# HG changeset patch
# User pjbriggs
# Date 1521559504 14400
# Node ID 4124781932dbacd6c6ed6d5bbd7cbd05a9a48905
# Parent  00d73c8123993124b9b0201611a36b2c7d3d82a5
Updated to MACS 2.1.1 and use conda for dependency resolution.

diff -r 00d73c812399 -r 4124781932db README.rst
--- a/README.rst	Wed Mar 22 11:36:07 2017 -0400
+++ b/README.rst	Tue Mar 20 11:25:04 2018 -0400
@@ -1,7 +1,7 @@
-MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0) peak calling
-==================================================================
+MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1) peak calling
+================================================================
 
-Galaxy tool wrapper for the peak calling function of MACS 2.1.0. MACS has been
+Galaxy tool wrapper for the peak calling function of MACS 2.1. MACS has been
 developed by Tao Lui
 https://github.com/taoliu/MACS/
 
@@ -15,7 +15,7 @@
 ======================
 
 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
-the MACS 2.1.0 program.
+the MACS 2.1 program.
 
 Manual Installation
 ===================
@@ -31,7 +31,7 @@
 
     <tool file="macs21/macs21_wrapper.xml" />
 
-You will also need to install MACS 2.1.0 and its dependencies:
+You will also need to install MACS 2.1 and its dependencies:
 
 - https://pypi.python.org/pypi/MACS2
 
@@ -52,13 +52,14 @@
 
 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 
 
-This version has been substantially modified both to adapt it to MACS 2.1.0, and
+This version has been substantially modified both to adapt it to MACS 2.1, and
 to re-implement the internal workings of the tool to conform with current
 practices in invoking commands from Galaxy, and to add new functionality.
 
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+2.1.1.0    - Update to use MACS 2.1.1 and use conda to resolve dependencies
 2.1.0-6    - Add bedSort step into bigWig file generation; terminate with error
              when MACS finishes with non-zero exit code.
 2.1.0-5    - User must explicitly specify the format for the inputs (to allow
diff -r 00d73c812399 -r 4124781932db macs21_wrapper.xml
--- a/macs21_wrapper.xml	Wed Mar 22 11:36:07 2017 -0400
+++ b/macs21_wrapper.xml	Tue Mar 20 11:25:04 2018 -0400
@@ -1,15 +1,17 @@
-<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-6">
+<tool id="macs2_1_peakcalling" name="MACS2.1.1" version="2.1.1.0">
   <description>Model-based Analysis of ChIP-Seq: peak calling</description>
   <requirements>
     <requirement type="package" version="2.7">python</requirement>
-    <requirement type="package" version="1.9">numpy</requirement>
-    <requirement type="package" version="2.1.0.20140616">macs2</requirement>
-    <requirement type="package" version="3.1.2">R</requirement>
-    <requirement type="package" version="2.0">ucsc_tools_for_macs21</requirement>
+    <requirement type="package" version="2.1.1">macs2</requirement>
+    <requirement type="package" version="3.4">R</requirement>
+    <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
+    <requirement type="package" version="357">ucsc-bedclip</requirement>
+    <requirement type="package" version="357">ucsc-bedsort</requirement>
+    <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
   </requirements>
   <version_command>macs2 --version</version_command>
-  <command interpreter="python">
-    macs21_wrapper.py callpeak
+  <command><![CDATA[
+    python $__tool_directory__/macs21_wrapper.py callpeak
     ##
     ## ChIP-seq input
     $input_chipseq_file1
@@ -96,10 +98,10 @@
     #else
        --output-peaks=$output_peaks_file
     #end if
-  </command>
+  ]]></command>
   <inputs>
     <!--experiment name used as base for output file names -->
-    <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50"
+    <param name="experiment_name" type="text" value="MACS2.1 in Galaxy" size="50"
 	   label="Experiment Name"/>
     <!--choose 'broad' or 'narrow' regions-->
     <conditional name="broad_options">
@@ -277,7 +279,7 @@
     <!-- Peak calling without bigwig output -->
     <test>
       <!-- Inputs -->
-      <param name="experiment_name" value="test_MACS2.1.0" />
+      <param name="experiment_name" value="test_MACS2.1.1" />
       <param name="broad_regions" value="" />
       <param name="format" value="BED" />
       <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
@@ -303,20 +305,20 @@
       <param name="nomodel_type_selector" value="nomodel" />
       <param name="nomodel_type|extsize" value="243" />
       <!-- Outputs -->
-      <output name="output_extra_files" file="test_MACS2.1.0_html_report.zip"
+      <output name="output_extra_files" file="test_MACS2.1.1_html_report.zip"
 	      compare="sim_size" delta="1500" />
-      <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" />
-      <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" />
+      <output name="output_summits_bed_file" file="test_MACS2.1.1_summits.bed" />
+      <output name="output_narrowpeaks_file" file="test_MACS2.1.1_peaks_narrowPeak.interval" />
       <output name="output_xls_to_interval_peaks_file"
-	      file="test_MACS2.1.0_peaks.xls.re_match"
+	      file="test_MACS2.1.1_peaks.xls.re_match"
 	      compare="re_match" lines_diff="1" />
-      <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" />
-      <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" />
+      <output name="output_treat_pileup_file" file="test_MACS2.1.1_treat_pileup.bdg" />
+      <output name="output_lambda_bedgraph_file" file="test_MACS2.1.1_control_lambda.bdg" />
     </test>
     <!-- Peak calling with bigwig output -->
     <test>
       <!-- Inputs -->
-      <param name="experiment_name" value="test_MACS2.1.0" />
+      <param name="experiment_name" value="test_MACS2.1.1" />
       <param name="broad_regions" value="" />
       <param name="format" value="BED" />
       <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"
@@ -342,23 +344,23 @@
       <param name="nomodel_type_selector" value="nomodel" />
       <param name="nomodel_type|extsize" value="243" />
       <!-- Outputs -->
-      <output name="output_extra_files" file="test_MACS2.1.0_bw_html_report.zip"
+      <output name="output_extra_files" file="test_MACS2.1.1_bw_html_report.zip"
 	      compare="sim_size" delta="2500" />
-      <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" />
-      <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" />
+      <output name="output_summits_bed_file" file="test_MACS2.1.1_summits.bed" />
+      <output name="output_narrowpeaks_file" file="test_MACS2.1.1_peaks_narrowPeak.interval" />
       <output name="output_xls_to_interval_peaks_file"
-	      file="test_MACS2.1.0_peaks.xls.re_match"
+	      file="test_MACS2.1.1_peaks.xls.re_match"
 	      compare="re_match" lines_diff="1" />
-      <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" />
-      <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" />
-      <output name="output_bigwig_file" file="test_MACS2.1.0_treat_pileup.bw"
+      <output name="output_treat_pileup_file" file="test_MACS2.1.1_treat_pileup.bdg" />
+      <output name="output_lambda_bedgraph_file" file="test_MACS2.1.1_control_lambda.bdg" />
+      <output name="output_bigwig_file" file="test_MACS2.1.1_treat_pileup.bw"
 	      compare="sim_size" />
     </test>
   </tests>
   <help>
 **What it does**
 
-MACS (Model-based Analysis of ChIP-seq) 2.1.0 provides algorithms for identifying
+MACS (Model-based Analysis of ChIP-seq) 2.1.1 provides algorithms for identifying
 transcript factor binding sites. The program can be used either for ChIP-Seq data alone,
 or with control sample data to improve specificity.
 
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_bw_html_report.zip
Binary file test-data/test_MACS2.1.0_bw_html_report.zip has changed
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_control_lambda.bdg
--- a/test-data/test_MACS2.1.0_control_lambda.bdg	Wed Mar 22 11:36:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,153 +0,0 @@
-chr26	0	4102915	0.31355
-chr26	4102915	4103978	486.00000
-chr26	4103978	4103998	972.00000
-chr26	4103998	4104449	1458.00000
-chr26	4104449	4105233	1944.00000
-chr26	4105233	4105326	2430.00000
-chr26	4105326	4105398	2916.00000
-chr26	4105398	4105644	3402.00024
-chr26	4105644	4105855	3888.00000
-chr26	4105855	4105980	4374.00000
-chr26	4105980	4106825	4860.00000
-chr26	4106825	4107471	5346.00049
-chr26	4107471	4107794	5832.00000
-chr26	4107794	4108037	20000.00000
-chr26	4108037	4108498	6804.00049
-chr26	4108498	4108857	9720.00000
-chr26	4108857	4108877	20000.00000
-chr26	4108877	4109100	40000.00000
-chr26	4109100	4109120	20000.00000
-chr26	4109120	4109327	14580.00000
-chr26	4109327	4109570	20000.00000
-chr26	4109570	4109733	8262.00000
-chr26	4109733	4109826	9720.00000
-chr26	4109826	4109898	14580.00000
-chr26	4109898	4109949	19440.00000
-chr26	4109949	4110111	14580.00000
-chr26	4110111	4110204	20000.00000
-chr26	4110204	4110276	40000.00000
-chr26	4110276	4110354	60000.00000
-chr26	4110354	4110447	40000.00000
-chr26	4110447	4110480	24300.00195
-chr26	4110480	4110733	29160.00000
-chr26	4110733	4110765	40000.00000
-chr26	4110765	4110826	24300.00195
-chr26	4110826	4110859	20000.00000
-chr26	4110859	4110976	40000.00000
-chr26	4110976	4111102	20000.00000
-chr26	4111102	4111144	14580.00000
-chr26	4111144	4111325	12150.00098
-chr26	4111325	4111355	14580.00000
-chr26	4111355	4111704	12636.00000
-chr26	4111704	4111947	20000.00000
-chr26	4111947	4112349	13608.00098
-chr26	4112349	4112592	20000.00000
-chr26	4112592	4112706	14580.00000
-chr26	4112706	4112862	20000.00000
-chr26	4112862	4112949	40000.00000
-chr26	4112949	4113105	20000.00000
-chr26	4113105	4113145	13608.00098
-chr26	4113145	4113327	14580.00000
-chr26	4113327	4113524	13608.00098
-chr26	4113524	4113767	20000.00000
-chr26	4113767	4113775	13608.00098
-chr26	4113775	4114145	14580.00000
-chr26	4114145	4114146	12636.00000
-chr26	4114146	4114154	20000.00000
-chr26	4114154	4114389	40000.00000
-chr26	4114389	4114686	24300.00195
-chr26	4114686	4114732	40000.00000
-chr26	4114732	4114855	60000.00000
-chr26	4114855	4114929	40000.00000
-chr26	4114929	4114975	20000.00000
-chr26	4114975	4115116	14580.00000
-chr26	4115116	4115234	19440.00000
-chr26	4115234	4115308	14580.00000
-chr26	4115308	4115326	12150.00098
-chr26	4115326	4115398	11664.00000
-chr26	4115398	4115495	11178.00000
-chr26	4115495	4115635	20000.00000
-chr26	4115635	4115837	24300.00195
-chr26	4115837	4115891	29160.00000
-chr26	4115891	4115990	40000.00000
-chr26	4115990	4116014	60000.00000
-chr26	4116014	4116072	80000.00000
-chr26	4116072	4116134	60000.00000
-chr26	4116134	4116215	40000.00000
-chr26	4116215	4116233	60000.00000
-chr26	4116233	4116257	40000.00000
-chr26	4116257	4116366	29160.00000
-chr26	4116366	4116450	34020.00000
-chr26	4116450	4116512	29160.00000
-chr26	4116512	4116611	24300.00195
-chr26	4116611	4116745	20000.00000
-chr26	4116745	4116831	40000.00000
-chr26	4116831	4116988	20000.00000
-chr26	4116988	4117136	11664.00000
-chr26	4117136	4117471	12150.00098
-chr26	4117471	4117730	11664.00000
-chr26	4117730	4117973	20000.00000
-chr26	4117973	4117983	11178.00000
-chr26	4117983	4118141	10692.00098
-chr26	4118141	4118645	11178.00000
-chr26	4118645	4118886	10692.00098
-chr26	4118886	4118904	11178.00000
-chr26	4118904	4119267	11664.00000
-chr26	4119267	4119275	11178.00000
-chr26	4119275	4119282	10692.00098
-chr26	4119282	4119525	20000.00000
-chr26	4119525	4119734	11178.00000
-chr26	4119734	4119808	10692.00098
-chr26	4119808	4119854	10206.00000
-chr26	4119854	4120286	9720.00000
-chr26	4120286	4120399	10206.00000
-chr26	4120399	4120642	20000.00000
-chr26	4120642	4120714	9720.00000
-chr26	4120714	4120957	20000.00000
-chr26	4120957	4120959	14580.00000
-chr26	4120959	4121021	19440.00000
-chr26	4121021	4121066	14580.00000
-chr26	4121066	4121216	19440.00000
-chr26	4121216	4121338	20000.00000
-chr26	4121338	4121445	40000.00000
-chr26	4121445	4121459	60000.00000
-chr26	4121459	4121581	40000.00000
-chr26	4121581	4121688	20000.00000
-chr26	4121688	4121837	19440.00000
-chr26	4121837	4121959	14580.00000
-chr26	4121959	4122015	9720.00000
-chr26	4122015	4122258	20000.00000
-chr26	4122258	4122851	8262.00000
-chr26	4122851	4123020	7776.00000
-chr26	4123020	4123263	20000.00000
-chr26	4123263	4123386	7776.00000
-chr26	4123386	4123404	9720.00000
-chr26	4123404	4123641	14580.00000
-chr26	4123641	4123764	9720.00000
-chr26	4123764	4123783	20000.00000
-chr26	4123783	4124007	40000.00000
-chr26	4124007	4124026	20000.00000
-chr26	4124026	4124386	14580.00000
-chr26	4124386	4124396	9720.00000
-chr26	4124396	4124639	20000.00000
-chr26	4124639	4124786	9234.00000
-chr26	4124786	4125017	9720.00000
-chr26	4125017	4125164	9234.00000
-chr26	4125164	4125407	20000.00000
-chr26	4125407	4125836	9234.00000
-chr26	4125836	4126337	8748.00000
-chr26	4126337	4126363	8262.00000
-chr26	4126363	4126459	9720.00000
-chr26	4126459	4126509	14580.00000
-chr26	4126509	4126699	19440.00000
-chr26	4126699	4126742	20000.00000
-chr26	4126742	4126837	40000.00000
-chr26	4126837	4126887	60000.00000
-chr26	4126887	4126942	80000.00000
-chr26	4126942	4126985	60000.00000
-chr26	4126985	4127080	40000.00000
-chr26	4127080	4127130	20000.00000
-chr26	4127130	4127320	19440.00000
-chr26	4127320	4127363	14580.00000
-chr26	4127363	4127459	9720.00000
-chr26	4127459	4127761	6804.00049
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_html_report.zip
Binary file test-data/test_MACS2.1.0_html_report.zip has changed
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_peaks.xls
--- a/test-data/test_MACS2.1.0_peaks.xls	Wed Mar 22 11:36:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#peaks file
-# This file is generated by MACS version 2.1.0.20140616
-# Command line: callpeak -t /home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_46.dat -c /home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_45.dat --format=BED --name=test_MACS2.1.0 --bw=300 --gsize=775000000.0 --nomodel --extsize=243 --qvalue=0.05 -B --SPMR --mfold 5 50 --keep-dup 1
-# ARGUMENTS LIST:
-# name = test_MACS2.1.0
-# format = BED
-# ChIP-seq file = ['/home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_46.dat']
-# control file = ['/home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_45.dat']
-# effective genome size = 7.75e+08
-# 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
-# MACS will save fragment pileup signal per million reads
-
-# tag size is determined as 50 bps
-# total tags in treatment: 50
-# tags after filtering in treatment: 50
-# maximum duplicate tags at the same position in treatment = 1
-# Redundant rate in treatment: 0.00
-# total tags in control: 50
-# tags after filtering in control: 50
-# maximum duplicate tags at the same position in control = 1
-# Redundant rate in control: 0.00
-# d = 243
-#chr	start	end	length	abs_summit	pileup	-log10(pvalue)	fold_enrichment	-log10(qvalue)	name
-chr26	4118914	4119282	369	4119130	9.00	9.13132	6.31632	2.51561	test_MACS2.1.0_peak_1
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_peaks.xls.re_match
--- a/test-data/test_MACS2.1.0_peaks.xls.re_match	Wed Mar 22 11:36:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-\#peaks\ file
-\#\ This\ file\ is\ generated\ by\ MACS\ version\ 2\.1\.0\.20140616
-\#\ Command\ line\:\ callpeak\ \-t\ .* \-c\ .* \-\-format\=BED\ \-\-name\=test\_MACS2\.1\.0\ \-\-bw\=300\ \-\-gsize\=775000000\.0\ \-\-nomodel\ \-\-extsize\=243\ \-\-qvalue\=0\.05\ \-B\ \-\-SPMR\ \-\-mfold\ 5\ 50\ \-\-keep\-dup\ 1
-\#\ ARGUMENTS\ LIST\:
-\#\ name\ \=\ test\_MACS2\.1\.0
-\#\ format\ \=\ BED
-\#\ ChIP\-seq\ file\ \=\ \[\'.*\'\]
-\#\ control\ file\ \=\ \[\'.*\'\]
-\#\ effective\ genome\ size\ \=\ 7\.75e\+08
-\#\ 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
-\#\ MACS\ will\ save\ fragment\ pileup\ signal\ per\ million\ reads
-
-\#\ tag\ size\ is\ determined\ as\ 50\ bps
-\#\ total\ tags\ in\ treatment\:\ 50
-\#\ tags\ after\ filtering\ in\ treatment\:\ 50
-\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ treatment\ \=\ 1
-\#\ Redundant\ rate\ in\ treatment\:\ 0\.00
-\#\ total\ tags\ in\ control\:\ 50
-\#\ tags\ after\ filtering\ in\ control\:\ 50
-\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ control\ \=\ 1
-\#\ Redundant\ rate\ in\ control\:\ 0\.00
-\#\ d\ \=\ 243
-\#chr\	start\	end\	length\	abs\_summit\	pileup\	\-log10\(pvalue\)\	fold\_enrichment\	\-log10\(qvalue\)\	name
-chr26\	4118914\	4119282\	369\	4119130\	9\.00\	9\.13132\	6\.31632\	2\.51561\	test\_MACS2\.1\.0\_peak\_1
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_peaks_narrowPeak.interval
--- a/test-data/test_MACS2.1.0_peaks_narrowPeak.interval	Wed Mar 22 11:36:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-chr26	4118913	4119282	test_MACS2.1.0_peak_1	25	.	6.31632	9.13132	2.51561	216
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_summits.bed
--- a/test-data/test_MACS2.1.0_summits.bed	Wed Mar 22 11:36:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-chr26	4119129	4119130	test_MACS2.1.0_peak_1	2.51561
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_treat_pileup.bdg
--- a/test-data/test_MACS2.1.0_treat_pileup.bdg	Wed Mar 22 11:36:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-chr26	0	4107561	0.00000
-chr26	4107561	4107804	20000.00000
-chr26	4107804	4108165	0.00000
-chr26	4108165	4108408	20000.00000
-chr26	4108408	4108531	0.00000
-chr26	4108531	4108774	20000.00000
-chr26	4108774	4109009	0.00000
-chr26	4109009	4109252	20000.00000
-chr26	4109252	4109506	0.00000
-chr26	4109506	4109749	20000.00000
-chr26	4109749	4109782	0.00000
-chr26	4109782	4110025	20000.00000
-chr26	4110025	4110080	0.00000
-chr26	4110080	4110323	20000.00000
-chr26	4110323	4111276	0.00000
-chr26	4111276	4111519	20000.00000
-chr26	4111519	4112110	0.00000
-chr26	4112110	4112353	20000.00000
-chr26	4112353	4112762	0.00000
-chr26	4112762	4113005	20000.00000
-chr26	4113005	4113579	0.00000
-chr26	4113579	4113822	20000.00000
-chr26	4113822	4113899	0.00000
-chr26	4113899	4114142	20000.00000
-chr26	4114142	4115021	0.00000
-chr26	4115021	4115264	20000.00000
-chr26	4115264	4115555	0.00000
-chr26	4115555	4115792	20000.00000
-chr26	4115792	4115798	40000.00000
-chr26	4115798	4116035	20000.00000
-chr26	4116035	4116615	0.00000
-chr26	4116615	4116858	20000.00000
-chr26	4116858	4116931	0.00000
-chr26	4116931	4116988	20000.00000
-chr26	4116988	4117174	40000.00000
-chr26	4117174	4117231	20000.00000
-chr26	4117231	4117308	0.00000
-chr26	4117308	4117551	20000.00000
-chr26	4117551	4117615	0.00000
-chr26	4117615	4117642	20000.00000
-chr26	4117642	4117737	40000.00000
-chr26	4117737	4117858	60000.00000
-chr26	4117858	4117885	40000.00000
-chr26	4117885	4117905	20000.00000
-chr26	4117905	4117980	40000.00000
-chr26	4117980	4118037	20000.00000
-chr26	4118037	4118122	40000.00000
-chr26	4118122	4118148	60000.00000
-chr26	4118148	4118280	40000.00000
-chr26	4118280	4118365	20000.00000
-chr26	4118365	4118516	0.00000
-chr26	4118516	4118531	20000.00000
-chr26	4118531	4118561	40000.00000
-chr26	4118561	4118753	60000.00000
-chr26	4118753	4118759	80000.00000
-chr26	4118759	4118774	60000.00000
-chr26	4118774	4118804	40000.00000
-chr26	4118804	4118812	20000.00000
-chr26	4118812	4118827	40000.00000
-chr26	4118827	4118852	60000.00000
-chr26	4118852	4118898	80000.00000
-chr26	4118898	4118913	100000.00000
-chr26	4118913	4118963	120000.00000
-chr26	4118963	4118967	140000.00000
-chr26	4118967	4118996	160000.00000
-chr26	4118996	4119022	140000.00000
-chr26	4119022	4119047	160000.00000
-chr26	4119047	4119055	180000.00000
-chr26	4119055	4119070	160000.00000
-chr26	4119070	4119077	140000.00000
-chr26	4119077	4119095	160000.00000
-chr26	4119095	4119103	140000.00000
-chr26	4119103	4119118	160000.00000
-chr26	4119118	4119141	180000.00000
-chr26	4119141	4119156	160000.00000
-chr26	4119156	4119163	140000.00000
-chr26	4119163	4119168	160000.00000
-chr26	4119168	4119206	180000.00000
-chr26	4119206	4119210	160000.00000
-chr26	4119210	4119265	140000.00000
-chr26	4119265	4119290	120000.00000
-chr26	4119290	4119320	100000.00000
-chr26	4119320	4119346	80000.00000
-chr26	4119346	4119361	60000.00000
-chr26	4119361	4119406	40000.00000
-chr26	4119406	4119411	20000.00000
-chr26	4119411	4122292	0.00000
-chr26	4122292	4122535	20000.00000
-chr26	4122535	4124351	0.00000
-chr26	4124351	4124452	20000.00000
-chr26	4124452	4124594	40000.00000
-chr26	4124594	4124695	20000.00000
-chr26	4124695	4125766	0.00000
-chr26	4125766	4125809	20000.00000
-chr26	4125809	4126009	40000.00000
-chr26	4126009	4126052	20000.00000
-chr26	4126052	4126452	0.00000
-chr26	4126452	4126695	20000.00000
-chr26	4126695	4127518	0.00000
-chr26	4127518	4127761	20000.00000
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_treat_pileup.bw
Binary file test-data/test_MACS2.1.0_treat_pileup.bw has changed
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_bw_html_report.zip
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_bw_html_report.zip	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,55 @@
+<html><head><title>Additional output created by MACS (test_MACS2.1.1)</title></head><body><h3>Additional Files:</h3><p><ul>
+<li><a href="test_MACS2.1.1_peaks.xls">test_MACS2.1.1_peaks.xls</a></li>
+<li><a href="test_MACS2.1.1_treat_pileup.bdg.clipped">test_MACS2.1.1_treat_pileup.bdg.clipped</a></li>
+<li><a href="test_MACS2.1.1_treat_pileup.bdg.clipped.sorted">test_MACS2.1.1_treat_pileup.bdg.clipped.sorted</a></li>
+</ul></p>
+<h3>Messages from MACS:</h3>
+<p><pre>INFO  @ Tue, 20 Mar 2018 14:21:47: 
+# Command line: callpeak -t /tmp/tmpHxmla3/files/000/dataset_9.dat -c /tmp/tmpHxmla3/files/000/dataset_10.dat --format=BED --name=test_MACS2.1.1 --bw=300 --gsize=775000000.0 --nomodel --extsize=243 --qvalue=0.05 -B --SPMR --mfold 5 50 --keep-dup 1
+# ARGUMENTS LIST:
+# name = test_MACS2.1.1
+# format = BED
+# ChIP-seq file = ['/tmp/tmpHxmla3/files/000/dataset_9.dat']
+# control file = ['/tmp/tmpHxmla3/files/000/dataset_10.dat']
+# effective genome size = 7.75e+08
+# 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
+# MACS will save fragment pileup signal per million reads
+ 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 read tag files... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 read treatment tags... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1.2 read input tags... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 tag size is determined as 50 bps 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 tag size = 50 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1  total tags in treatment: 50 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 user defined the maximum tags... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1  tags after filtering in treatment: 50 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1  Redundant rate of treatment: 0.00 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1  total tags in control: 50 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 user defined the maximum tags... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1  tags after filtering in control: 50 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1  Redundant rate of control: 0.00 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #1 finished! 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #2 Build Peak Model... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #2 Skipped... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #2 Use 243 as fragment length 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #3 Call peaks... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #3 Pre-compute pvalue-qvalue table... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #3 In the peak calling step, the following will be performed simultaneously: 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... test_MACS2.1.1_treat_pileup.bdg 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #3   Write bedGraph files for control lambda (after scaling if necessary)... test_MACS2.1.1_control_lambda.bdg 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #3 Call peaks for each chromosome... 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #4 Write output xls file... test_MACS2.1.1_peaks.xls 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #4 Write peak in narrowPeak format file... test_MACS2.1.1_peaks.narrowPeak 
+INFO  @ Tue, 20 Mar 2018 14:21:47: #4 Write summits bed file... test_MACS2.1.1_summits.bed 
+INFO  @ Tue, 20 Mar 2018 14:21:47: Done! 
+</pre></p>
+</body></html>
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_control_lambda.bdg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_control_lambda.bdg	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,153 @@
+chr26	0	4102915	0.31355
+chr26	4102915	4103978	486.00000
+chr26	4103978	4103998	972.00000
+chr26	4103998	4104449	1458.00000
+chr26	4104449	4105233	1944.00000
+chr26	4105233	4105326	2430.00000
+chr26	4105326	4105398	2916.00000
+chr26	4105398	4105644	3402.00000
+chr26	4105644	4105855	3888.00000
+chr26	4105855	4105980	4374.00000
+chr26	4105980	4106825	4860.00000
+chr26	4106825	4107471	5346.00000
+chr26	4107471	4107794	5832.00000
+chr26	4107794	4108037	20000.00000
+chr26	4108037	4108498	6804.00000
+chr26	4108498	4108857	9720.00000
+chr26	4108857	4108877	20000.00000
+chr26	4108877	4109100	40000.00000
+chr26	4109100	4109120	20000.00000
+chr26	4109120	4109327	14579.99902
+chr26	4109327	4109570	20000.00000
+chr26	4109570	4109733	8262.00000
+chr26	4109733	4109826	9720.00000
+chr26	4109826	4109898	14579.99902
+chr26	4109898	4109949	19440.00000
+chr26	4109949	4110111	14579.99902
+chr26	4110111	4110204	20000.00000
+chr26	4110204	4110276	40000.00000
+chr26	4110276	4110354	60000.00000
+chr26	4110354	4110447	40000.00000
+chr26	4110447	4110480	24300.00000
+chr26	4110480	4110733	29159.99805
+chr26	4110733	4110765	40000.00000
+chr26	4110765	4110826	24300.00000
+chr26	4110826	4110859	20000.00000
+chr26	4110859	4110976	40000.00000
+chr26	4110976	4111102	20000.00000
+chr26	4111102	4111144	14579.99902
+chr26	4111144	4111325	12150.00000
+chr26	4111325	4111355	14579.99902
+chr26	4111355	4111704	12636.00000
+chr26	4111704	4111947	20000.00000
+chr26	4111947	4112349	13608.00000
+chr26	4112349	4112592	20000.00000
+chr26	4112592	4112706	14579.99902
+chr26	4112706	4112862	20000.00000
+chr26	4112862	4112949	40000.00000
+chr26	4112949	4113105	20000.00000
+chr26	4113105	4113145	13608.00000
+chr26	4113145	4113327	14579.99902
+chr26	4113327	4113524	13608.00000
+chr26	4113524	4113767	20000.00000
+chr26	4113767	4113775	13608.00000
+chr26	4113775	4114145	14579.99902
+chr26	4114145	4114146	12636.00000
+chr26	4114146	4114154	20000.00000
+chr26	4114154	4114389	40000.00000
+chr26	4114389	4114686	24300.00000
+chr26	4114686	4114732	40000.00000
+chr26	4114732	4114855	60000.00000
+chr26	4114855	4114929	40000.00000
+chr26	4114929	4114975	20000.00000
+chr26	4114975	4115116	14579.99902
+chr26	4115116	4115234	19440.00000
+chr26	4115234	4115308	14579.99902
+chr26	4115308	4115326	12150.00000
+chr26	4115326	4115398	11664.00000
+chr26	4115398	4115495	11178.00000
+chr26	4115495	4115635	20000.00000
+chr26	4115635	4115837	24300.00000
+chr26	4115837	4115891	29159.99805
+chr26	4115891	4115990	40000.00000
+chr26	4115990	4116014	60000.00000
+chr26	4116014	4116072	80000.00000
+chr26	4116072	4116134	60000.00000
+chr26	4116134	4116215	40000.00000
+chr26	4116215	4116233	60000.00000
+chr26	4116233	4116257	40000.00000
+chr26	4116257	4116366	29159.99805
+chr26	4116366	4116450	34020.00000
+chr26	4116450	4116512	29159.99805
+chr26	4116512	4116611	24300.00000
+chr26	4116611	4116745	20000.00000
+chr26	4116745	4116831	40000.00000
+chr26	4116831	4116988	20000.00000
+chr26	4116988	4117136	11664.00000
+chr26	4117136	4117471	12150.00000
+chr26	4117471	4117730	11664.00000
+chr26	4117730	4117973	20000.00000
+chr26	4117973	4117983	11178.00000
+chr26	4117983	4118141	10692.00000
+chr26	4118141	4118645	11178.00000
+chr26	4118645	4118886	10692.00000
+chr26	4118886	4118904	11178.00000
+chr26	4118904	4119267	11664.00000
+chr26	4119267	4119275	11178.00000
+chr26	4119275	4119282	10692.00000
+chr26	4119282	4119525	20000.00000
+chr26	4119525	4119734	11178.00000
+chr26	4119734	4119808	10692.00000
+chr26	4119808	4119854	10206.00000
+chr26	4119854	4120286	9720.00000
+chr26	4120286	4120399	10206.00000
+chr26	4120399	4120642	20000.00000
+chr26	4120642	4120714	9720.00000
+chr26	4120714	4120957	20000.00000
+chr26	4120957	4120959	14579.99902
+chr26	4120959	4121021	19440.00000
+chr26	4121021	4121066	14579.99902
+chr26	4121066	4121216	19440.00000
+chr26	4121216	4121338	20000.00000
+chr26	4121338	4121445	40000.00000
+chr26	4121445	4121459	60000.00000
+chr26	4121459	4121581	40000.00000
+chr26	4121581	4121688	20000.00000
+chr26	4121688	4121837	19440.00000
+chr26	4121837	4121959	14579.99902
+chr26	4121959	4122015	9720.00000
+chr26	4122015	4122258	20000.00000
+chr26	4122258	4122851	8262.00000
+chr26	4122851	4123020	7776.00000
+chr26	4123020	4123263	20000.00000
+chr26	4123263	4123386	7776.00000
+chr26	4123386	4123404	9720.00000
+chr26	4123404	4123641	14579.99902
+chr26	4123641	4123764	9720.00000
+chr26	4123764	4123783	20000.00000
+chr26	4123783	4124007	40000.00000
+chr26	4124007	4124026	20000.00000
+chr26	4124026	4124386	14579.99902
+chr26	4124386	4124396	9720.00000
+chr26	4124396	4124639	20000.00000
+chr26	4124639	4124786	9234.00000
+chr26	4124786	4125017	9720.00000
+chr26	4125017	4125164	9234.00000
+chr26	4125164	4125407	20000.00000
+chr26	4125407	4125836	9234.00000
+chr26	4125836	4126337	8748.00000
+chr26	4126337	4126363	8262.00000
+chr26	4126363	4126459	9720.00000
+chr26	4126459	4126509	14579.99902
+chr26	4126509	4126699	19440.00000
+chr26	4126699	4126742	20000.00000
+chr26	4126742	4126837	40000.00000
+chr26	4126837	4126887	60000.00000
+chr26	4126887	4126942	80000.00000
+chr26	4126942	4126985	60000.00000
+chr26	4126985	4127080	40000.00000
+chr26	4127080	4127130	20000.00000
+chr26	4127130	4127320	19440.00000
+chr26	4127320	4127363	14579.99902
+chr26	4127363	4127459	9720.00000
+chr26	4127459	4127761	6804.00000
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_html_report.zip
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_html_report.zip	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,53 @@
+<html><head><title>Additional output created by MACS (test_MACS2.1.1)</title></head><body><h3>Additional Files:</h3><p><ul>
+<li><a href="test_MACS2.1.1_peaks.xls">test_MACS2.1.1_peaks.xls</a></li>
+</ul></p>
+<h3>Messages from MACS:</h3>
+<p><pre>INFO  @ Tue, 20 Mar 2018 14:21:02: 
+# Command line: callpeak -t /tmp/tmpHxmla3/files/000/dataset_1.dat -c /tmp/tmpHxmla3/files/000/dataset_2.dat --format=BED --name=test_MACS2.1.1 --bw=300 --gsize=775000000.0 --nomodel --extsize=243 --qvalue=0.05 -B --SPMR --mfold 5 50 --keep-dup 1
+# ARGUMENTS LIST:
+# name = test_MACS2.1.1
+# format = BED
+# ChIP-seq file = ['/tmp/tmpHxmla3/files/000/dataset_1.dat']
+# control file = ['/tmp/tmpHxmla3/files/000/dataset_2.dat']
+# effective genome size = 7.75e+08
+# 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
+# MACS will save fragment pileup signal per million reads
+ 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 read tag files... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 read treatment tags... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1.2 read input tags... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 tag size is determined as 50 bps 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 tag size = 50 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1  total tags in treatment: 50 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 user defined the maximum tags... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1  tags after filtering in treatment: 50 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1  Redundant rate of treatment: 0.00 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1  total tags in control: 50 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 user defined the maximum tags... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1  tags after filtering in control: 50 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1  Redundant rate of control: 0.00 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #1 finished! 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #2 Build Peak Model... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #2 Skipped... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #2 Use 243 as fragment length 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #3 Call peaks... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #3 Pre-compute pvalue-qvalue table... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #3 In the peak calling step, the following will be performed simultaneously: 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... test_MACS2.1.1_treat_pileup.bdg 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #3   Write bedGraph files for control lambda (after scaling if necessary)... test_MACS2.1.1_control_lambda.bdg 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #3 Call peaks for each chromosome... 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #4 Write output xls file... test_MACS2.1.1_peaks.xls 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #4 Write peak in narrowPeak format file... test_MACS2.1.1_peaks.narrowPeak 
+INFO  @ Tue, 20 Mar 2018 14:21:02: #4 Write summits bed file... test_MACS2.1.1_summits.bed 
+INFO  @ Tue, 20 Mar 2018 14:21:02: Done! 
+</pre></p>
+</body></html>
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_peaks.xls
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_peaks.xls	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,30 @@
+#peaks file
+# This file is generated by MACS version 2.1.1.20160309
+# Command line: callpeak -t /tmp/tmpHxmla3/files/000/dataset_9.dat -c /tmp/tmpHxmla3/files/000/dataset_10.dat --format=BED --name=test_MACS2.1.1 --bw=300 --gsize=775000000.0 --nomodel --extsize=243 --qvalue=0.05 -B --SPMR --mfold 5 50 --keep-dup 1
+# ARGUMENTS LIST:
+# name = test_MACS2.1.1
+# format = BED
+# ChIP-seq file = ['/tmp/tmpHxmla3/files/000/dataset_9.dat']
+# control file = ['/tmp/tmpHxmla3/files/000/dataset_10.dat']
+# effective genome size = 7.75e+08
+# 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
+# MACS will save fragment pileup signal per million reads
+
+# tag size is determined as 50 bps
+# total tags in treatment: 50
+# tags after filtering in treatment: 50
+# maximum duplicate tags at the same position in treatment = 1
+# Redundant rate in treatment: 0.00
+# total tags in control: 50
+# tags after filtering in control: 50
+# maximum duplicate tags at the same position in control = 1
+# Redundant rate in control: 0.00
+# d = 243
+#chr	start	end	length	abs_summit	pileup	-log10(pvalue)	fold_enrichment	-log10(qvalue)	name
+chr26	4118914	4119282	369	4119130	9.00	9.13132	6.31632	2.51561	test_MACS2.1.1_peak_1
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_peaks.xls.re_match
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_peaks.xls.re_match	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,30 @@
+\#peaks\ file
+\#\ This\ file\ is\ generated\ by\ MACS\ version\ 2\.1\.1\.20160309
+\#\ Command\ line\:\ callpeak\ \-t\ \/tmp\/tmpHxmla3\/files\/000\/dataset\_9\.dat\ \-c\ \/tmp\/tmpHxmla3\/files\/000\/dataset\_10\.dat\ \-\-format\=BED\ \-\-name\=test\_MACS2\.1\.1\ \-\-bw\=300\ \-\-gsize\=775000000\.0\ \-\-nomodel\ \-\-extsize\=243\ \-\-qvalue\=0\.05\ \-B\ \-\-SPMR\ \-\-mfold\ 5\ 50\ \-\-keep\-dup\ 1
+\#\ ARGUMENTS\ LIST\:
+\#\ name\ \=\ test\_MACS2\.1\.1
+\#\ format\ \=\ BED
+\#\ ChIP\-seq\ file\ \=\ \[\'.*\'\]
+\#\ control\ file\ \=\ \[\'.*\'\]
+\#\ effective\ genome\ size\ \=\ 7\.75e\+08
+\#\ 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
+\#\ MACS\ will\ save\ fragment\ pileup\ signal\ per\ million\ reads
+
+\#\ tag\ size\ is\ determined\ as\ 50\ bps
+\#\ total\ tags\ in\ treatment\:\ 50
+\#\ tags\ after\ filtering\ in\ treatment\:\ 50
+\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ treatment\ \=\ 1
+\#\ Redundant\ rate\ in\ treatment\:\ 0\.00
+\#\ total\ tags\ in\ control\:\ 50
+\#\ tags\ after\ filtering\ in\ control\:\ 50
+\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ control\ \=\ 1
+\#\ Redundant\ rate\ in\ control\:\ 0\.00
+\#\ d\ \=\ 243
+\#chr\	start\	end\	length\	abs\_summit\	pileup\	\-log10\(pvalue\)\	fold\_enrichment\	\-log10\(qvalue\)\	name
+chr26\	4118914\	4119282\	369\	4119130\	9\.00\	9\.13132\	6\.31632\	2\.51561\	test\_MACS2\.1\.1\_peak\_1
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_peaks.xls.re_match~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_peaks.xls.re_match~	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,30 @@
+\#peaks\ file
+\#\ This\ file\ is\ generated\ by\ MACS\ version\ 2\.1\.1\.20160309
+\#\ Command\ line\:\ callpeak\ \-t\ \/tmp\/tmpHxmla3\/files\/000\/dataset\_9\.dat\ \-c\ \/tmp\/tmpHxmla3\/files\/000\/dataset\_10\.dat\ \-\-format\=BED\ \-\-name\=test\_MACS2\.1\.1\ \-\-bw\=300\ \-\-gsize\=775000000\.0\ \-\-nomodel\ \-\-extsize\=243\ \-\-qvalue\=0\.05\ \-B\ \-\-SPMR\ \-\-mfold\ 5\ 50\ \-\-keep\-dup\ 1
+\#\ ARGUMENTS\ LIST\:
+\#\ name\ \=\ test\_MACS2\.1\.1
+\#\ format\ \=\ BED
+\#\ ChIP\-seq\ file\ \=\ \[\'\/tmp\/tmpHxmla3\/files\/000\/dataset\_9\.dat\'\]
+\#\ control\ file\ \=\ \[\'\/tmp\/tmpHxmla3\/files\/000\/dataset\_10\.dat\'\]
+\#\ effective\ genome\ size\ \=\ 7\.75e\+08
+\#\ 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
+\#\ MACS\ will\ save\ fragment\ pileup\ signal\ per\ million\ reads
+
+\#\ tag\ size\ is\ determined\ as\ 50\ bps
+\#\ total\ tags\ in\ treatment\:\ 50
+\#\ tags\ after\ filtering\ in\ treatment\:\ 50
+\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ treatment\ \=\ 1
+\#\ Redundant\ rate\ in\ treatment\:\ 0\.00
+\#\ total\ tags\ in\ control\:\ 50
+\#\ tags\ after\ filtering\ in\ control\:\ 50
+\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ control\ \=\ 1
+\#\ Redundant\ rate\ in\ control\:\ 0\.00
+\#\ d\ \=\ 243
+\#chr\	start\	end\	length\	abs\_summit\	pileup\	\-log10\(pvalue\)\	fold\_enrichment\	\-log10\(qvalue\)\	name
+chr26\	4118914\	4119282\	369\	4119130\	9\.00\	9\.13132\	6\.31632\	2\.51561\	test\_MACS2\.1\.1\_peak\_1
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_peaks_narrowPeak.interval
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_peaks_narrowPeak.interval	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,1 @@
+chr26	4118913	4119282	test_MACS2.1.1_peak_1	25	.	6.31632	9.13132	2.51561	216
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_summits.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_summits.bed	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,1 @@
+chr26	4119129	4119130	test_MACS2.1.1_peak_1	2.51561
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_treat_pileup.bdg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_MACS2.1.1_treat_pileup.bdg	Tue Mar 20 11:25:04 2018 -0400
@@ -0,0 +1,100 @@
+chr26	0	4107561	0.00000
+chr26	4107561	4107804	20000.00000
+chr26	4107804	4108165	0.00000
+chr26	4108165	4108408	20000.00000
+chr26	4108408	4108531	0.00000
+chr26	4108531	4108774	20000.00000
+chr26	4108774	4109009	0.00000
+chr26	4109009	4109252	20000.00000
+chr26	4109252	4109506	0.00000
+chr26	4109506	4109749	20000.00000
+chr26	4109749	4109782	0.00000
+chr26	4109782	4110025	20000.00000
+chr26	4110025	4110080	0.00000
+chr26	4110080	4110323	20000.00000
+chr26	4110323	4111276	0.00000
+chr26	4111276	4111519	20000.00000
+chr26	4111519	4112110	0.00000
+chr26	4112110	4112353	20000.00000
+chr26	4112353	4112762	0.00000
+chr26	4112762	4113005	20000.00000
+chr26	4113005	4113579	0.00000
+chr26	4113579	4113822	20000.00000
+chr26	4113822	4113899	0.00000
+chr26	4113899	4114142	20000.00000
+chr26	4114142	4115021	0.00000
+chr26	4115021	4115264	20000.00000
+chr26	4115264	4115555	0.00000
+chr26	4115555	4115792	20000.00000
+chr26	4115792	4115798	40000.00000
+chr26	4115798	4116035	20000.00000
+chr26	4116035	4116615	0.00000
+chr26	4116615	4116858	20000.00000
+chr26	4116858	4116931	0.00000
+chr26	4116931	4116988	20000.00000
+chr26	4116988	4117174	40000.00000
+chr26	4117174	4117231	20000.00000
+chr26	4117231	4117308	0.00000
+chr26	4117308	4117551	20000.00000
+chr26	4117551	4117615	0.00000
+chr26	4117615	4117642	20000.00000
+chr26	4117642	4117737	40000.00000
+chr26	4117737	4117858	60000.00000
+chr26	4117858	4117885	40000.00000
+chr26	4117885	4117905	20000.00000
+chr26	4117905	4117980	40000.00000
+chr26	4117980	4118037	20000.00000
+chr26	4118037	4118122	40000.00000
+chr26	4118122	4118148	60000.00000
+chr26	4118148	4118280	40000.00000
+chr26	4118280	4118365	20000.00000
+chr26	4118365	4118516	0.00000
+chr26	4118516	4118531	20000.00000
+chr26	4118531	4118561	40000.00000
+chr26	4118561	4118753	60000.00000
+chr26	4118753	4118759	80000.00000
+chr26	4118759	4118774	60000.00000
+chr26	4118774	4118804	40000.00000
+chr26	4118804	4118812	20000.00000
+chr26	4118812	4118827	40000.00000
+chr26	4118827	4118852	60000.00000
+chr26	4118852	4118898	80000.00000
+chr26	4118898	4118913	100000.00000
+chr26	4118913	4118963	120000.00000
+chr26	4118963	4118967	140000.00000
+chr26	4118967	4118996	160000.00000
+chr26	4118996	4119022	140000.00000
+chr26	4119022	4119047	160000.00000
+chr26	4119047	4119055	180000.00000
+chr26	4119055	4119070	160000.00000
+chr26	4119070	4119077	140000.00000
+chr26	4119077	4119095	160000.00000
+chr26	4119095	4119103	140000.00000
+chr26	4119103	4119118	160000.00000
+chr26	4119118	4119141	180000.00000
+chr26	4119141	4119156	160000.00000
+chr26	4119156	4119163	140000.00000
+chr26	4119163	4119168	160000.00000
+chr26	4119168	4119206	180000.00000
+chr26	4119206	4119210	160000.00000
+chr26	4119210	4119265	140000.00000
+chr26	4119265	4119290	120000.00000
+chr26	4119290	4119320	100000.00000
+chr26	4119320	4119346	80000.00000
+chr26	4119346	4119361	60000.00000
+chr26	4119361	4119406	40000.00000
+chr26	4119406	4119411	20000.00000
+chr26	4119411	4122292	0.00000
+chr26	4122292	4122535	20000.00000
+chr26	4122535	4124351	0.00000
+chr26	4124351	4124452	20000.00000
+chr26	4124452	4124594	40000.00000
+chr26	4124594	4124695	20000.00000
+chr26	4124695	4125766	0.00000
+chr26	4125766	4125809	20000.00000
+chr26	4125809	4126009	40000.00000
+chr26	4126009	4126052	20000.00000
+chr26	4126052	4126452	0.00000
+chr26	4126452	4126695	20000.00000
+chr26	4126695	4127518	0.00000
+chr26	4127518	4127761	20000.00000
diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_treat_pileup.bw
Binary file test-data/test_MACS2.1.1_treat_pileup.bw has changed
diff -r 00d73c812399 -r 4124781932db tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 22 11:36:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <!-- Dependencies from main/test toolsheds -->
-  <package name="numpy" version="1.9">
-    <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="R" version="3.1.2">
-    <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <!-- Subset of UCSC tools -->
-  <package name="ucsc_tools_for_macs21" version="2.0">
-      <install version="1.0">
-            <actions>
-	      <!-- fetchChromSizes -->
-              <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
-              </action>
-              <action type="chmod">
-                <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
-              </action>
-	      <!-- bedClip -->
-              <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
-              </action>
-              <action type="chmod">
-                <file mode="755">$INSTALL_DIR/bedClip</file>
-              </action>
-	      <!-- bedSort -->
-              <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort</url_template>
-              </action>
-              <action type="chmod">
-                <file mode="755">$INSTALL_DIR/bedSort</file>
-              </action>
-	      <!-- bedGraphToBigWig -->
-              <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
-              </action>
-              <action type="chmod">
-                <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
-              </action>
-              <action type="set_environment">
-                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
-              </action>
-	    </actions>
-      </install>
-  </package>
-  <!-- MACS 2.1.0 -->
-  <package name="macs2" version="2.1.0.20140616">
-      <install version="1.0">
-            <actions>
-              <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
-	      <!-- Install environment for main & test toolsheds -->
-              <action type="set_environment_for_install">
-		<repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-		  <package name="numpy" version="1.9" />
-		</repository>
-	      </action>
-              <action type="make_directory">$INSTALL_DIR/lib/python</action>
-              <action type="shell_command">
-                export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
-                python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
-              </action>
-              <action type="set_environment">
-                <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-              </action>
-            </actions>
-      </install>
-      <readme>Macs2.1 depends on having python2.7 and numpy 1.8 installed on all nodes of the work cluster</readme>
-    </package>
-</tool_dependency>