Mercurial > repos > iuc > multiqc

changeset 11:f0ec41881020 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
author iuc
date Mon, 06 Aug 2018 10:42:11 -0400
parents ce0f144f4835
children 1c2db0054039
files multiqc.xml test-data/aligner_soft_stats.tabular test-data/macs_1.txt test-data/macs_2.txt test-data/macs_stats.tabular
diffstat 5 files changed, 243 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/multiqc.xml	Sun Aug 05 18:26:28 2018 -0400
+++ b/multiqc.xml	Mon Aug 06 10:42:11 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.2">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
         <token name="@WRAPPER_VERSION@">1.5</token>
@@ -216,6 +216,14 @@
     #elif str($repeat.software_cond.software) == "kallisto"
         #set $pattern = "finding pseudoalignments for the reads"
         @LN_FILES@
+    #elif str($repeat.software_cond.software) == "macs2"
+        #set $pattern = "# This file is generated by MACS"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls')
+            grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
+            ln -s '$file' '$file_path' &&
+        #end for
     #elif str($repeat.software_cond.software) == "picard"
         #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
             #if str($repeat2.type) == "alignment_metrics"
@@ -505,7 +513,7 @@
                     <!--<option value="jellyfish">Jellyfish</option>-->
                     <option value="kallisto">Kallisto</option>
                     <!--<option value="leehom">leeHom</option>-->
-                    <!--<option value="macs2">MACS2</option>-->
+                    <option value="macs2">MACS2</option>
                     <!--<option value="methylQA">methylQA</option>-->
                     <!--<option value="peddy">Peddy</option>-->
                     <option value="picard">Picard</option>
@@ -614,6 +622,9 @@
                 <when value="kallisto">
                     <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Kallisto" help="It should contain '[quant] finding pseudoalignments for the reads'"/>
                 </when>
+                <when value="macs2">
+                    <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of MACS2" help="It should be a tabular file containing '# This file is generated by MACS'"/>
+                </when>
                 <when value="picard">
                     <repeat name="output" title="Picard output" min="1">
                         <param name="type" type="select" label="Type of Picard output?">
@@ -887,6 +898,12 @@
             </repeat>
             <repeat name="results">
                 <conditional name="software_cond">
+                    <param name="software" value="macs2" />
+                    <param name="input" value="macs_1.txt,macs_2.txt" />
+                </conditional>
+            </repeat>
+            <repeat name="results">
+                <conditional name="software_cond">
                     <param name="software" value="star" />
                     <repeat name="output">
                         <conditional name="type">
@@ -915,6 +932,7 @@
                     <has_text text="bowtie2_se_plot" />
                     <has_text text="hisat2_se_plot" />
                     <has_text text="kallisto_alignment" />
+                    <has_text text="MACS2" />
                     <has_text text="star_alignment_plot" />
                     <has_text text="tophat_alignment" />
                     <has_text text="hicexplorer" />
@@ -928,6 +946,7 @@
                 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/>
                 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
                 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
+                <element name="macs" file="macs_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
             </output_collection>
--- a/test-data/aligner_soft_stats.tabular	Sun Aug 05 18:26:28 2018 -0400
+++ b/test-data/aligner_soft_stats.tabular	Mon Aug 06 10:42:11 2018 -0400
@@ -1,17 +1,19 @@
-Sample	Cutadapt_mqc-generalstats-percent_trimmed	Kallisto_mqc-generalstats-percent_aligned	Kallisto_mqc-generalstats-fragment_length	Kallisto_mqc-generalstats-pseudoaligned_reads	Bismark_mqc-generalstats-percent_aligned	Bismark_mqc-generalstats-aligned_reads	Bowtie 2_mqc-generalstats-overall_alignment_rate	HiCExplorer_mqc-generalstats-Pairs_used	HiCExplorer_mqc-generalstats-Min_rest_site_distance	HiCExplorer_mqc-generalstats-Mapped	HiCExplorer_mqc-generalstats-Max_rest_site_distance	HiCExplorer_mqc-generalstats-Pairs_considered	HISAT2_mqc-generalstats-overall_alignment_rate	STAR_mqc-generalstats-uniquely_mapped	STAR_mqc-generalstats-uniquely_mapped_percent	Tophat_mqc-generalstats-aligned_not_multimapped_discordant	Tophat_mqc-generalstats-overall_aligned_percent
-HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1	5.880883098970165																
-HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1		83.65114569077758	167.866	48531088.0													
-HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2	31.038195169381073																
-HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1	7.7267901650356645																
-HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1		84.50278473550448	169.418	59280920.0													
-HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2	32.18485266309055																
-bismark_SE_report					69.71079996207212	220558.0											
-bowtie2_1							98.33										
-bowtie2_2							98.31										
-hicexplorer_hicexplorer1_1_small_test								0.3732734564876029	303.0	0.08778492343698428	800.0	99983.0					
-hicexplorer_hicexplorer1_small_test								0.3732734564876029	303.0	0.08778492343698428	800.0	99983.0					
-hicexplorer_hicexplorer2_small_test_rf								0.35940109818669175	152.0	0.08778492343698428	1500.0	99983.0					
-hisat2_1													96.15				
-hisat2_2													96.15				
-star_log														89.0	89.0		
-tophat_align																307733.0	99.5
+Sample	Cutadapt_mqc-generalstats-percent_trimmed	Kallisto_mqc-generalstats-fragment_length	Kallisto_mqc-generalstats-percent_aligned	Kallisto_mqc-generalstats-pseudoaligned_reads	Bismark_mqc-generalstats-aligned_reads	Bismark_mqc-generalstats-percent_aligned	Bowtie 2_mqc-generalstats-overall_alignment_rate	HiCExplorer_mqc-generalstats-Pairs_considered	HiCExplorer_mqc-generalstats-Pairs_used	HiCExplorer_mqc-generalstats-Mapped	HiCExplorer_mqc-generalstats-Min_rest_site_distance	HiCExplorer_mqc-generalstats-Max_rest_site_distance	HISAT2_mqc-generalstats-overall_alignment_rate	STAR_mqc-generalstats-uniquely_mapped_percent	STAR_mqc-generalstats-uniquely_mapped	Tophat_mqc-generalstats-overall_aligned_percent	Tophat_mqc-generalstats-aligned_not_multimapped_discordant	MACS2_mqc-generalstats-d	MACS2_mqc-generalstats-treatment_redundant_rate	MACS2_mqc-generalstats-control_redundant_rate
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1	5.880883098970165																			
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1		167.866	83.65114569077758	48531088.0																
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2	31.038195169381073																			
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1	7.7267901650356645																			
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1		169.418	84.50278473550448	59280920.0																
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2	32.18485266309055																			
+bismark_txt_SE_report					220558.0	69.71079996207212														
+bowtie2_1_txt							98.33													
+bowtie2_2_txt							98.31													
+hicexplorer_3_hicexplorer1_log_1_small_test								99983.0	0.3732734564876029	0.08778492343698428	303.0	800.0								
+hicexplorer_3_hicexplorer1_log_small_test								99983.0	0.3732734564876029	0.08778492343698428	303.0	800.0								
+hicexplorer_3_hicexplorer2_log_small_test_rf								99983.0	0.35940109818669175	0.08778492343698428	152.0	1500.0								
+hisat2_1_txt													96.15							
+hisat2_2_txt													96.15							
+star_log_txt														89.0	89.0					
+tophat_txtalign																99.5	307733.0			
+treat1																		254.0	0.0	0.0
+treat2																		254.0	0.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/macs_1.txt	Mon Aug 06 10:42:11 2018 -0400
@@ -0,0 +1,100 @@
+# This file is generated by MACS version 2.1.1.20160309
+# Command line: callpeak --name treat1 -t /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_1.dat -c /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_2.dat --format BED --gsize 2700000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300
+# ARGUMENTS LIST:
+# name = treat1
+# format = BED
+# ChIP-seq file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_1.dat']
+# control file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_2.dat']
+# effective genome size = 2.70e+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	10.71801	4.90785	7.08620	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	8.29236	3.92628	4.97243	MACS2_peak_4
+chr1	994763	995016	254	994906	3.00	8.29236	3.92628	4.97243	MACS2_peak_5
+chr1	1057395	1057648	254	1057509	3.00	8.29236	3.92628	4.97243	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	10.71801	4.90785	7.08620	MACS2_peak_9
+chr1	1555433	1555725	293	1555571	4.00	10.71801	4.90785	7.08620	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	13.22276	5.88942	9.29290	MACS2_peak_13
+chr1	1976400	1976653	254	1976469	3.00	8.29236	3.92628	4.97243	MACS2_peak_14
+chr1	2071302	2071627	326	2071423	4.00	10.71801	4.90785	7.08620	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	13.22276	5.88942	9.29290	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	8.29236	3.92628	4.97243	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	8.29236	3.92628	4.97243	MACS2_peak_23
+chr1	3400441	3400769	329	3400610	4.00	10.71801	4.90785	7.08620	MACS2_peak_24
+chr1	3407841	3408094	254	3407975	3.00	8.29236	3.92628	4.97243	MACS2_peak_25
+chr1	3481748	3482245	498	3481863	4.00	10.71801	4.90785	7.08620	MACS2_peak_26
+chr1	3535562	3535821	260	3535663	3.00	8.29236	3.92628	4.97243	MACS2_peak_27
+chr1	3537757	3538010	254	3537960	3.00	8.29236	3.92628	4.97243	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	18.42402	7.85256	13.89198	MACS2_peak_32
+chr1	3827306	3827722	417	3827525	5.00	13.22276	5.88942	9.29290	MACS2_peak_33
+chr1	4712784	4713037	254	4712904	3.00	8.29236	3.92628	4.97243	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	10.71801	4.90785	7.08620	MACS2_peak_36
+chr1	5574777	5575080	304	5574838	3.00	8.29236	3.92628	4.97243	MACS2_peak_37
+chr1	5805838	5806091	254	5805965	2.00	5.96348	2.94471	2.92914	MACS2_peak_38
+chr1	5976146	5976399	254	5976235	3.00	8.29236	3.92628	4.97243	MACS2_peak_39
+chr1	6094646	6094899	254	6094678	2.00	5.96348	2.94471	2.92914	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	8.29236	3.92628	4.97243	MACS2_peak_43
+chr1	6306874	6307127	254	6307013	3.00	8.29236	3.92628	4.97243	MACS2_peak_44
+chr1	6403481	6403843	363	6403679	6.00	15.79441	6.87099	11.56042	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	8.29236	3.92628	4.97243	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	13.22276	5.88942	9.29290	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	13.22276	5.88942	9.29290	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	15.79441	6.87099	11.56042	MACS2_peak_53
+chr1	6787475	6787900	426	6787704	7.00	18.42402	7.85256	13.89198	MACS2_peak_54
+chr1	6949953	6950377	425	6950153	5.00	10.64473	5.71033	7.08620	MACS2_peak_55
+chr1	7102753	7103077	325	7102915	4.00	10.71801	4.90785	7.08620	MACS2_peak_56
+chr1	7278317	7278718	402	7278483	6.00	15.79441	6.87099	11.56042	MACS2_peak_57
+chr1	7868456	7868722	267	7868577	4.00	10.71801	4.90785	7.08620	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	5.22097	MACS2_peak_62
+chr1	8091217	8091506	290	8091352	4.00	10.71801	4.90785	7.08620	MACS2_peak_63
+chr1	8374359	8374715	357	8374570	6.00	15.79441	6.87099	11.56042	MACS2_peak_64
+chr1	8408996	8409352	357	8409218	4.00	10.71801	4.90785	7.08620	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	13.22276	5.88942	9.29290	MACS2_peak_69
+chr1	9048092	9048380	289	9048260	4.00	8.57130	4.75861	5.22097	MACS2_peak_70
+chr1	9065105	9065592	488	9065349	5.00	13.22276	5.88942	9.29290	MACS2_peak_71
+chr1	9069997	9070429	433	9070211	4.00	10.71801	4.90785	7.08620	MACS2_peak_72
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/macs_2.txt	Mon Aug 06 10:42:11 2018 -0400
@@ -0,0 +1,100 @@
+# This file is generated by MACS version 2.1.1.20160309
+# Command line: callpeak --name treat2 -t /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_8.dat -c /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_2.dat --format BED --gsize 2700000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300
+# ARGUMENTS LIST:
+# name = treat2
+# format = BED
+# ChIP-seq file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_8.dat']
+# control file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_2.dat']
+# effective genome size = 2.70e+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: 100000
+# tags after filtering in treatment: 99795
+# 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	115538	115791	254	115665	1.00	4.35859	1.98140	1.67749	MACS2_peak_1
+chr1	237644	237935	292	237790	2.00	6.86347	2.97210	3.86269	MACS2_peak_2
+chr1	542564	542817	254	542691	1.00	4.35859	1.98140	1.67749	MACS2_peak_3
+chr1	652482	652735	254	652609	1.00	4.35859	1.98140	1.67749	MACS2_peak_4
+chr1	675967	676220	254	676094	1.00	4.35859	1.98140	1.67749	MACS2_peak_5
+chr1	739125	739378	254	739252	1.00	4.35859	1.98140	1.67749	MACS2_peak_6
+chr1	785730	785983	254	785857	1.00	4.35859	1.98140	1.67749	MACS2_peak_7
+chr1	805192	805536	345	805364	2.00	6.47268	2.96243	3.63723	MACS2_peak_8
+chr1	811789	812361	573	811916	1.00	3.49990	1.95053	1.44931	MACS2_peak_9
+chr1	840079	840401	323	840240	4.00	12.21969	4.95350	8.64187	MACS2_peak_10
+chr1	858769	859114	346	858942	2.00	6.47268	2.96243	3.63723	MACS2_peak_11
+chr1	875785	876038	254	875912	1.00	4.09830	1.97495	1.67749	MACS2_peak_12
+chr1	902086	902339	254	902213	1.00	4.09830	1.97495	1.67749	MACS2_peak_13
+chr1	911342	911595	254	911469	1.00	4.35859	1.98140	1.67749	MACS2_peak_14
+chr1	919315	919929	615	919550	5.00	14.24284	5.92486	10.53337	MACS2_peak_15
+chr1	937147	937603	457	937375	4.00	11.56776	4.93738	8.14431	MACS2_peak_16
+chr1	953008	953261	254	953135	1.00	4.35859	1.98140	1.67749	MACS2_peak_17
+chr1	954263	955017	755	954814	3.00	9.49316	3.96280	6.20710	MACS2_peak_18
+chr1	994723	995089	367	994906	3.00	9.49316	3.96280	6.20710	MACS2_peak_19
+chr1	999268	999578	311	999423	2.00	6.86347	2.97210	3.86269	MACS2_peak_20
+chr1	1004656	1004909	254	1004783	1.00	4.35859	1.98140	1.67749	MACS2_peak_21
+chr1	1044551	1044804	254	1044678	1.00	4.35859	1.98140	1.67749	MACS2_peak_22
+chr1	1057326	1057692	367	1057509	3.00	9.49316	3.96280	6.20710	MACS2_peak_23
+chr1	1105615	1105868	254	1105742	1.00	3.49990	1.95053	1.44931	MACS2_peak_24
+chr1	1115032	1115285	254	1115159	1.00	4.35859	1.98140	1.67749	MACS2_peak_25
+chr1	1142348	1142601	254	1142475	1.00	4.09830	1.97495	1.67749	MACS2_peak_26
+chr1	1143298	1143551	254	1143425	1.00	4.09830	1.97495	1.67749	MACS2_peak_27
+chr1	1166225	1166478	254	1166352	1.00	4.35859	1.98140	1.67749	MACS2_peak_28
+chr1	1204174	1204427	254	1204301	1.00	4.35859	1.98140	1.67749	MACS2_peak_29
+chr1	1220904	1221157	254	1221031	1.00	4.09830	1.97495	1.67749	MACS2_peak_30
+chr1	1225704	1225957	254	1225831	1.00	4.35859	1.98140	1.67749	MACS2_peak_31
+chr1	1227178	1227443	266	1227311	2.00	6.86347	2.97210	3.86269	MACS2_peak_32
+chr1	1240549	1241123	575	1240777	3.00	8.97181	3.94991	5.83616	MACS2_peak_33
+chr1	1241426	1241846	421	1241636	2.00	6.47268	2.96243	3.63723	MACS2_peak_34
+chr1	1284325	1284888	564	1284452	1.00	4.35859	1.98140	1.67749	MACS2_peak_35
+chr1	1307376	1307825	450	1307601	5.00	14.24284	5.92486	10.53337	MACS2_peak_36
+chr1	1310554	1310807	254	1310681	1.00	4.09830	1.97495	1.67749	MACS2_peak_37
+chr1	1316444	1316697	254	1316571	1.00	4.09830	1.97495	1.67749	MACS2_peak_38
+chr1	1318227	1318480	254	1318354	1.00	4.35859	1.98140	1.67749	MACS2_peak_39
+chr1	1334774	1335027	254	1334901	1.00	3.49990	1.95053	1.44931	MACS2_peak_40
+chr1	1365743	1365996	254	1365870	1.00	4.09830	1.97495	1.67749	MACS2_peak_41
+chr1	1406356	1406609	254	1406483	1.00	4.35859	1.98140	1.67749	MACS2_peak_42
+chr1	1440209	1440715	507	1440462	4.00	12.21969	4.95350	8.64187	MACS2_peak_43
+chr1	1440989	1441242	254	1441116	1.00	4.35859	1.98140	1.67749	MACS2_peak_44
+chr1	1487432	1487685	254	1487559	1.00	4.09830	1.97495	1.67749	MACS2_peak_45
+chr1	1506072	1506325	254	1506199	1.00	4.09830	1.97495	1.67749	MACS2_peak_46
+chr1	1549214	1549467	254	1549341	1.00	4.09830	1.97495	1.67749	MACS2_peak_47
+chr1	1555404	1555738	335	1555571	4.00	12.21969	4.95350	8.64187	MACS2_peak_48
+chr1	1556892	1557145	254	1557019	1.00	4.35859	1.98140	1.67749	MACS2_peak_49
+chr1	1590595	1591084	490	1590840	4.00	11.56776	4.93738	8.14431	MACS2_peak_50
+chr1	1609355	1609608	254	1609482	1.00	4.35859	1.98140	1.67749	MACS2_peak_51
+chr1	1610353	1610772	420	1610563	2.00	6.86347	2.97210	3.86269	MACS2_peak_52
+chr1	1619961	1620214	254	1620088	1.00	4.09830	1.97495	1.67749	MACS2_peak_53
+chr1	1655695	1656225	531	1655822	1.00	4.09830	1.97495	1.67749	MACS2_peak_54
+chr1	1657692	1657945	254	1657819	1.00	4.09830	1.97495	1.67749	MACS2_peak_55
+chr1	1680363	1680616	254	1680490	1.00	4.35859	1.98140	1.67749	MACS2_peak_56
+chr1	1720444	1720697	254	1720571	1.00	4.35859	1.98140	1.67749	MACS2_peak_57
+chr1	1728043	1728296	254	1728170	1.00	4.09830	1.97495	1.67749	MACS2_peak_58
+chr1	1734745	1734998	254	1734872	1.00	4.35859	1.98140	1.67749	MACS2_peak_59
+chr1	1743661	1743914	254	1743788	1.00	4.09830	1.97495	1.67749	MACS2_peak_60
+chr1	1756326	1756579	254	1756453	1.00	3.49990	1.95053	1.44931	MACS2_peak_61
+chr1	1760856	1761109	254	1760983	1.00	3.49990	1.95053	1.44931	MACS2_peak_62
+chr1	1766488	1766741	254	1766615	1.00	3.49990	1.95053	1.44931	MACS2_peak_63
+chr1	1787177	1787430	254	1787304	1.00	4.35859	1.98140	1.67749	MACS2_peak_64
+chr1	1791336	1791589	254	1791463	1.00	4.09830	1.97495	1.67749	MACS2_peak_65
+chr1	1830665	1830918	254	1830792	1.00	4.09830	1.97495	1.67749	MACS2_peak_66
+chr1	1837638	1838133	496	1837886	6.00	16.98484	6.91233	12.98445	MACS2_peak_67
+chr1	1839919	1840172	254	1840046	1.00	4.09830	1.97495	1.67749	MACS2_peak_68
+chr1	1840298	1841007	710	1840547	5.00	15.02536	5.94420	11.12772	MACS2_peak_69
+chr1	1891434	1891687	254	1891561	1.00	4.35859	1.98140	1.67749	MACS2_peak_70
+chr1	1938174	1938427	254	1938301	1.00	4.35859	1.98140	1.67749	MACS2_peak_71
+chr1	1974716	1975076	361	1974896	2.00	6.47268	2.96243	3.63723	MACS2_peak_72
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/macs_stats.tabular	Mon Aug 06 10:42:11 2018 -0400
@@ -0,0 +1,3 @@
+Sample	fragment_size	treatment_fragments_total	treatment_fragments_after_filtering	treatment_max_duplicates	treatment_redundant_rate	control_fragments_total	control_fragments_after_filtering	control_max_duplicates	control_redundant_rate	d
+treat1	100.0	199977.0	199583.0	1.0	0.0	199978.0	199867.0	1.0	0.0	254.0
+treat2	100.0	100000.0	99795.0	1.0	0.0	199978.0	199867.0	1.0	0.0	254.0