| Previous changeset 4:11cf21ee4242 (2018-12-12) |
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Commit message:
New version 2.1.2-galaxy1 (updates UCSC dependencies) |
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modified:
README.rst macs21_wrapper.xml |
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removed:
test-data/test_MACS2.1.1_peaks.xls.re_match~ |
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| diff -r 11cf21ee4242 -r 3c435705aca5 README.rst --- a/README.rst Wed Dec 12 08:26:16 2018 -0500 +++ b/README.rst Tue Jun 27 07:54:55 2023 +0000 |
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| @@ -56,21 +56,22 @@ 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 ----------- ---------------------------------------------------------------------- -2.1.2.0 - Update to use MACS 2.1.2 -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 - for paired-end data) -2.1.0-4 - Remove 'bdgcmp' functionality. -2.1.0-3 - Add tool tests -2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with -B - option; make --mfold defaults consistent. -2.1.0-1 - Initial version -========== ====================================================================== +============= ================================================================= +Version Changes +------------- ----------------------------------------------------------------- +2.1.2-galaxy1 - Update UCSC tool dependencies to version 357 +2.1.2.0 - Update to use MACS 2.1.2 +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 for paired-end data) +2.1.0-4 - Remove 'bdgcmp' functionality. +2.1.0-3 - Add tool tests +2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with + ``-B`` option; make ``--mfold`` defaults consistent. +2.1.0-1 - Initial version +============= ================================================================= Developers |
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| diff -r 11cf21ee4242 -r 3c435705aca5 macs21_wrapper.xml --- a/macs21_wrapper.xml Wed Dec 12 08:26:16 2018 -0500 +++ b/macs21_wrapper.xml Tue Jun 27 07:54:55 2023 +0000 |
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| @@ -1,13 +1,13 @@ -<tool id="macs2_1_peakcalling" name="MACS2.1.2" version="2.1.2.0"> +<tool id="macs2_1_peakcalling" name="MACS2.1.2" version="2.1.2-galaxy1"> <description>Model-based Analysis of ChIP-Seq: peak calling</description> <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="2.1.2">macs2</requirement> <requirement type="package" version="3.5">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> + <requirement type="package" version="377">ucsc-fetchchromsizes</requirement> + <requirement type="package" version="377">ucsc-bedclip</requirement> + <requirement type="package" version="377">ucsc-bedsort</requirement> + <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement> </requirements> <version_command>macs2 --version</version_command> <command><![CDATA[ |
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| diff -r 11cf21ee4242 -r 3c435705aca5 test-data/test_MACS2.1.1_peaks.xls.re_match~ --- a/test-data/test_MACS2.1.1_peaks.xls.re_match~ Wed Dec 12 08:26:16 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,30 +0,0 @@ -\#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 |