| Next changeset 1:e726f7546561 (2018-04-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324 |
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added:
damidseq_findpeaks.xml find_peaks test-data/hp1.bed test-data/peaks.gff |
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| diff -r 000000000000 -r be830200e987 damidseq_findpeaks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/damidseq_findpeaks.xml Fri Apr 20 04:34:17 2018 -0400 |
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| @@ -0,0 +1,68 @@ +<tool id="damidseq_find_peaks" name="damidseq find peaks" version="0.1.3"> + <description>Simple FDR random permutation peak caller</description> + <requirements> + <requirement type="package" version="5.26">perl</requirement> + </requirements> + <version_command><![CDATA['$__tool_directory__/find_peaks' --help 2>&1| grep find_peaks]]></version_command> + <command detect_errors="aggressive"><![CDATA[ +'$__tool_directory__/find_peaks' + --fdr=$fdr + --frac=$fdr + --min_count=$min_count + --min_quant=$min_quant + --n=$n + --step=$step + --unified_peaks=$unified_peaks + '$input_file' && +mv peak_analysis*/*.gff peaks.gff && +mv peak_analysis*/*data log.txt + ]]></command> + <inputs> + <param name="input_file" type="data" format="gff,bed,bedgraph" label="Select dam-fusion/dam ratio files" help="You can use damidseq_core to produce this file."/> + <param argument="--fdr" type="float" min="0" max="1" value="0.01" label="Set the False Discovery Rate (FDR)"/> + <param argument="--frac" type="float" min="0" max="1" value="0.01" label="Number of random fragments to consider per iteration"/> + <param argument="--min_count" type="integer" min="1" value="2" label="Minimum number of fragments to consider as a peak"/> + <param argument="--min_quant" type="float" min="0" max="1" value="0.95" label="Minimum quantile for considering peaks"/> + <param argument="--n" type="integer" min="1" value="100" label="Number of iterations"/> + <param argument="--step" type="float" min="0" max="1" value="0.01" label="Stepping for quantiles"/> + <param argument="--unified_peaks" type="select" label="Set the False Discovery Rate (FDR)"> + <option value="max">call maximum overlap as peak</option> + <option value="min">call minimum overlap as peak</option> + </param> + </inputs> + <outputs> + <data name="peaks" format="gff3" from_work_dir="peaks.gff" label="${tool.name} on ${on_string}"/> + <data name="logs" format="txt" hidden="true" from_work_dir="log.txt" label="${tool.name} logs on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="input_file" value="hp1.bed" ftype="bed"/> + <param name="min_count" value="1"/> + <param name="fdr" value="0.1"/> + <output name="peaks" value="peaks.gff"/> + </test> + </tests> + <help><![CDATA[ + +Options: + --fdr False discovery rate value + [Current value: 0.01] + --frac Number of random fragments to consider per iteration + --min_count Minimum number of fragments to consider as a peak + [Current value: 2] + --min_quant Minimum quantile for considering peaks + [Current value: 0.95] + --n Number of iterations + [Current value: 100] + --step Stepping for quantiles + [Current value: 0.01] + --unified_peaks Method for calling peak overlaps (two options): + 'min': call minimum overlapping peak area + 'max': call maximum overlap as peak + [Current value: max] + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btv386</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r be830200e987 find_peaks --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/find_peaks Fri Apr 20 04:34:17 2018 -0400 |
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| b'@@ -0,0 +1,633 @@\n+#!/usr/bin/perl -w\n+\n+# Copyright \xa9 2012-2015, Owen Marshall\n+\n+# This program is free software; you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation; either version 2 of the License, or (at\n+# your option) any later version. \n+# \n+# This program is distributed in the hope that it will be useful, but\n+# WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\n+# General Public License for more details. \n+# \n+# You should have received a copy of the GNU General Public License\n+# along with this program; if not, write to the Free Software\n+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 \n+# USA\n+\n+use strict;\n+use File::Basename;\n+use 5.010;\n+$|++;\n+\n+my $version = "1.0.1";\n+\n+print STDERR "\\nfind_peaks v$version\\nCopyright \xa9 2012-15, Owen Marshall\\n\\n";\n+\n+my %vars = (\n+\t\'fdr\' => 0.01,\n+\t\'min_count\' => 2,\n+\t\'n\' => 100,\n+\t\'frac\' => 0,\n+\t\'min_quant\' => 0.95,\n+\t\'step\' => 0.01,\n+\t\'unified_peaks\' => \'max\',\n+);\n+\n+my %vars_details = (\n+\t\'fdr\' => \'False discovery rate value\',\n+\t\'min_count\' => \'Minimum number of fragments to consider as a peak\',\n+\t\'n\' => \'Number of iterations\',\n+\t\'frac\' => \'Number of random fragments to consider per iteration\',\n+\t\'min_quant\' => \'Minimum quantile for considering peaks\',\n+\t\'step\' => \'Stepping for quantiles\',\n+\t\'unified_peaks\' => "Method for calling peak overlaps (two options):\\n\\r\'min\': call minimum overlapping peak area\\n\\r\'max\': call maximum overlap as peak",\n+);\n+\n+\n+my @in_files;\n+process_cli();\n+\n+# Time and date\n+my ($sec,$min,$hour,$mday,$mon,$year) = localtime();\n+my $date = sprintf("%04d-%02d-%02d.%02d-%02d-%02d",$year+1900,$mon+1,$mday,$hour,$min,$sec);\n+\n+help() unless @in_files;\n+\n+foreach my $fn (@in_files) {\n+\tmy @in;\n+\tmy @unified_peaks;\n+\tmy @sig_peaks;\n+\tmy @peakmins;\n+\t\n+\tmy %peaks;\n+\tmy %peak_count;\n+\tmy %peak_count_real;\n+\tmy %log_scores;\n+\tmy %regression;\n+\tmy %peak_fdr_cutoff;\n+\tmy %fdr;\n+\t\n+\t# Output file names\n+\tmy ($name,$dir,$ext) = fileparse($fn, qr/\\.[^.]*/);\n+\t\n+\t# filenames\n+\tmy $fn_base_date = "peak_analysis.".$name.".$date";\n+\tmy $base_dir = "$fn_base_date/";\n+\tmy $out = "$base_dir"."$name-FDR$vars{\'fdr\'}";\n+\tmy $out_peak_unified_track = $out.".peaks.gff";\n+\tmy $out_peaks = $out."_FDR-data";\n+\t\n+\t# Load gff data files\n+\tload_gff(FILE=>$fn, IN_REF=>\\@in);\n+\t\n+\tmy $probes = @in;\n+\t\n+\tfind_quants(IN_REF=>\\@in, PEAKMINS_REF=>\\@peakmins);\n+\tfind_randomised_peaks(IN_REF=>\\@in, PEAKMINS_REF=>\\@peakmins, PEAK_COUNT=>\\%peak_count, PEAKS=>\\%peaks);\n+\t\n+\t# Make directory\n+\tmkdir($base_dir);\n+\t\n+\t# Open peaks file for writing\n+\topen(OUTP, ">$out_peaks")|| die "Cannot open peak file for writing: $!\\n";\n+\tprint OUTP "FDR peak call v$version\\n\\n";\n+\tprint OUTP "Input file: $fn\\n";\n+\t\n+\tcalculate_regressions(IN_REF=>\\@in, PEAKMINS_REF=>\\@peakmins, PEAK_COUNT=>\\%peak_count, PEAKS=>\\%peaks, LOG_SCORES=>\\%log_scores, REGRESSION=>\\%regression);\n+\t\n+\tcall_peaks_unified_redux(ITER=>1, REAL=>1, AREF=>\\@in, PEAKMINS_REF=>\\@peakmins, PEAK_COUNT=>\\%peak_count, PEAK_COUNT_REAL=>\\%peak_count_real, PEAKS=>\\%peaks);\n+\t\n+\tcalculate_fdr(IN_REF=>\\@in, PEAKMINS_REF=>\\@peakmins, PEAK_COUNT=>\\%peak_count, PEAK_COUNT_REAL=>\\%peak_count_real, PEAK_FDR_CUTOFF=>\\%peak_fdr_cutoff, FDR=>\\%fdr, LOG_SCORES=>\\%log_scores, REGRESSION=>\\%regression);\n+\t\n+\tfind_significant_peaks(PEAKMINS=>\\@peakmins, SIG_PEAKS=>\\@sig_peaks, PEAKS=>\\%peaks, PEAK_FDR_CUTOFF=>\\%peak_fdr_cutoff, FDR=>\\%fdr);\n+\t\n+\tmake_unified_peaks(SIG_PEAKS=>\\@sig_peaks, UNIFIED_PEAKS=>\\@unified_peaks, OUT=>$out_peak_unified_track, TYPE=>$vars{\'unified_peaks\'});\n+\t\n+\tprint STDERR "$#unified_peaks peaks found.\\n\\n";\n+\t\n+\tclose OUTP;\n+}\n+\n+print STDERR "All done.\\n\\n";\n+exit 0;\n+\n+\n+######################\n+# Subroutines start here\n+#\n+\n+sub find_significant_peaks {\n+\tmy (%opts) = @_;\n+\t\n+\tmy $peakmins = $opts{PEAKMINS};\n+\tmy $peaks = $opts{PEAKS};\n+\tmy $sig_p'..b'ts{OUT};\n+\tmy $unified_peaks = $opts{UNIFIED_PEAKS};\n+\tmy $type = $opts{TYPE};\n+\tmy $total = @$ref;\n+\t\t\n+\t# Unify overlapping peaks, and make significant peaks file\n+\tmy $skipped_peaks;\n+\tprint STDERR "Combining significant peaks ...\\n";\n+\t\n+\t# unroll chromosomes for speed\n+\tforeach my $chr (uniq( map @{$_}[0], @$ref )) {\n+\t\tmy @c = grep {@{$_}[0] eq $chr} @$ref;\n+\t\t\n+\t\tmy @unified_peaks_chr;\n+\t\tforeach my $ar (@c) {\n+\t\t\tif (state $i++ % 100 == 0) {\n+\t\t\t\t\tmy $pc = sprintf("%0.2f",($i*100)/$total);\n+\t\t\t\t\tprint STDERR "$pc\\% processed ...\\r";\n+\t\t\t}\n+\t\t\t\n+\t\t\tmy ($chra, $start, $end, $score, $total_score, $count, $peaklen, $fdr) = @$ar;\n+\t\t\t\n+\t\t\t# next if @unified_peaks_chr already overlaps\n+\t\t\tnext if grep {\n+\t\t\t\t\t\t@{$_}[3] < $end\n+\t\t\t\t\t\t&& @{$_}[4] > $start\n+\t\t\t\t\t} @unified_peaks_chr;\n+\t\t\t\n+\t\t\t# Grab all elements that overlap\n+\t\t\tmy @test = grep {\n+\t\t\t\t\t\t@{$_}[1] < $end\n+\t\t\t\t\t\t&& @{$_}[2] > $start\n+\t\t\t\t\t} @c;\n+\t\t\t\n+\t\t\tfor my $j (0 .. $#test) {\n+\t\t\t\tmy ($chr1, $start1, $end1, $score1, $total_score1, $count1, $peaklen1, $fdr1) = @{$test[$j]};\n+\t\t\t\t\n+\t\t\t\tnext unless $start1 < $end;\n+\t\t\t\tnext unless $end1 > $start;\n+\t\t\t\t\n+\t\t\t\tif ($type eq \'min\') {\n+\t\t\t\t\t$start = max($start, $start1);\n+\t\t\t\t\t$end = min($end, $end1);\n+\t\t\t\t} else {\n+\t\t\t\t\t$start = min($start, $start1);\n+\t\t\t\t\t$end = max($end, $end1);\n+\t\t\t\t}\n+\t\t\t\t\n+\t\t\t\t$score = max($score, $score1);\n+\t\t\t\t$fdr = min($fdr, $fdr1);\n+\t\t\t}\n+\t\t\t\n+\t\t\tpush @unified_peaks_chr, [($chr, \'.\', \'.\', $start, $end, $score, \'.\', \'.\', "FDR=$fdr")];\n+\t\t}\n+\t\t\n+\t\t@$unified_peaks = (@$unified_peaks, @unified_peaks_chr);\n+\t}\n+\t\n+\t$total = $#$unified_peaks;\n+\t\n+\tprint STDERR "Sorting unified peaks ...\\n";\n+\t@$unified_peaks = sort { $a->[3] <=> $b->[3] } @$unified_peaks;\n+\t@$unified_peaks = sort { $a->[0] cmp $b->[0] } @$unified_peaks;\n+\t\n+\tprint STDERR "Writing unified peaks file ...\\n";\n+\topen(PEAKOUTUNI, ">$out_peak_unified_track") || die "Unable to open peak output track for writing: $!\\n\\n"; \n+\tfor my $j (0 .. $#$unified_peaks) {\n+\t\tprint PEAKOUTUNI join("\\t", @{$$unified_peaks[$j]}), "\\n";\n+\t}\n+}\n+\n+sub max {\n+ my ($max, @vars) = @_;\n+\tmy $index=0;\n+\t$max||=0;\n+ for my $i (0..$#vars) {\n+ ($max, $index) = ($vars[$i], $i+1) if $vars[$i] > $max;\n+ }\n+ return $max;\n+}\n+\n+sub min {\n+ my ($min, @vars) = @_;\n+\tmy $index=0;\n+\t$min||=0;\n+ for my $i (0..$#vars) {\n+ ($min, $index) = ($vars[$i],$i+1) if $vars[$i] < $min;\n+ }\n+ return $min;\n+}\n+\n+sub uniq {\n+\tmy %seen;\n+\treturn grep { !$seen{$_}++ } @_;\n+}\n+\n+\n+\n+sub process_cli {\n+\tforeach (@ARGV) {\n+\t\tif (/--(.*)=(.*)/) {\n+\t\t\tunless (defined($vars{$1})) {\n+\t\t\t\tprint STDERR "Did not understand $_ ...\\n";\n+\t\t\t\thelp();\n+\t\t\t}\n+\t\t\tmy ($v, $opt) = ($1,$2);\n+\t\t\t$vars{$v} = $opt;\n+\t\t\tnext;\n+\t\t} elsif (/--h[elp]*/) {\n+\t\t\thelp();\n+\t\t} elsif (/--(.*)/) {\n+\t\t\tprint STDERR "Please add a parameter to $_ ...\\n\\n";\n+\t\t\texit 1;\n+\t\t}\n+\t\tpush @in_files, $_;\n+\t}\n+}\n+\n+\n+sub help {\n+\tprint STDOUT <<EOT;\n+Simple FDR random permutation peak caller\n+Usage: [options] [files in bedgraph or GFF format]\n+\t\n+Options:\n+EOT\n+\t\n+\tmy $opt_len = 0;\n+\tforeach (keys %vars) {\n+\t\tmy $l = length($_);\n+\t\t$opt_len = $l if $l > $opt_len;\n+\t}\n+\t\n+\t$opt_len+=2;\n+\t\n+\tmy $cols= `tput cols` || 80;\n+\t\n+\tmy ($v, $val, $def, $def_format);\n+\tmy $help_format = "format STDOUT =\\n"\n+\t\t.\' \'.\'^\'.\'<\'x$opt_len . \' \'. \'^\' . \'<\'x($cols-$opt_len-4) . "\\n"\n+\t\t.\'$v, $def_format\'."\\n"\n+\t\t.\' \'.\'^\'.\'<\'x$opt_len . \' \'. \'^\' . \'<\'x($cols-$opt_len-6) . "~~\\n"\n+\t\t.\'$v, $def_format\'."\\n"\n+\t\t.".\\n";\n+\t\t\n+\teval $help_format;\n+\tdie $@ if $@;\n+\t\n+\tforeach my $k (sort (keys %vars)) {\n+\t\t($v, $val, $def) = ($k, $vars{$k}, $vars_details{$k});\n+\t\t$def||="";\n+\t\t$def_format = $val ? "$def\\n\\r[Current value: $val]" : $def;\n+\t\t$v = "--$v";\n+#\t\tformat =\n+# ^<<<<<<<<<<<<<<<<<<<< ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n+#$v, $def_format\n+# ^<<<<<<<<<<<<<<<<<<<< ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< ~~\n+#$v, $def_format\n+#.\n+\n+\t\twrite();\n+\t\t\n+\t}\n+\tprint STDOUT "\\n";\n+\texit 1;\n+}\n' |
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| diff -r 000000000000 -r be830200e987 test-data/hp1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hp1.bed Fri Apr 20 04:34:17 2018 -0400 |
| b |
| b'@@ -0,0 +1,2000 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|
| b |
| diff -r 000000000000 -r be830200e987 test-data/peaks.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks.gff Fri Apr 20 04:34:17 2018 -0400 |
| b |
| @@ -0,0 +1,43 @@ +3L . . 17416196 17416656 2.06 . . FDR=0.0434782608695652 +3L . . 17428494 17428708 4.60 . . FDR=0.25 +3L . . 17434875 17435361 2.36 . . FDR=0.0434782608695652 +3L . . 17436191 17436240 1.55 . . FDR=0.0434782608695652 +3L . . 17454392 17455057 1.47 . . FDR=0.0434782608695652 +3L . . 17469263 17469357 1.76 . . FDR=0.25 +3L . . 17474212 17474436 2.67 . . FDR=0.1 +3L . . 17478792 17479470 2.71 . . FDR=0.25 +3L . . 17480437 17480672 4.80 . . FDR=0.1 +3L . . 17484190 17484263 1.55 . . FDR=0.0434782608695652 +3L . . 17493333 17493632 2.10 . . FDR=0.0434782608695652 +3L . . 17509604 17509706 2.15 . . FDR=0.0434782608695652 +3L . . 17548916 17549057 1.90 . . FDR=0.0434782608695652 +3L . . 17629032 17629240 1.43 . . FDR=0.0434782608695652 +3L . . 17637540 17637772 3.90 . . FDR=0.1 +3L . . 17639208 17639274 1.55 . . FDR=0.0434782608695652 +3L . . 17655832 17656401 4.47 . . FDR=0.0555555555555556 +3L . . 17663729 17663765 2.15 . . FDR=0.0434782608695652 +3L . . 17745743 17745838 1.47 . . FDR=0.0434782608695652 +3L . . 17748063 17748387 2.92 . . FDR=0.0434782608695652 +3L . . 17753481 17753917 4.56 . . FDR=0.1 +3L . . 17756873 17757959 1.63 . . FDR=0.0434782608695652 +3L . . 17801230 17802045 1.85 . . FDR=0.0434782608695652 +3L . . 17841131 17842320 2.31 . . FDR=1 +3L . . 17853549 17854148 1.90 . . FDR=0.0555555555555556 +3L . . 17858323 17858952 1.68 . . FDR=0.111111111111111 +3L . . 17859435 17859724 1.64 . . FDR=0.0555555555555556 +3L . . 17861050 17861152 2.02 . . FDR=0.0434782608695652 +3L . . 17869953 17870956 2.56 . . FDR=0.25 +3L . . 17872304 17873275 2.92 . . FDR=0.25 +3L . . 17874546 17875836 3.37 . . FDR=0.25 +3L . . 17910607 17910788 2.74 . . FDR=0.1 +3L . . 17918198 17918586 1.62 . . FDR=0.0434782608695652 +3L . . 17936813 17937334 1.85 . . FDR=0.0434782608695652 +3L . . 17999429 17999479 2.15 . . FDR=0.0434782608695652 +3L . . 18008966 18009131 2.85 . . FDR=0.1 +3L . . 18016765 18016884 1.47 . . FDR=0.0434782608695652 +3L . . 18017196 18017386 2.02 . . FDR=0.0555555555555556 +3L . . 18018167 18018993 1.65 . . FDR=0.0434782608695652 +3L . . 18036026 18036121 4.10 . . FDR=0.0434782608695652 +3L . . 18079650 18079739 2.15 . . FDR=0.0434782608695652 +3L . . 18110932 18111360 1.88 . . FDR=0.1 +3L . . 18131560 18131987 3.45 . . FDR=1 |