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changeset 14:c16dbe4e2db2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
author iuc
date Mon, 06 Aug 2018 10:41:57 -0400
parents 01cded2297b7
children c33686854b19
files macs2_callpeak.xml test-data/callpeak_bampe_narrow.bed test-data/callpeak_part.tabular
diffstat 3 files changed, 137 insertions(+), 133 deletions(-) [+]
line wrap: on
line diff
--- a/macs2_callpeak.xml	Fri May 04 21:39:56 2018 -0400
+++ b/macs2_callpeak.xml	Mon Aug 06 10:41:57 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3" profile="17.09">
+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.4" profile="17.09">
     <description>Call peaks from alignment results</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -8,21 +8,25 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
+        #import re
+
         @home_dir@
-
         #set $temp_stderr = 'macs2_stderr'
+
         (macs2 callpeak
 
-            --name 'MACS2'
-
             ## Treatment File(s)
 
             #if str($treatment.t_multi_select) == "Yes":
                 -t ${ ' '.join( [ "'%s'" %  $x for $x in $treatment.input_treatment_file] ) }
+                #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file[0].element_identifier))
             #else
                 -t '$treatment.input_treatment_file'
+                #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file.element_identifier))
             #end if
 
+            --name $identifier
+
             ## Control File(s)
 
             #if str($control.c_select) == "Yes":
@@ -98,24 +102,24 @@
         2>&1 > $temp_stderr)
         #if "peaks_tabular" in str($outputs).split(','):
             &&
-            cp MACS2_peaks.xls '${ output_tabular }'
+            cp ${identifier}_peaks.xls '${ output_tabular }'
         #end if
 
         ## run R to create pdf from model script
         #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE":
             &&
-            Rscript MACS2_model.r > MACS2_model.r.log
+            Rscript ${identifier}_model.r > ${identifier}_model.r.log
         #end if
 
         #if 'html' in str($outputs).split(','):
             ## if output files exists, move them to the files_path and create a html result page linking to them
             &&
             (
-            count=`ls -1 MACS2* 2>/dev/null | wc -l`;
+            count=`ls -1 ${identifier}* 2>/dev/null | wc -l`;
             if [ \$count != 0 ];
             then
                 mkdir '${ output_extra_files.files_path }' &&
-                cp -r MACS2* '${ output_extra_files.files_path }' &&
+                cp -r ${identifier}* '${ output_extra_files.files_path }' &&
                 python '$__tool_directory__/dir2html.py'
                     '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }';
             fi;
@@ -202,7 +206,7 @@
         </conditional>
 
         <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built">
-            <option value="peaks_tabular">Peaks as tabular file</option>
+            <option value="peaks_tabular">Peaks as tabular file (compatible wih MultiQC)</option>
             <option value="summits">Peak summits</option>
             <option value="bdg" >Scores in bedGraph files (--bdg)</option>
             <option value="html">Summary page (html)</option>
@@ -246,31 +250,31 @@
         <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
             <filter> outputs and 'peaks_tabular' in outputs</filter>
         </data>
-        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
+        <data name="output_broadpeaks" format="bed" from_work_dir="*_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
             <filter>
             ((
               advanced_options['broad_options']['broad_options_selector'] == "broad"
             ))
             </filter>
         </data>
-        <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
+        <data name="output_gappedpeaks" format="bed" from_work_dir="*_peaks.gappedPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
             <filter>
             ((
               advanced_options['broad_options']['broad_options_selector'] == "broad"
             ))
             </filter>
         </data>
-        <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
+        <data name="output_narrowpeaks" format="bed" from_work_dir="*_peaks.narrowPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
             <filter>
             ((
               advanced_options['broad_options']['broad_options_selector'] == "nobroad"
             ))
             </filter>
         </data>
-        <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
+        <data name="output_summits" format="bed" from_work_dir="*_summits.bed" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
             <filter>outputs and 'summits' in outputs</filter>
         </data>
-        <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (plot)">
+        <data name="output_plot" format="pdf" from_work_dir="*_model.pdf" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (plot)">
             <filter>
             ((
               outputs and 'pdf' in outputs and
@@ -279,10 +283,10 @@
             ))
             </filter>
         </data>
-        <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
+        <data name="output_treat_pileup" format="bedgraph" from_work_dir="*_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
             <filter>outputs and 'bdg' in outputs</filter>
         </data>
-        <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
+        <data name="output_control_lambda" format="bedgraph" from_work_dir="*_control_lambda.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
             <filter>outputs and 'bdg' in outputs</filter>
         </data>
         <data name="output_extra_files" format="html" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (html report)">
@@ -305,7 +309,7 @@
             <param name="upper" value="50" />
             <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
             <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
-            <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/>
+            <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/>
             <output name="output_extra_files">
                 <assert_contents>
                     <has_text text="Additional output created by MACS2" />
@@ -379,7 +383,7 @@
 This tool produces a BED file of narrowPeaks as default output. It can also produce additional outputs, which can be selected under the **Additional Outputs** option above.
 
     * **a BED file of peaks** (default)
-    * a tabular file of peaks
+    * a tabular file of peaks (compatible wih MultiQC)
     * a BED file of peak summits
     * two bedGraph files of scores, for treatment pileup and control lambda
     * a HTML summary page
@@ -396,9 +400,9 @@
     ======= ========= ======= ============ ==== === ======= ======== ======= =======
     1          2        3          4        5    6     7       8         9   **10**
     ======= ========= ======= ============ ==== === ======= ======== ======= =======
-    chr1    840081    840400  MACS2_peak_1  69   .  4.89872 10.50944 6.91052 158
-    chr1    919419    919785  MACS2_peak_2  87   .  5.85158 12.44148 8.70936 130
-    chr1    937220    937483  MACS2_peak_3  66   .  4.87632 10.06728 6.61759 154
+    chr1    840081    840400  treat1_peak_1  69   .  4.89872 10.50944 6.91052 158
+    chr1    919419    919785  treat1_peak_2  87   .  5.85158 12.44148 8.70936 130
+    chr1    937220    937483  treat1_peak_3  66   .  4.87632 10.06728 6.61759 154
     ======= ========= ======= ============ ==== === ======= ======== ======= =======
 
     Columns contain the following data:
@@ -417,16 +421,16 @@
 
 **Peaks tabular File**
 
-A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions.
+A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions. This file is compatible with **MultiQC**.
 
     Example:
 
     ======= ========= ======= ========== ============== ========== ==================  =================== ================== =============
     **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)**  **fold_enrichment** **-log10(qvalue)**  **name**
     ======= ========= ======= ========== ============== ========== ==================  =================== ================== =============
-    chr1    840082    840400  319        840240         4.00       10.50944            4.89872             6.91052             MACS2_peak_1
-    chr1    919420    919785  366        919550         5.00       12.44148            5.85158             8.70936             MACS2_peak_2
-    chr1    937221    937483  263        937375         4.00       10.06728            4.87632             6.61759             MACS2_peak_3
+    chr1    840082    840400  319        840240         4.00       10.50944            4.89872             6.91052             treat1_peak_1
+    chr1    919420    919785  366        919550         5.00       12.44148            5.85158             8.70936             treat1_peak_2
+    chr1    937221    937483  263        937375         4.00       10.06728            4.87632             6.61759             treat1_peak_3
     ======= ========= ======= ========== ============== ========== ==================  =================== ================== =============
 
     Columns contain the following data:
@@ -454,9 +458,9 @@
     ======= ========= ======= ============ =======
     1          2        3          4        **5**
     ======= ========= ======= ============ =======
-    chr1    840239    840240  MACS2_peak_1 6.91052
-    chr1    919549    919550  MACS2_peak_2 8.70936
-    chr1    937374    937375  MACS2_peak_3 6.61759
+    chr1    840239    840240  treat1_peak_1 6.91052
+    chr1    919549    919550  treat1_peak_2 8.70936
+    chr1    937374    937375  treat1_peak_3 6.61759
     ======= ========= ======= ============ =======
 
     Columns contain the following data:
@@ -513,9 +517,9 @@
     ======= ========= ======= ============ ==== === ======= ======= =======
     1        2         3       4            5    6   7       8       9
     ======= ========= ======= ============ ==== === ======= ======= =======
-    chr1    840081    840400  MACS2_peak_1  52   .  4.08790 8.57605 5.21506
-    chr1    919419    919785  MACS2_peak_2  56   .  4.37270 8.90436 5.60462
-    chr1    937220    937483  MACS2_peak_3  48   .  4.02343 8.06676 4.86861
+    chr1    840081    840400  treat1_peak_1  52   .  4.08790 8.57605 5.21506
+    chr1    919419    919785  treat1_peak_2  56   .  4.37270 8.90436 5.60462
+    chr1    937220    937483  treat1_peak_3  48   .  4.02343 8.06676 4.86861
     ======= ========= ======= ============ ==== === ======= ======= =======
 
 
@@ -541,9 +545,9 @@
     ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
     1       2         3       4            5    6    7       8       9   10  11  12  13      14     15
     ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
-    chr1    840081    840400  MACS2_peak_1  52   .  840081  840400   0   1  319  0  4.08790 8.57605 5.21506
-    chr1    919419    919785  MACS2_peak_2  56   .  919419  919785   0   1  366  0  4.37270 8.90436 5.60462
-    chr1    937220    937483  MACS2_peak_3  48   .  937220  937483   0   1  263  0  4.02343 8.06676 4.86861
+    chr1    840081    840400  treat1_peak_1  52   .  840081  840400   0   1  319  0  4.08790 8.57605 5.21506
+    chr1    919419    919785  treat1_peak_2  56   .  919419  919785   0   1  366  0  4.37270 8.90436 5.60462
+    chr1    937220    937483  treat1_peak_3  48   .  937220  937483   0   1  263  0  4.02343 8.06676 4.86861
     ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
 
 Columns contain the following data:
--- a/test-data/callpeak_bampe_narrow.bed	Fri May 04 21:39:56 2018 -0400
+++ b/test-data/callpeak_bampe_narrow.bed	Mon Aug 06 10:41:57 2018 -0400
@@ -1,1 +1,1 @@
-gi|251831106|ref|NC_012920.1|	0	251	MACS2_peak_1	3056	.	44.99989	308.04297	305.64328	56
+gi|251831106|ref|NC_012920.1|	0	251	bwa-mem-test1_bam_peak_1	3056	.	44.99989	308.04297	305.64328	56
--- a/test-data/callpeak_part.tabular	Fri May 04 21:39:56 2018 -0400
+++ b/test-data/callpeak_part.tabular	Mon Aug 06 10:41:57 2018 -0400
@@ -1,100 +1,100 @@
+# This file is generated by MACS version 2.1.1.20160309
+# Command line: callpeak -t /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_8.dat --name ChIP_200K_bed -c /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_9.dat --format BED --gsize 3300000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300
+# ARGUMENTS LIST:
+# name = ChIP_200K_bed
+# format = BED
+# ChIP-seq file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_8.dat']
+# control file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_9.dat']
+# effective genome size = 3.30e+09
+# band width = 300
+# model fold = [5, 50]
+# qvalue cutoff = 5.00e-02
+# Larger dataset will be scaled towards smaller dataset.
+# Range for calculating regional lambda is: 1000 bps and 10000 bps
+# Broad region calling is off
+# Paired-End mode is off
 
+# tag size is determined as 100 bps
+# total tags in treatment: 199977
+# tags after filtering in treatment: 199583
+# maximum duplicate tags at the same position in treatment = 1
+# Redundant rate in treatment: 0.00
+# total tags in control: 199978
+# tags after filtering in control: 199867
+# maximum duplicate tags at the same position in control = 1
+# Redundant rate in control: 0.00
+# d = 254
+# alternative fragment length(s) may be 254 bps
 chr	start	end	length	abs_summit	pileup	-log10(pvalue)	fold_enrichment	-log10(qvalue)	name
-chr1	840082	840400	319	840240	4.00	11.15252	4.92435	7.51486	MACS2_peak_1
-chr1	919420	919785	366	919550	5.00	12.44148	5.85158	8.70936	MACS2_peak_2
-chr1	937221	937483	263	937375	4.00	10.06728	4.87632	6.61759	MACS2_peak_3
-chr1	954743	954996	254	954814	3.00	8.63977	3.93948	5.28944	MACS2_peak_4
-chr1	994763	995016	254	994906	3.00	8.63977	3.93948	5.28944	MACS2_peak_5
-chr1	1057395	1057648	254	1057509	3.00	8.63977	3.93948	5.28944	MACS2_peak_6
-chr1	1240580	1241004	425	1240777	3.00	7.77216	3.90105	4.60940	MACS2_peak_7
-chr1	1307393	1307735	343	1307601	5.00	12.44148	5.85158	8.70936	MACS2_peak_8
-chr1	1440351	1440633	283	1440462	4.00	11.15252	4.92435	7.51486	MACS2_peak_9
-chr1	1555433	1555725	293	1555571	4.00	11.15252	4.92435	7.51486	MACS2_peak_10
-chr1	1590668	1590946	279	1590840	4.00	10.06728	4.87632	6.61759	MACS2_peak_11
-chr1	1837669	1838104	436	1837886	6.00	14.88256	6.82684	10.84922	MACS2_peak_12
-chr1	1840366	1840828	463	1840547	5.00	13.74439	5.90922	9.80598	MACS2_peak_13
-chr1	1976400	1976653	254	1976469	3.00	8.63977	3.93948	5.28944	MACS2_peak_14
-chr1	2071302	2071627	326	2071423	4.00	11.15252	4.92435	7.51486	MACS2_peak_15
-chr1	2105717	2106140	424	2105919	4.00	7.70001	4.64644	4.60940	MACS2_peak_16
-chr1	2126522	2126861	340	2126648	4.00	10.06728	4.87632	6.61759	MACS2_peak_17
-chr1	2246521	2246954	434	2246712	5.00	9.59761	5.57573	6.23289	MACS2_peak_18
-chr1	2313158	2313560	403	2313353	5.00	13.74439	5.90922	9.80598	MACS2_peak_19
-chr1	2345828	2346242	415	2346028	7.00	17.38158	7.80211	13.02598	MACS2_peak_20
-chr1	2510055	2510308	254	2510213	3.00	8.63977	3.93948	5.28944	MACS2_peak_21
-chr1	3341408	3341661	254	3341461	3.00	7.77216	3.90105	4.60940	MACS2_peak_22
-chr1	3369639	3369892	254	3369863	3.00	8.63977	3.93948	5.28944	MACS2_peak_23
-chr1	3400441	3400769	329	3400610	4.00	11.15252	4.92435	7.51486	MACS2_peak_24
-chr1	3407841	3408094	254	3407975	3.00	8.63977	3.93948	5.28944	MACS2_peak_25
-chr1	3481748	3482245	498	3481863	4.00	11.15252	4.92435	7.51486	MACS2_peak_26
-chr1	3535562	3535821	260	3535663	3.00	8.63977	3.93948	5.28944	MACS2_peak_27
-chr1	3537757	3538010	254	3537960	3.00	8.63977	3.93948	5.28944	MACS2_peak_28
-chr1	3593610	3593863	254	3593838	3.00	7.77216	3.90105	4.60940	MACS2_peak_29
-chr1	3640884	3641366	483	3641134	12.00	30.54970	12.67843	24.90331	MACS2_peak_30
-chr1	3702144	3702397	254	3702260	3.00	7.77216	3.90105	4.60940	MACS2_peak_31
-chr1	3773699	3774058	360	3773876	7.00	19.11990	7.87896	14.58582	MACS2_peak_32
-chr1	3827306	3827722	417	3827525	5.00	13.74439	5.90922	9.80598	MACS2_peak_33
-chr1	4712784	4713037	254	4712904	3.00	8.63977	3.93948	5.28944	MACS2_peak_34
-chr1	4886187	4886440	254	4886326	3.00	7.77216	3.90105	4.60940	MACS2_peak_35
-chr1	5569919	5570198	280	5570056	4.00	11.15252	4.92435	7.51486	MACS2_peak_36
-chr1	5574777	5575080	304	5574838	3.00	8.63977	3.93948	5.28944	MACS2_peak_37
-chr1	5805838	5806091	254	5805965	2.00	6.22382	2.95461	3.18932	MACS2_peak_38
-chr1	5976146	5976399	254	5976235	3.00	8.63977	3.93948	5.28944	MACS2_peak_39
-chr1	6094646	6094899	254	6094678	2.00	6.22382	2.95461	3.18932	MACS2_peak_40
-chr1	6112957	6113210	254	6113135	3.00	6.57684	3.80689	3.50364	MACS2_peak_41
-chr1	6265253	6265640	388	6265437	6.00	11.56197	6.50502	7.91704	MACS2_peak_42
-chr1	6305229	6305482	254	6305299	3.00	8.63977	3.93948	5.28944	MACS2_peak_43
-chr1	6306874	6307127	254	6307013	3.00	8.63977	3.93948	5.28944	MACS2_peak_44
-chr1	6403481	6403843	363	6403679	6.00	16.40316	6.89409	12.16639	MACS2_peak_45
-chr1	6464657	6465096	440	6464869	6.00	11.56197	6.50502	7.91704	MACS2_peak_46
-chr1	6483604	6483857	254	6483739	3.00	8.63977	3.93948	5.28944	MACS2_peak_47
-chr1	6498110	6498494	385	6498258	6.00	14.88256	6.82684	10.84922	MACS2_peak_48
-chr1	6535513	6535838	326	6535591	5.00	13.74439	5.90922	9.80598	MACS2_peak_49
-chr1	6614468	6614882	415	6614708	4.00	10.06728	4.87632	6.61759	MACS2_peak_50
-chr1	6706586	6706931	346	6706743	5.00	13.74439	5.90922	9.80598	MACS2_peak_51
-chr1	6761833	6762203	371	6762039	7.00	14.98313	7.61377	10.92185	MACS2_peak_52
-chr1	6780092	6780471	380	6780329	6.00	16.40316	6.89409	12.16639	MACS2_peak_53
-chr1	6787475	6787900	426	6787704	7.00	19.11990	7.87896	14.58582	MACS2_peak_54
-chr1	6949953	6950377	425	6950153	5.00	10.64473	5.71033	7.17293	MACS2_peak_55
-chr1	7102753	7103077	325	7102915	4.00	11.15252	4.92435	7.51486	MACS2_peak_56
-chr1	7278317	7278718	402	7278483	6.00	16.40316	6.89409	12.16639	MACS2_peak_57
-chr1	7868456	7868722	267	7868577	4.00	11.15252	4.92435	7.51486	MACS2_peak_58
-chr1	7962797	7963068	272	7962862	3.00	7.77216	3.90105	4.60940	MACS2_peak_59
-chr1	8042368	8042722	355	8042491	6.00	14.88256	6.82684	10.84922	MACS2_peak_60
-chr1	8075039	8075466	428	8075252	6.00	12.78498	6.66205	9.02328	MACS2_peak_61
-chr1	8076577	8076851	275	8076739	4.00	8.57130	4.75861	5.28944	MACS2_peak_62
-chr1	8091217	8091506	290	8091352	4.00	11.15252	4.92435	7.51486	MACS2_peak_63
-chr1	8374359	8374715	357	8374570	6.00	16.40316	6.89409	12.16639	MACS2_peak_64
-chr1	8408996	8409352	357	8409218	4.00	11.15252	4.92435	7.51486	MACS2_peak_65
-chr1	8731417	8731750	334	8731570	4.00	10.06728	4.87632	6.61759	MACS2_peak_66
-chr1	8786590	8786948	359	8786756	7.00	12.59445	7.26312	8.86075	MACS2_peak_67
-chr1	8908916	8909169	254	8909002	2.00	5.57376	2.92579	2.70690	MACS2_peak_68
-chr1	8978204	8978524	321	8978356	5.00	13.74439	5.90922	9.80598	MACS2_peak_69
-chr1	9048092	9048380	289	9048260	4.00	8.57130	4.75861	5.28944	MACS2_peak_70
-chr1	9065105	9065592	488	9065349	5.00	13.74439	5.90922	9.80598	MACS2_peak_71
-chr1	9069997	9070429	433	9070211	4.00	11.15252	4.92435	7.51486	MACS2_peak_72
-chr1	9161571	9162021	451	9161797	4.00	11.15252	4.92435	7.51486	MACS2_peak_73
-chr1	9202271	9202685	415	9202502	8.00	21.88778	8.86384	17.04807	MACS2_peak_74
-chr1	9349089	9349445	357	9349217	7.00	13.58418	7.43431	9.80598	MACS2_peak_75
-chr1	9515790	9516185	396	9515967	5.00	12.44148	5.85158	8.70936	MACS2_peak_76
-chr1	9551082	9551430	349	9551283	8.00	19.93173	8.77737	15.26509	MACS2_peak_77
-chr1	9555243	9555566	324	9555465	4.00	8.57130	4.75861	5.28944	MACS2_peak_78
-chr1	9633765	9634090	326	9633928	4.00	11.15252	4.92435	7.51486	MACS2_peak_79
-chr1	9686945	9687456	512	9687169	8.00	21.88778	8.86384	17.04807	MACS2_peak_80
-chr1	9785163	9785490	328	9785327	4.00	11.15252	4.92435	7.51486	MACS2_peak_81
-chr1	9844609	9845020	412	9844800	7.00	17.38158	7.80211	13.02598	MACS2_peak_82
-chr1	9927528	9927906	379	9927732	6.00	16.40316	6.89409	12.16639	MACS2_peak_83
-chr1	9934881	9935311	431	9935118	10.00	27.55640	10.83358	22.22258	MACS2_peak_84
-chr1	10002416	10002754	339	10002612	6.00	14.88256	6.82684	10.84922	MACS2_peak_85
-chr1	10094609	10094862	254	10094709	3.00	7.77216	3.90105	4.60940	MACS2_peak_86
-chr1	10213081	10213334	254	10213170	3.00	8.63977	3.93948	5.28944	MACS2_peak_87
-chr1	10270278	10270531	254	10270454	3.00	7.77216	3.90105	4.60940	MACS2_peak_88
-chr1	10398111	10398364	254	10398242	3.00	8.63977	3.93948	5.28944	MACS2_peak_89
-chr1	10437538	10437866	329	10437672	4.00	10.06728	4.87632	6.61759	MACS2_peak_90
-chr1	10488119	10488390	272	10488249	4.00	11.15252	4.92435	7.51486	MACS2_peak_91
-chr1	10490217	10490601	385	10490448	3.00	8.63977	3.93948	5.28944	MACS2_peak_92
-chr1	10555092	10555459	368	10555262	5.00	13.74439	5.90922	9.80598	MACS2_peak_93
-chr1	10567501	10567905	405	10567666	8.00	17.23237	8.56549	12.97384	MACS2_peak_94
-chr1	10590401	10590654	254	10590532	3.00	8.63977	3.93948	5.28944	MACS2_peak_95
-chr1	11002044	11002404	361	11002212	5.00	13.74439	5.90922	9.80598	MACS2_peak_96
-chr1	11021083	11021336	254	11021260	3.00	8.63977	3.93948	5.28944	MACS2_peak_97
-chr1	11346323	11346576	254	11346452	3.00	8.63977	3.93948	5.28944	MACS2_peak_98
+chr1	840082	840400	319	840240	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_1
+chr1	919420	919785	366	919550	5.00	12.44148	5.85158	8.70936	ChIP_200K_bed_peak_2
+chr1	937221	937483	263	937375	4.00	10.06728	4.87632	6.61759	ChIP_200K_bed_peak_3
+chr1	954743	954996	254	954814	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_4
+chr1	994763	995016	254	994906	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_5
+chr1	1057395	1057648	254	1057509	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_6
+chr1	1240580	1241004	425	1240777	3.00	7.77216	3.90105	4.60940	ChIP_200K_bed_peak_7
+chr1	1307393	1307735	343	1307601	5.00	12.44148	5.85158	8.70936	ChIP_200K_bed_peak_8
+chr1	1440351	1440633	283	1440462	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_9
+chr1	1555433	1555725	293	1555571	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_10
+chr1	1590668	1590946	279	1590840	4.00	10.06728	4.87632	6.61759	ChIP_200K_bed_peak_11
+chr1	1837669	1838104	436	1837886	6.00	14.88256	6.82684	10.84922	ChIP_200K_bed_peak_12
+chr1	1840366	1840828	463	1840547	5.00	13.74439	5.90922	9.80598	ChIP_200K_bed_peak_13
+chr1	1976400	1976653	254	1976469	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_14
+chr1	2071302	2071627	326	2071423	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_15
+chr1	2105717	2106140	424	2105919	4.00	7.70001	4.64644	4.60940	ChIP_200K_bed_peak_16
+chr1	2126522	2126861	340	2126648	4.00	10.06728	4.87632	6.61759	ChIP_200K_bed_peak_17
+chr1	2246521	2246954	434	2246712	5.00	9.59761	5.57573	6.23289	ChIP_200K_bed_peak_18
+chr1	2313158	2313560	403	2313353	5.00	13.74439	5.90922	9.80598	ChIP_200K_bed_peak_19
+chr1	2345828	2346242	415	2346028	7.00	17.38158	7.80211	13.02598	ChIP_200K_bed_peak_20
+chr1	2510055	2510308	254	2510213	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_21
+chr1	3341408	3341661	254	3341461	3.00	7.77216	3.90105	4.60940	ChIP_200K_bed_peak_22
+chr1	3369639	3369892	254	3369863	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_23
+chr1	3400441	3400769	329	3400610	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_24
+chr1	3407841	3408094	254	3407975	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_25
+chr1	3481748	3482245	498	3481863	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_26
+chr1	3535562	3535821	260	3535663	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_27
+chr1	3537757	3538010	254	3537960	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_28
+chr1	3593610	3593863	254	3593838	3.00	7.77216	3.90105	4.60940	ChIP_200K_bed_peak_29
+chr1	3640884	3641366	483	3641134	12.00	30.54970	12.67843	24.90331	ChIP_200K_bed_peak_30
+chr1	3702144	3702397	254	3702260	3.00	7.77216	3.90105	4.60940	ChIP_200K_bed_peak_31
+chr1	3773699	3774058	360	3773876	7.00	19.11990	7.87896	14.58582	ChIP_200K_bed_peak_32
+chr1	3827306	3827722	417	3827525	5.00	13.74439	5.90922	9.80598	ChIP_200K_bed_peak_33
+chr1	4712784	4713037	254	4712904	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_34
+chr1	4886187	4886440	254	4886326	3.00	7.77216	3.90105	4.60940	ChIP_200K_bed_peak_35
+chr1	5569919	5570198	280	5570056	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_36
+chr1	5574777	5575080	304	5574838	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_37
+chr1	5805838	5806091	254	5805965	2.00	6.22382	2.95461	3.18932	ChIP_200K_bed_peak_38
+chr1	5976146	5976399	254	5976235	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_39
+chr1	6094646	6094899	254	6094678	2.00	6.22382	2.95461	3.18932	ChIP_200K_bed_peak_40
+chr1	6112957	6113210	254	6113135	3.00	6.57684	3.80689	3.50364	ChIP_200K_bed_peak_41
+chr1	6265253	6265640	388	6265437	6.00	11.56197	6.50502	7.91704	ChIP_200K_bed_peak_42
+chr1	6305229	6305482	254	6305299	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_43
+chr1	6306874	6307127	254	6307013	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_44
+chr1	6403481	6403843	363	6403679	6.00	16.40316	6.89409	12.16639	ChIP_200K_bed_peak_45
+chr1	6464657	6465096	440	6464869	6.00	11.56197	6.50502	7.91704	ChIP_200K_bed_peak_46
+chr1	6483604	6483857	254	6483739	3.00	8.63977	3.93948	5.28944	ChIP_200K_bed_peak_47
+chr1	6498110	6498494	385	6498258	6.00	14.88256	6.82684	10.84922	ChIP_200K_bed_peak_48
+chr1	6535513	6535838	326	6535591	5.00	13.74439	5.90922	9.80598	ChIP_200K_bed_peak_49
+chr1	6614468	6614882	415	6614708	4.00	10.06728	4.87632	6.61759	ChIP_200K_bed_peak_50
+chr1	6706586	6706931	346	6706743	5.00	13.74439	5.90922	9.80598	ChIP_200K_bed_peak_51
+chr1	6761833	6762203	371	6762039	7.00	14.98313	7.61377	10.92185	ChIP_200K_bed_peak_52
+chr1	6780092	6780471	380	6780329	6.00	16.40316	6.89409	12.16639	ChIP_200K_bed_peak_53
+chr1	6787475	6787900	426	6787704	7.00	19.11990	7.87896	14.58582	ChIP_200K_bed_peak_54
+chr1	6949953	6950377	425	6950153	5.00	10.64473	5.71033	7.17293	ChIP_200K_bed_peak_55
+chr1	7102753	7103077	325	7102915	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_56
+chr1	7278317	7278718	402	7278483	6.00	16.40316	6.89409	12.16639	ChIP_200K_bed_peak_57
+chr1	7868456	7868722	267	7868577	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_58
+chr1	7962797	7963068	272	7962862	3.00	7.77216	3.90105	4.60940	ChIP_200K_bed_peak_59
+chr1	8042368	8042722	355	8042491	6.00	14.88256	6.82684	10.84922	ChIP_200K_bed_peak_60
+chr1	8075039	8075466	428	8075252	6.00	12.78498	6.66205	9.02328	ChIP_200K_bed_peak_61
+chr1	8076577	8076851	275	8076739	4.00	8.57130	4.75861	5.28944	ChIP_200K_bed_peak_62
+chr1	8091217	8091506	290	8091352	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_63
+chr1	8374359	8374715	357	8374570	6.00	16.40316	6.89409	12.16639	ChIP_200K_bed_peak_64
+chr1	8408996	8409352	357	8409218	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_65
+chr1	8731417	8731750	334	8731570	4.00	10.06728	4.87632	6.61759	ChIP_200K_bed_peak_66
+chr1	8786590	8786948	359	8786756	7.00	12.59445	7.26312	8.86075	ChIP_200K_bed_peak_67
+chr1	8908916	8909169	254	8909002	2.00	5.57376	2.92579	2.70690	ChIP_200K_bed_peak_68
+chr1	8978204	8978524	321	8978356	5.00	13.74439	5.90922	9.80598	ChIP_200K_bed_peak_69
+chr1	9048092	9048380	289	9048260	4.00	8.57130	4.75861	5.28944	ChIP_200K_bed_peak_70
+chr1	9065105	9065592	488	9065349	5.00	13.74439	5.90922	9.80598	ChIP_200K_bed_peak_71
+chr1	9069997	9070429	433	9070211	4.00	11.15252	4.92435	7.51486	ChIP_200K_bed_peak_72