From a6a57ef7e5654afa8a1be2dfc5526875d13dea5d Mon Sep 17 00:00:00 2001 From: npinter Date: Sun, 25 Feb 2024 23:06:54 +0100 Subject: [PATCH 1/5] Initial commit --- tools/peakzilla/.shed.yml | 10 + tools/peakzilla/peakzilla.xml | 158 + tools/peakzilla/test-data/chip.bed | 9953 +++++++++++++++++++++++++ tools/peakzilla/test-data/input.bed | 9569 ++++++++++++++++++++++++ tools/peakzilla/test-data/results.tsv | 2 + 5 files changed, 19692 insertions(+) create mode 100644 tools/peakzilla/.shed.yml create mode 100644 tools/peakzilla/peakzilla.xml create mode 100644 tools/peakzilla/test-data/chip.bed create mode 100644 tools/peakzilla/test-data/input.bed create mode 100644 tools/peakzilla/test-data/results.tsv diff --git a/tools/peakzilla/.shed.yml b/tools/peakzilla/.shed.yml new file mode 100644 index 00000000000..f3af2836c54 --- /dev/null +++ b/tools/peakzilla/.shed.yml @@ -0,0 +1,10 @@ +name: peakzilla +owner: iuc +categories: + - ChIP-seq +description: Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. +long_description: | + Peakzilla is a tool for identifying sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at high accuracy and resolution. It is designed to work with data from any species and is suitable for both single and paired end data from any sequencing platform. +homepage_url: https://github.com/steinmann/peakzilla +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla +type: unrestricted diff --git a/tools/peakzilla/peakzilla.xml b/tools/peakzilla/peakzilla.xml new file mode 100644 index 00000000000..f18226e5d40 --- /dev/null +++ b/tools/peakzilla/peakzilla.xml @@ -0,0 +1,158 @@ + + Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments + + python + peakzilla + + + + + + + 1.0 + 1 + + + '$results' + ]]> + + + + +
+ + + + + + +
+
+ + +
+ + + + + log + + negative + + + + + + + + + + + + + Peak_1 + + + + + input.bam + samtools view -bS chip.sam > chip.bam + + # convert to BED format + bamToBed -i input.bam > input.bed + bamToBed -i chip.bam > chip.bed + + # run peakzilla + python peakzilla.py chip.bed input.bed > chip_peaks.tsv + + # Comparison of 2 datasets + # Determine significant peaks with a score threshold of 10 + python peakzilla.py -s 10 chip1.bed input1.bed > chip1_s10_peaks.tsv + # Determine enriched regions with a score threshold of 2 + python peakzilla.py -s 2 chip2.bed input2.bed > chip2_s2_peaks.tsv + # Overlap significant peaks from chip1 with enriched regions from chip2 + intersectBed -a chip1_s10_peaks.tsv -b chip2_s2_peaks.tsv > intersect_peaks.tsv + + For example datasets as well as an example of a computational pipeline for the comparative analysis of ChIP-seq datasets, please refer to our publication: Bardet AF et al. A computational pipeline for comparative ChIP-seq analyses. Nature Protocols (2011) 7(1):45-61 (http://www.starklab.org/data/bardet_natprotoc_2011/) + + OPTIONS + ------- + One of peakzilla's design goals is to learn all the necessary information + from the data. The usage of the options should therefore not be required. + + OUTPUT FORMAT + ------------- + * Results are printed as a table of tab delimited values to stdout + * Logs are appended to logs.txt in the current directory or a custom directory/filename specified by the -l option + * Enriched regions in the control sample are written to negative_peaks.tsv or a custom directory/filename specified by the -n option + * Columns represent Chromosome / Start / End / Name / Summit / Score / ChIP / Control / FoldEnrichment / DistributionScore / FDR (%) + ]]> + + + @article{bardet2012computational, + title={A computational pipeline for comparative ChIP-seq analyses}, + author={Bardet, Ana{\"\i}s F and He, Qiye and Zeitlinger, Julia and Stark, Alexander}, + journal={Nature protocols}, + volume={7}, + number={1}, + pages={45--61}, + year={2012}, + publisher={Nature Publishing Group UK London} + } + + + \ No newline at end of file diff --git a/tools/peakzilla/test-data/chip.bed b/tools/peakzilla/test-data/chip.bed new file mode 100644 index 00000000000..590f8a64065 --- /dev/null +++ b/tools/peakzilla/test-data/chip.bed @@ -0,0 +1,9953 @@ +2R 19906658 19906694 V00-HWI-EAS132:1:1:1570:58#0/1 255 + +2R 3777007 3777043 V00-HWI-EAS132:1:1:1570:1202#0/1 255 - 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- 1.0 - 1 - - + log + negative - + + + Peak_1 + + + Peakzilla + + + + + Peak_1 + + Date: Mon, 26 Feb 2024 10:46:50 +0100 Subject: [PATCH 3/5] Fix linting errors and test --- tools/peakzilla/peakzilla.xml | 40 ++++++++++++-------- tools/peakzilla/test-data/log.txt | 15 ++++++++ tools/peakzilla/test-data/negative_peaks.tsv | 1 + 3 files changed, 41 insertions(+), 15 deletions(-) create mode 100644 tools/peakzilla/test-data/log.txt create mode 100644 tools/peakzilla/test-data/negative_peaks.tsv diff --git a/tools/peakzilla/peakzilla.xml b/tools/peakzilla/peakzilla.xml index 053614f7286..5e95c7e6f6d 100644 --- a/tools/peakzilla/peakzilla.xml +++ b/tools/peakzilla/peakzilla.xml @@ -1,13 +1,13 @@ Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments - - python - peakzilla - 1.0 1 + + python + peakzilla + '$results' + + ## copy the log file to the output if it was requested + #if $outputs.log + && cp log.txt $log + #end if + + ## copy the negative peaks file to the output if it was requested + #if $outputs.negative + && cp negative_peaks.tsv $negative_peaks + #end if ]]> @@ -65,7 +75,7 @@ log - + negative @@ -80,19 +90,19 @@ - - Peak_1 - + + + - - - Peakzilla - + + + + - - Peak_1 - + + + diff --git a/tools/peakzilla/test-data/log.txt b/tools/peakzilla/test-data/log.txt new file mode 100644 index 00000000000..2804954943b --- /dev/null +++ b/tools/peakzilla/test-data/log.txt @@ -0,0 +1,15 @@ +10:13:55 Loading tags ... +10:13:55 Tags in IP: 9953 +10:13:55 Tags in control: 9569 +10:13:55 Fragment size was set manually to 50 bp +10:13:55 Peak size is 101 bp +10:13:55 Estimating tag distribution using gaussian ... +10:13:55 Finding peaks in ChIP sample ... +10:13:55 Finding peaks in control sample ... +10:13:55 Calculating peak scores ... +10:13:55 Calculating FDR ... +10:13:55 1 peaks detected +10:13:55 Enrichment cutoff: 2.0 +10:13:55 Score cutoff: 1.0 +10:13:55 Writing input peaks to negative_peaks.tsv +10:13:55 Done! diff --git a/tools/peakzilla/test-data/negative_peaks.tsv b/tools/peakzilla/test-data/negative_peaks.tsv new file mode 100644 index 00000000000..2401cf247c4 --- /dev/null +++ b/tools/peakzilla/test-data/negative_peaks.tsv @@ -0,0 +1 @@ +#Chromosome Start End Name Summit Score ChIP Control FoldEnrichment DistributionScore From f97c8330a74a2b9911291973f0be206230a860e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 26 Feb 2024 11:20:23 +0100 Subject: [PATCH 4/5] last fixes --- tools/peakzilla/peakzilla.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/peakzilla/peakzilla.xml b/tools/peakzilla/peakzilla.xml index 5e95c7e6f6d..e5bb9fa6d70 100644 --- a/tools/peakzilla/peakzilla.xml +++ b/tools/peakzilla/peakzilla.xml @@ -2,11 +2,11 @@ Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments 1.0 - 1 + 0 python - peakzilla + peakzilla @@ -174,4 +174,4 @@ } - \ No newline at end of file + From 0d8f2965e86ef39abcaa9e220fbfb87dfcb98bf3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 26 Feb 2024 11:24:48 +0100 Subject: [PATCH 5/5] ok, now last fixes --- tools/peakzilla/peakzilla.xml | 45 +++++++++++------------------------ 1 file changed, 14 insertions(+), 31 deletions(-) diff --git a/tools/peakzilla/peakzilla.xml b/tools/peakzilla/peakzilla.xml index e5bb9fa6d70..d302018c582 100644 --- a/tools/peakzilla/peakzilla.xml +++ b/tools/peakzilla/peakzilla.xml @@ -42,16 +42,6 @@ -l log.txt #end if '$chip_bed' '$input_bed' > '$results' - - ## copy the log file to the output if it was requested - #if $outputs.log - && cp log.txt $log - #end if - - ## copy the negative peaks file to the output if it was requested - #if $outputs.negative - && cp negative_peaks.tsv $negative_peaks - #end if ]]> @@ -72,10 +62,10 @@ - + log - + negative @@ -109,15 +99,18 @@ intersect_peaks.tsv - For example datasets as well as an example of a computational pipeline for the comparative analysis of ChIP-seq datasets, please refer to our publication: Bardet AF et al. A computational pipeline for comparative ChIP-seq analyses. Nature Protocols (2011) 7(1):45-61 (http://www.starklab.org/data/bardet_natprotoc_2011/) + For example datasets as well as an example of a computational pipeline for the comparative analysis of ChIP-seq datasets, please refer to our + publication: Bardet AF et al. A computational pipeline for comparative ChIP-seq analyses. Nature Protocols (2011) 7(1):45-61 (http://www.starklab.org/data/bardet_natprotoc_2011/) *OPTIONS* One of peakzilla's design goals is to learn all the necessary information from the data. The usage of the options should therefore not be required. *OUTPUT FORMAT* - * Results are printed as a table of tab delimited values to stdout + * Results are printed as a table of tab-delimited values to stdout * Logs are appended to logs.txt in the current directory or a custom directory/filename specified by the -l option * Enriched regions in the control sample are written to negative_peaks.tsv or a custom directory/filename specified by the -n option * Columns represent Chromosome / Start / End / Name / Summit / Score / ChIP / Control / FoldEnrichment / DistributionScore / FDR (%) ]]> - - @article{bardet2012computational, - title={A computational pipeline for comparative ChIP-seq analyses}, - author={Bardet, Ana{\"\i}s F and He, Qiye and Zeitlinger, Julia and Stark, Alexander}, - journal={Nature protocols}, - volume={7}, - number={1}, - pages={45--61}, - year={2012}, - publisher={Nature Publishing Group UK London} - } - + 10.1038/nprot.2011.420