# HG changeset patch # User iuc # Date 1516864312 18000 # Node ID acbd3fb47f90a778e53840538a061045da373713 # Parent e8a060164e11b0b802627ef6ca8a6e3d3cd2023c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2 diff -r e8a060164e11 -r acbd3fb47f90 macs2_bdgbroadcall.xml --- a/macs2_bdgbroadcall.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_bdgbroadcall.xml Thu Jan 25 02:11:52 2018 -0500 @@ -8,8 +8,8 @@ - - '${ outfile }' - ]]> - + ]]> - - - + ]]> diff -r e8a060164e11 -r acbd3fb47f90 macs2_bdgdiff.xml --- a/macs2_bdgdiff.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_bdgdiff.xml Thu Jan 25 02:11:52 2018 -0500 @@ -8,8 +8,8 @@ - - '${ output_cond1 }' && awk '!/^track name/' "c2.bed" > '${ output_cond1 }' && awk '!/^track name/' "both.bed" > '${ output_both }' - - ]]> - + ]]> diff -r e8a060164e11 -r acbd3fb47f90 macs2_bdgpeakcall.xml --- a/macs2_bdgpeakcall.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_bdgpeakcall.xml Thu Jan 25 02:11:52 2018 -0500 @@ -6,9 +6,8 @@ - - - + ]]> + Call peaks from alignment results macs2_macros.xml @@ -8,6 +8,8 @@ &1 > $temp_stderr) @@ -111,7 +115,7 @@ if [ \$count != 0 ]; then mkdir '${ output_extra_files.files_path }' && - cp MACS2* '${ output_extra_files.files_path }' && + cp -r MACS2* '${ output_extra_files.files_path }' && python '$__tool_directory__/dir2html.py' '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }'; fi; @@ -138,8 +142,8 @@ - - + + @@ -158,13 +162,31 @@ - + + + + + - - + + + + + + + + + + + + + + + + @@ -175,19 +197,7 @@ - - - - - - - - - - - - - + @@ -199,24 +209,19 @@ - - - - - - - + - - + + - - + help="(--ratio) Default: ignore"/> + + @@ -234,9 +239,7 @@ - - - + @@ -246,7 +249,6 @@ (( - advanced_options['advanced_options_selector'] == "on" and advanced_options['broad_options']['broad_options_selector'] == "broad" )) @@ -254,17 +256,13 @@ (( - advanced_options['advanced_options_selector'] == "on" and advanced_options['broad_options']['broad_options_selector'] == "broad" )) - ( - advanced_options['advanced_options_selector'] == "off" or - ( - advanced_options['advanced_options_selector'] == "on" and + (( advanced_options['broad_options']['broad_options_selector'] == "nobroad" )) @@ -295,6 +293,7 @@ + @@ -311,13 +310,13 @@ - + @@ -328,6 +327,16 @@ + + + + + + + + + + + + - - - - - + Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. Sizes are from the MACS2 website (--gsize)"> + + + + - - - - - + + + + diff -r e8a060164e11 -r acbd3fb47f90 macs2_predictd.xml --- a/macs2_predictd.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_predictd.xml Thu Jan 25 02:11:52 2018 -0500 @@ -6,8 +6,8 @@ - - - + ]]> - + diff -r e8a060164e11 -r acbd3fb47f90 macs2_randsample.xml --- a/macs2_randsample.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_randsample.xml Thu Jan 25 02:11:52 2018 -0500 @@ -6,8 +6,8 @@ - - - + ]]> diff -r e8a060164e11 -r acbd3fb47f90 macs2_refinepeak.xml --- a/macs2_refinepeak.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_refinepeak.xml Thu Jan 25 02:11:52 2018 -0500 @@ -6,8 +6,8 @@ - - - + ]]> diff -r e8a060164e11 -r acbd3fb47f90 test-data/bwa-mem-test1.bam Binary file test-data/bwa-mem-test1.bam has changed diff -r e8a060164e11 -r acbd3fb47f90 test-data/callpeak_bampe_narrow.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/callpeak_bampe_narrow.bed Thu Jan 25 02:11:52 2018 -0500 @@ -0,0 +1,1 @@ +gi|251831106|ref|NC_012920.1| 0 251 MACS2_peak_1 3056 . 44.99989 308.04297 305.64328 56