124470	41125450	68	0	146.790438	0.001000
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+chr19	21851155	21850910	21851340	3	4	5.752407	1.000000
+chr19	53306355	53306120	53306590	3	4	5.752407	1.000000
+chr19	44909225	44908970	44909480	3	4	5.752407	1.000000
+chr19	43643065	43642820	43643310	3	4	5.752407	1.000000
+chr19	47496375	47496160	47496590	3	4	5.752407	1.000000
+chr19	37642155	37641960	37642440	3	4	5.752407	1.000000
+chr19	25418055	25417860	25418400	3	4	5.752407	1.000000
+chr19	28974665	28974450	28974870	3	4	5.752407	1.000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.significant.region	Fri Dec 03 16:27:57 2021 +0000
@@ -0,0 +1,2808 @@
+chr19	44636155	44635690	44637010	138	2	281.402772	0.001000
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+chr19	53306355	53306120	53306590	3	4	5.752407	1.000000
+chr19	21851155	21850910	21851340	3	4	5.752407	1.000000
+chr19	43643065	43642820	43643310	3	4	5.752407	1.000000
+chr19	37642155	37641960	37642440	3	4	5.752407	1.000000
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+chr19	25418055	25417860	25418400	3	4	5.752407	1.000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.top100000.peak	Fri Dec 03 16:27:57 2021 +0000
@@ -0,0 +1,2946 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_GFP_chr19.bed	Fri Dec 03 16:27:57 2021 +0000
@@ -0,0 +1,97149 @@
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+chr19	34799301	34799326	0	0	+
+chr19	22917107	22917132	0	0	-
--- a/test-data/a.tab	Tue Jul 21 14:13:34 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 16:27:57 2021 +0000
@@ -0,0 +1,1 @@
+config_TF	config_TF	${__HERE__}/config_TF.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chipseq_enriched.bed	Fri Dec 03 16:27:57 2021 +0000
@@ -0,0 +1,10000 @@
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Binary file test-data/chipseq_enriched.bed.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chipseq_input.bed	Fri Dec 03 16:27:57 2021 +0000
@@ -0,0 +1,10000 @@
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+chr1	4635312	4635348	region_9805	0	+
+chr1	4635363	4635399	region_9806	0	-
+chr1	4635456	4635492	region_9807	0	+
+chr1	4636007	4636043	region_9808	0	+
+chr1	4636146	4636182	region_9809	0	-
+chr1	4636163	4636199	region_9810	0	-
+chr1	4636189	4636225	region_9811	0	-
+chr1	4636190	4636226	region_9812	0	-
+chr1	4636300	4636336	region_9813	0	+
+chr1	4636411	4636447	region_9814	0	+
+chr1	4636424	4636460	region_9815	0	+
+chr1	4636432	4636468	region_9816	0	-
+chr1	4636510	4636546	region_9817	0	-
+chr1	4636524	4636560	region_9818	0	+
+chr1	4636587	4636623	region_9819	0	-
+chr1	4636746	4636782	region_9820	0	-
+chr1	4636772	4636808	region_9821	0	+
+chr1	4636838	4636874	region_9822	0	-
+chr1	4636854	4636890	region_9823	0	+
+chr1	4636872	4636908	region_9824	0	+
+chr1	4636902	4636938	region_9825	0	-
+chr1	4637144	4637180	region_9826	0	-
+chr1	4637146	4637182	region_9827	0	-
+chr1	4637147	4637183	region_9828	0	-
+chr1	4637203	4637239	region_9829	0	-
+chr1	4637203	4637239	region_9830	0	-
+chr1	4637211	4637247	region_9831	0	+
+chr1	4637427	4637463	region_9832	0	-
+chr1	4637434	4637470	region_9833	0	+
+chr1	4637457	4637493	region_9834	0	-
+chr1	4637613	4637649	region_9835	0	+
+chr1	4637635	4637671	region_9836	0	+
+chr1	4637715	4637751	region_9837	0	+
+chr1	4638113	4638149	region_9838	0	+
+chr1	4638156	4638192	region_9839	0	-
+chr1	4638493	4638529	region_9840	0	-
+chr1	4638527	4638563	region_9841	0	+
+chr1	4638579	4638615	region_9842	0	-
+chr1	4638640	4638676	region_9843	0	-
+chr1	4638736	4638772	region_9844	0	+
+chr1	4638803	4638839	region_9845	0	-
+chr1	4638946	4638982	region_9846	0	-
+chr1	4638984	4639020	region_9847	0	-
+chr1	4639170	4639206	region_9848	0	-
+chr1	4639244	4639280	region_9849	0	-
+chr1	4639871	4639907	region_9850	0	+
+chr1	4640788	4640824	region_9851	0	+
+chr1	4641241	4641277	region_9852	0	-
+chr1	4641335	4641371	region_9853	0	-
+chr1	4641576	4641612	region_9854	0	+
+chr1	4641663	4641699	region_9855	0	-
+chr1	4641690	4641726	region_9856	0	+
+chr1	4641708	4641744	region_9857	0	-
+chr1	4641729	4641765	region_9858	0	-
+chr1	4641729	4641765	region_9859	0	+
+chr1	4641745	4641781	region_9860	0	+
+chr1	4641824	4641860	region_9861	0	-
+chr1	4643758	4643794	region_9862	0	+
+chr1	4643866	4643902	region_9863	0	-
+chr1	4643894	4643930	region_9864	0	+
+chr1	4644047	4644083	region_9865	0	+
+chr1	4644097	4644133	region_9866	0	-
+chr1	4644105	4644141	region_9867	0	-
+chr1	4644703	4644739	region_9868	0	-
+chr1	4644800	4644836	region_9869	0	+
+chr1	4644873	4644909	region_9870	0	+
+chr1	4645099	4645135	region_9871	0	+
+chr1	4645149	4645185	region_9872	0	-
+chr1	4645237	4645273	region_9873	0	-
+chr1	4645247	4645283	region_9874	0	+
+chr1	4645497	4645533	region_9875	0	-
+chr1	4645690	4645726	region_9876	0	-
+chr1	4645789	4645825	region_9877	0	-
+chr1	4645840	4645876	region_9878	0	+
+chr1	4645843	4645879	region_9879	0	+
+chr1	4645969	4646005	region_9880	0	-
+chr1	4646136	4646172	region_9881	0	+
+chr1	4646149	4646185	region_9882	0	+
+chr1	4646157	4646193	region_9883	0	+
+chr1	4646298	4646334	region_9884	0	-
+chr1	4646461	4646497	region_9885	0	-
+chr1	4646527	4646563	region_9886	0	+
+chr1	4646550	4646586	region_9887	0	-
+chr1	4646675	4646711	region_9888	0	+
+chr1	4646719	4646755	region_9889	0	-
+chr1	4646799	4646835	region_9890	0	+
+chr1	4646807	4646843	region_9891	0	-
+chr1	4646812	4646848	region_9892	0	+
+chr1	4646879	4646915	region_9893	0	-
+chr1	4646916	4646952	region_9894	0	-
+chr1	4646928	4646964	region_9895	0	+
+chr1	4646987	4647023	region_9896	0	-
+chr1	4647000	4647036	region_9897	0	+
+chr1	4647088	4647124	region_9898	0	-
+chr1	4647181	4647217	region_9899	0	+
+chr1	4647281	4647317	region_9900	0	+
+chr1	4647559	4647595	region_9901	0	-
+chr1	4647582	4647618	region_9902	0	-
+chr1	4647591	4647627	region_9903	0	+
+chr1	4647654	4647690	region_9904	0	+
+chr1	4647696	4647732	region_9905	0	-
+chr1	4647722	4647758	region_9906	0	+
+chr1	4647755	4647791	region_9907	0	+
+chr1	4648124	4648160	region_9908	0	-
+chr1	4648129	4648165	region_9909	0	-
+chr1	4648179	4648215	region_9910	0	-
+chr1	4648461	4648497	region_9911	0	+
+chr1	4648523	4648559	region_9912	0	-
+chr1	4648532	4648568	region_9913	0	+
+chr1	4648554	4648590	region_9914	0	-
+chr1	4650071	4650107	region_9915	0	+
+chr1	4650119	4650155	region_9916	0	-
+chr1	4650645	4650681	region_9917	0	-
+chr1	4652025	4652061	region_9918	0	-
+chr1	4652316	4652352	region_9919	0	+
+chr1	4652334	4652370	region_9920	0	+
+chr1	4652368	4652404	region_9921	0	-
+chr1	4652487	4652523	region_9922	0	-
+chr1	4652666	4652702	region_9923	0	+
+chr1	4652701	4652737	region_9924	0	-
+chr1	4653073	4653109	region_9925	0	-
+chr1	4653175	4653211	region_9926	0	-
+chr1	4653188	4653224	region_9927	0	+
+chr1	4653199	4653235	region_9928	0	-
+chr1	4653277	4653313	region_9929	0	+
+chr1	4653345	4653381	region_9930	0	+
+chr1	4653387	4653423	region_9931	0	-
+chr1	4653471	4653507	region_9932	0	-
+chr1	4653503	4653539	region_9933	0	-
+chr1	4653574	4653610	region_9934	0	-
+chr1	4653665	4653701	region_9935	0	+
+chr1	4655248	4655284	region_9936	0	+
+chr1	4655485	4655521	region_9937	0	+
+chr1	4656708	4656744	region_9938	0	-
+chr1	4656721	4656757	region_9939	0	-
+chr1	4656752	4656788	region_9940	0	+
+chr1	4656810	4656846	region_9941	0	-
+chr1	4657008	4657044	region_9942	0	-
+chr1	4657224	4657260	region_9943	0	-
+chr1	4657264	4657300	region_9944	0	+
+chr1	4657354	4657390	region_9945	0	+
+chr1	4657366	4657402	region_9946	0	+
+chr1	4657389	4657425	region_9947	0	+
+chr1	4657454	4657490	region_9948	0	+
+chr1	4657590	4657626	region_9949	0	-
+chr1	4657717	4657753	region_9950	0	-
+chr1	4657724	4657760	region_9951	0	-
+chr1	4657774	4657810	region_9952	0	+
+chr1	4657836	4657872	region_9953	0	-
+chr1	4657909	4657945	region_9954	0	-
+chr1	4657912	4657948	region_9955	0	+
+chr1	4657928	4657964	region_9956	0	-
+chr1	4657951	4657987	region_9957	0	+
+chr1	4658311	4658347	region_9958	0	-
+chr1	4658321	4658357	region_9959	0	+
+chr1	4658371	4658407	region_9960	0	+
+chr1	4658397	4658433	region_9961	0	+
+chr1	4658487	4658523	region_9962	0	+
+chr1	4658664	4658700	region_9963	0	-
+chr1	4658713	4658749	region_9964	0	-
+chr1	4658824	4658860	region_9965	0	-
+chr1	4658866	4658902	region_9966	0	-
+chr1	4658905	4658941	region_9967	0	+
+chr1	4658955	4658991	region_9968	0	+
+chr1	4658971	4659007	region_9969	0	-
+chr1	4659035	4659071	region_9970	0	-
+chr1	4659244	4659280	region_9971	0	-
+chr1	4659387	4659423	region_9972	0	+
+chr1	4659465	4659501	region_9973	0	-
+chr1	4659470	4659506	region_9974	0	-
+chr1	4659504	4659540	region_9975	0	-
+chr1	4659504	4659540	region_9976	0	-
+chr1	4659511	4659547	region_9977	0	-
+chr1	4659523	4659559	region_9978	0	+
+chr1	4659530	4659566	region_9979	0	-
+chr1	4659563	4659599	region_9980	0	-
+chr1	4659578	4659614	region_9981	0	-
+chr1	4659619	4659655	region_9982	0	+
+chr1	4659698	4659734	region_9983	0	+
+chr1	4659803	4659839	region_9984	0	+
+chr1	4659846	4659882	region_9985	0	+
+chr1	4659880	4659916	region_9986	0	-
+chr1	4660125	4660161	region_9987	0	-
+chr1	4660236	4660272	region_9988	0	+
+chr1	4660334	4660370	region_9989	0	+
+chr1	4660404	4660440	region_9990	0	+
+chr1	4660431	4660467	region_9991	0	-
+chr1	4661109	4661145	region_9992	0	+
+chr1	4661186	4661222	region_9993	0	+
+chr1	4661332	4661368	region_9994	0	+
+chr1	4661506	4661542	region_9995	0	+
+chr1	4661557	4661593	region_9996	0	-
+chr1	4661619	4661655	region_9997	0	-
+chr1	4662104	4662140	region_9998	0	-
+chr1	4662148	4662184	region_9999	0	+
Binary file test-data/chipseq_input.bed.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/config_TF.txt	Fri Dec 03 16:27:57 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 16:27:57 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 16:27:57 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 Jul 21 14:13:34 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 Jul 21 14:13:34 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 Jul 21 14:13:34 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
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-chr1	5161975	5161200	5162750	4	0	12\.\d+	0\.193000
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-chr1	4895575	4889250	4896100	4	0	12\.\d+	0\.193000
-chr1	4323875	4323250	4324550	47	4	11\.\d+	1\.000000
-chr1	4629425	4629150	4629700	9	1	7\.\d+	1\.000000
-chr1	3462625	3462250	3463300	8	1	6\.\d+	1\.000000
-chr1	3559825	3559550	3560150	7	1	5\.\d+	1\.000000
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--- a/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match	Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,272 +0,0 @@
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-chr1	5237875	5228750	5242150	4	0	14\.\d+	1\.000000
-chr1	4984925	4978900	4987150	4	0	14\.\d+	1\.000000
-chr1	5302025	5300700	5319250	4	0	14\.\d+	1\.000000
-chr1	5381625	5368500	5389350	4	0	14\.\d+	1\.000000
-chr1	5033175	5032000	5036100	4	0	14\.\d+	1\.000000
-chr1	4408525	4407200	4409200	88	13	6\.\d+	1\.000000
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--- a/test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match	Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,183 +0,0 @@
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-chr1	4885925	4885150	4886550	5	0	15\.\d+	0\.193000
-chr1	5540175	5539550	5541750	5	0	15\.\d+	0\.193000
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-chr1	3832625	3831950	3833100	5	0	15\.\d+	0\.193000
-chr1	5655975	5655300	5656700	5	0	15\.\d+	0\.193000
-chr1	4727375	4725950	4728150	5	0	15\.\d+	0\.193000
-chr1	5633525	5631850	5636000	5	0	15\.\d+	0\.193000
-chr1	4674175	4673500	4675550	5	0	15\.\d+	0\.193000
-chr1	5497825	5495700	5499250	5	0	15\.\d+	0\.193000
-chr1	4092425	4091800	4092950	5	0	15\.\d+	0\.193000
-chr1	5506125	5501700	5509950	5	0	15\.\d+	0\.193000
-chr1	5487775	5487100	5488500	5	0	15\.\d+	0\.193000
-chr1	5666675	5666250	5667300	5	0	15\.\d+	0\.193000
-chr1	5606575	5604350	5609750	5	0	15\.\d+	0\.193000
-chr1	5137425	5136800	5138000	5	0	15\.\d+	0\.193000
-chr1	5370725	5369000	5375550	5	0	15\.\d+	0\.193000
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-chr1	5356225	5353400	5357000	5	0	15\.\d+	0\.193000
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-chr1	5164475	5163800	5165200	5	0	15\.\d+	0\.193000
-chr1	5148625	5148200	5150600	5	0	15\.\d+	0\.193000
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-chr1	5142775	5141600	5144200	5	0	15\.\d+	0\.193000
-chr1	5475625	5475100	5477300	5	0	15\.\d+	0\.193000
-chr1	5292275	5291650	5293450	5	0	15\.\d+	0\.193000
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-chr1	5288675	5288100	5291550	5	0	15\.\d+	0\.193000
-chr1	3054875	3054500	3055300	5	0	15\.\d+	0\.193000
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-chr1	5603725	5602100	5604250	4	0	12\.\d+	0\.193000
-chr1	5205775	5205150	5206300	4	0	12\.\d+	0\.193000
-chr1	5395225	5394650	5396000	4	0	12\.\d+	0\.193000
-chr1	5396675	5396050	5398750	4	0	12\.\d+	0\.193000
-chr1	5431675	5430850	5433300	4	0	12\.\d+	0\.193000
-chr1	5660625	5659950	5661050	4	0	12\.\d+	0\.193000
-chr1	5161975	5161200	5162750	4	0	12\.\d+	0\.193000
-chr1	5657525	5657150	5658300	4	0	12\.\d+	0\.193000
-chr1	4975375	4974700	4976400	4	0	12\.\d+	0\.193000
-chr1	4887025	4886600	4887750	4	0	12\.\d+	0\.193000
-chr1	3196025	3195750	3196350	4	0	12\.\d+	0\.193000
-chr1	5257475	5257000	5258200	4	0	12\.\d+	0\.193000
-chr1	4852675	4852100	4853850	4	0	12\.\d+	0\.193000
-chr1	4877275	4876500	4878000	4	0	12\.\d+	0\.193000
-chr1	5317175	5316400	5318750	4	0	12\.\d+	0\.193000
-chr1	4781125	4780750	4781850	4	0	12\.\d+	0\.193000
-chr1	4841375	4840600	4842150	4	0	12\.\d+	0\.193000
-chr1	5232925	5232400	5233500	4	0	12\.\d+	0\.193000
-chr1	5712725	5712200	5713300	4	0	12\.\d+	0\.193000
-chr1	4784375	4783850	4785000	4	0	12\.\d+	0\.193000
-chr1	5381625	5381000	5383200	4	0	12\.\d+	0\.193000
-chr1	5234475	5233800	5237550	4	0	12\.\d+	0\.193000
-chr1	3062525	3062250	3062900	4	0	12\.\d+	0\.193000
-chr1	5440025	5439250	5440800	4	0	12\.\d+	0\.193000
-chr1	5694925	5694400	5696050	4	0	12\.\d+	0\.193000
-chr1	5139025	5138250	5139800	4	0	12\.\d+	0\.193000
-chr1	5529975	5529250	5531450	4	0	12\.\d+	0\.193000
-chr1	5434275	5433650	5434750	4	0	12\.\d+	0\.193000
-chr1	5074275	5073700	5074850	4	0	12\.\d+	0\.193000
-chr1	5524325	5523650	5525000	4	0	12\.\d+	0\.193000
-chr1	4323875	4323250	4324550	47	4	11\.\d+	1\.000000
-chr1	4629425	4629150	4629700	9	1	7\.\d+	1\.000000
-chr1	3462625	3462250	3463300	8	1	6\.\d+	1\.000000
-chr1	3677375	3677100	3677700	7	1	5\.\d+	1\.000000
-chr1	3559825	3559550	3560150	7	1	5\.\d+	1\.000000
-chr1	4247375	4247100	4247650	11	2	5\.\d+	1\.000000
--- a/test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match	Tue Jul 21 14:13:34 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
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-chr1	5106525	5105050	5117450	11	0	40\.\d+	0\.034000
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-chr1	5448375	5445350	5450050	9	0	32\.\d+	0\.034000
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-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
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-chr1	5324575	5322550	5334750	8	0	29\.\d+	0\.034000
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-chr1	5548775	5547250	5552250	7	0	25\.\d+	0\.135000
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-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
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-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
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-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
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--- a/test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match	Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,884 +0,0 @@
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-chr1	5746675	5743300	5747400	5	0	15\.\d+	0\.193000
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--- a/test-data/peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match	Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,673 +0,0 @@
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-chr1	5510825	5501200	5517200	12	0	43\.\d+	0\.025000
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-chr1	5524125	5521900	5536850	5	0	18\.\d+	0\.199000
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-chr1	5632975	5631350	5638100	6	0	21\.\d+	0\.135000
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-chr1	5651825	5645550	5668850	9	0	32\.\d+	0\.034000
-chr1	5653275	5645550	5668850	11	0	40\.\d+	0\.034000
-chr1	5656025	5645550	5668850	6	0	21\.\d+	0\.135000
-chr1	5660675	5645550	5668850	4	0	14\.\d+	1\.000000
-chr1	5664225	5645550	5668850	5	0	18\.\d+	0\.199000
-chr1	5666375	5645550	5668850	6	0	21\.\d+	0\.135000
-chr1	5679325	5675600	5681850	8	0	29\.\d+	0\.034000
-chr1	5688775	5687300	5691900	6	0	21\.\d+	0\.135000
-chr1	5695175	5693900	5701400	7	0	25\.\d+	0\.135000
-chr1	5696975	5693900	5701400	7	0	25\.\d+	0\.135000
-chr1	5699925	5693900	5701400	4	0	14\.\d+	1\.000000
-chr1	5706725	5703650	5710750	8	0	29\.\d+	0\.034000
-chr1	5712725	5711700	5719950	4	0	14\.\d+	1\.000000
-chr1	5716025	5711700	5719950	7	0	25\.\d+	0\.135000
-chr1	5718625	5711700	5719950	7	0	25\.\d+	0\.135000
-chr1	5722875	5720500	5731000	5	0	18\.\d+	0\.199000
-chr1	5726025	5720500	5731000	11	0	40\.\d+	0\.034000
-chr1	5742375	5741000	5748200	7	0	25\.\d+	0\.135000
-chr1	5744425	5741000	5748200	6	0	21\.\d+	0\.135000
-chr1	5746175	5741000	5748200	9	0	32\.\d+	0\.034000
-chr1	5751925	5749150	5753500	7	0	25\.\d+	0\.135000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Dec 03 16:27:57 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 Jul 21 14:13:34 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="b65b1bab9226" name="package_ccat_3_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>