| Previous changeset 2:00d73c812399 (2017-03-22) Next changeset 4:11cf21ee4242 (2018-12-12) |
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Commit message:
Updated to MACS 2.1.1 and use conda for dependency resolution. |
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modified:
README.rst macs21_wrapper.xml |
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added:
test-data/test_MACS2.1.1_bw_html_report.zip test-data/test_MACS2.1.1_control_lambda.bdg test-data/test_MACS2.1.1_html_report.zip test-data/test_MACS2.1.1_peaks.xls test-data/test_MACS2.1.1_peaks.xls.re_match test-data/test_MACS2.1.1_peaks.xls.re_match~ test-data/test_MACS2.1.1_peaks_narrowPeak.interval test-data/test_MACS2.1.1_summits.bed test-data/test_MACS2.1.1_treat_pileup.bdg test-data/test_MACS2.1.1_treat_pileup.bw |
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removed:
test-data/test_MACS2.1.0_bw_html_report.zip test-data/test_MACS2.1.0_control_lambda.bdg test-data/test_MACS2.1.0_html_report.zip test-data/test_MACS2.1.0_peaks.xls test-data/test_MACS2.1.0_peaks.xls.re_match test-data/test_MACS2.1.0_peaks_narrowPeak.interval test-data/test_MACS2.1.0_summits.bed test-data/test_MACS2.1.0_treat_pileup.bdg test-data/test_MACS2.1.0_treat_pileup.bw tool_dependencies.xml |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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. |
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| diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_bw_html_report.zip |
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| 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 |
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| @@ -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 |
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| diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_html_report.zip |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -1,1 +0,0 @@ -chr26 4118913 4119282 test_MACS2.1.0_peak_1 25 . 6.31632 9.13132 2.51561 216 |
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| 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 |
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| @@ -1,1 +0,0 @@ -chr26 4119129 4119130 test_MACS2.1.0_peak_1 2.51561 |
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| 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 |
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| @@ -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 |
| b |
| diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.0_treat_pileup.bw |
| b |
| Binary file test-data/test_MACS2.1.0_treat_pileup.bw has changed |
| b |
| 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> |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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> |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,1 @@ +chr26 4118913 4119282 test_MACS2.1.1_peak_1 25 . 6.31632 9.13132 2.51561 216 |
| b |
| 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 |
| b |
| @@ -0,0 +1,1 @@ +chr26 4119129 4119130 test_MACS2.1.1_peak_1 2.51561 |
| b |
| 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 |
| b |
| @@ -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 |
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| diff -r 00d73c812399 -r 4124781932db test-data/test_MACS2.1.1_treat_pileup.bw |
| b |
| Binary file test-data/test_MACS2.1.1_treat_pileup.bw has changed |
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| 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 |
| b |
| @@ -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 && - 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> |