# HG changeset patch
# User iuc
# Date 1430275567 14400
# Node ID a2b093982c38c9fb176471b3227e18195356b047
# Parent 059d9131dce76751b78cc39630e78bd709af08ca
Uploaded
diff -r 059d9131dce7 -r a2b093982c38 dir2html.py
--- a/dir2html.py Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-import os
-import sys
-from xml.sax.saxutils import escape
-
-def make_table( directory ):
- ret = ['\n']
- for file in os.listdir( directory ):
- ret.append('| %s |
\n' % ( file, escape(file).replace( 'MACS2_', '' ) ))
- ret.append('
')
- return ''.join(ret)
-
-def make_html( directory, stderr ):
- return '\n'.join([''
- '',
- ' Additional output created by MACS2',
- ' ',
- '',
- '',
- 'Additional Files:
',
- make_table( directory ),
- 'Messages from MACS2:
',
- stderr.read().replace('\n', '
'),
- '',
- ''])
-
-if __name__ == '__main__':
- if len(sys.argv) == 3:
- directory_path = sys.argv[1]
- stderr = open( sys.argv[2] )
- print make_html( directory_path, stderr )
- else:
- sys.exit( 'Two parameter expected: directory path and stderr path' )
-
diff -r 059d9131dce7 -r a2b093982c38 macs2_bdgbroadcall.xml
--- a/macs2_bdgbroadcall.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-
- Call broad peaks from bedGraph output
-
- gnu_awk
-
-
-
- macs2_macros.xml
-
-
- macs2 bdgbroadcall
- --ifile "${ infile }"
- --cutoff-peak "${ cutoffpeak }"
- --cutoff-link "${ cutofflink }"
- --min-length "${ minlen }"
- --lvl1-max-gap "${ LVL1MAXGAP }"
- --lvl2-max-gap "${ LVL2MAXGAP }"
- --ofile "macs2_bdgbroadcall.bdg"
- &&
- awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }"
-
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-**What it does**
-
-Call broad peaks from bedGraph output.
-bdgbroadcall from macs2
-
-@citation@
-
-
-
diff -r 059d9131dce7 -r a2b093982c38 macs2_bdgcmp.xml
--- a/macs2_bdgcmp.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-
- Deduct noise by comparing two signal tracks in bedGraph
-
-
-
- macs2_macros.xml
-
-
- macs2 bdgcmp
- -t "${ infile_treatment }"
- -c "${ infile_control }"
-
- -m "${ bdgcmp_options.bdgcmp_options_selector }"
- #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']:
- -p "${ bdgcmp_options.pseudocount }"
- #end if
- -o "${ outfile }"
-
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-**What it does**
-
-With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
-is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
-identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
-binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
-
-View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
-
-------
-
-**Usage**
-
-**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
-
-
-@citation@
-
-
-
diff -r 059d9131dce7 -r a2b093982c38 macs2_bdgdiff.xml
--- a/macs2_bdgdiff.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-
- Differential peak detection based on paired four bedgraph files
-
-
-
- macs2_macros.xml
-
-
- macs2 bdgdiff
- --t1 "${ infile_pileup_cond1 }"
- --t2 "${ infile_pileup_cond2 }"
- --c1 "${ infile_control_cond1 }"
- --c2 "${ infile_control_cond2 }"
- --cutoff "${ cutoff }"
- --min-len "${ minlen }"
- --depth1 "${ depth1 }"
- --depth2 "${ depth2 }"
- --max-gap "${ maxgap }"
- --o-prefix MACS2
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- '--ofile-cond1' in outputs
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- '--ofile-cond2' in outputs
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- '--ofile-both-conditions' in outputs
-
-
-
-
-
-
-
-**What it does**
-
-bdgdiff from macs2
-
-
-@citation@
-
-
-
diff -r 059d9131dce7 -r a2b093982c38 macs2_bdgpeakcall.xml
--- a/macs2_bdgpeakcall.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-
- Call peaks from bedGraph output
-
- gnu_awk
-
-
-
- macs2_macros.xml
-
-
- macs2 bdgpeakcall
- --ifile "${ infile }"
- --cutoff "${ cutoff }"
- --min-length "${ minlen }"
- --max-gap "${ maxgap }"
- ${ callsummits }
- ${ notrackline }
- --ofile "macs2_bdgpeakcall.bdg"
- &&
- awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }"
-
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-**What it does**
-
-Call peaks from bedGraph output.
-bdgpeakcall from macs2
-
-
-@citation@
-
-
-
diff -r 059d9131dce7 -r a2b093982c38 macs2_callpeak.xml
--- a/macs2_callpeak.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,291 +0,0 @@
-
- Call peaks from alignment results
-
- R_3_0_1
- gnu_awk
- MACS2_SCRIPT_PATH
-
-
-
- macs2_macros.xml
-
-
- #set $temp_stderr = 'macs2_stderr'
- (macs2 callpeak
-
- --name "MACS2"
- -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_treatment_file ) ) }
-
- #if str( $input_control_file ) != 'None':
- -c ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_control_file ) ) }
- #end if
-
- #for $ifile in $input_treatment_file:
- #if $ifile.ext.upper() == 'BAM' and $bampe:
- --format BAMPE
- #else
- --format='$ifile.ext.upper()'
- #end if
- #end for
-
- @effective_genome_size@
-
- --bw='$band_width'
-
- ## advanced options
- #if $advanced_options.advanced_options_selector == 'on':
- $advanced_options.nolambda
- $advanced_options.to_large
- --ratio $advanced_options.ratio
- --slocal $advanced_options.slocal
- --llocal $advanced_options.llocal
- #if $advanced_options.broad_options.broad_options_selector == 'broad':
- --broad
- --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
- #else:
- $advanced_options.broad_options.call_summits
- #end if
-
- #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
- --keep-dup "${ advanced_options.keep_dup_options.user_keepdup }"
- #else
- --keep-dup "${ advanced_options.keep_dup_options.keep_dup_options_selector }"
- #end if
-
- #end if
-
- ## With --bdg two additional output files will be generated.
- #if 'bdg' in str($outputs).split(','):
- --bdg
- #end if
-
- ## cutoff selection
- #if str( $cutoff_options.cutoff_options_selector ) == 'qvalue':
- --qvalue "${ cutoff_options.qvalue }"
- #elif str( $cutoff_options.cutoff_options_selector ) == 'pvalue':
- #if str($cutoff_options.pvalue).strip() != '':
- --pvalue "${ cutoff_options.pvalue }"
- #end if
- #else:
- --foldenrichment "${ cutoff_options.foldenrichment }"
- #end if
-
- ## model options
- #if $nomodel_type.nomodel_type_selector == 'nomodel':
- --nomodel
- ##--shiftsize '$nomodel_type.shiftsize'
- --extsize '${ nomodel_type.extsize }'
- #end if
-
- 2> $temp_stderr)
- #if 'peaks_bed' in str($outputs).split(','):
- &&
- awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\t' '$1=$1' | tail -n+3 > "${ output_bed }"
- #end if
-
- ## run R to create pdf from model script
- #if 'pdf' in str($outputs).split(','):
- &&
- Rscript MACS2_model.r > MACS2_model.r.log
- #end if
-
- #if 'html' in str($outputs).split(','):
- ## if output files exists, move them to the files_path and create a html result page linking to them
- &&
- (
- count=`ls -1 MACS2* 2>/dev/null | wc -l`;
- if [ \$count != 0 ];
- then
- mkdir "${ output_extra_files.files_path }";
- cp MACS2* "${ output_extra_files.files_path }";
- python "\$MACS2_SCRIPT_PATH/dir2html.py" "${ output_extra_files.files_path }" $temp_stderr > "${ output_extra_files }";
- fi;
- )
- #end if
- ;
- exit_code_for_galaxy=\$?;
- cat $temp_stderr 2>&1;
- (exit \$exit_code_for_galaxy)
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- 'peaks_bed' in outputs
-
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- ((
- advanced_options['advanced_options_selector'] == "on" and
- advanced_options['broad_options']['broad_options_selector'] == "broad"
- ))
-
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-
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- ((
- advanced_options['advanced_options_selector'] == "on" and
- advanced_options['broad_options']['broad_options_selector'] == "broad"
- ))
-
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-
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- (
- advanced_options['advanced_options_selector'] == "off" or
- (
- advanced_options['advanced_options_selector'] == "on" and
- advanced_options['broad_options']['broad_options_selector'] == "nobroad"
- ))
-
-
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- 'summits' in outputs
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- 'pdf' in outputs
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- 'bdg' in outputs
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- 'bdg' in outputs
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- 'html' in outputs
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-
-
-**What it does**
-
-With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
-is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
-identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
-binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
-
-View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
-
-------
-
-**Usage**
-
-**Peak Calling**: Main MACS2 Function to Call peaks from alignment results.
-
-If you choose "Scores in bedGraph files" MACS will output the fragment pileup, control lambda, -log10-pvalue and -log10-qvalue scores in bedGraph files.
-The peaks in BED format contain the following colomns: chr end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name
-
-**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
-
-
-@citation@
-
-
-
diff -r 059d9131dce7 -r a2b093982c38 macs2_filterdup.xml
--- a/macs2_filterdup.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-
- Remove duplicate reads at the same position
-
-
-
- macs2_macros.xml
-
-
- macs2 filterdup
- -i "${ infile }"
- -o temp_outfile
-
- --format '${ infile.extension.upper() }'
- @effective_genome_size@
- @tag_size@
- --pvalue "${ pvalue }"
- #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
- --keep-dup "${ keep_dup_options.user_keepdup }"
- #else
- --keep-dup "${ keep_dup_options.keep_dup_options_selector }"
- #end if
- ;
- mv temp_outfile "${ outfile }"
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-**What it does**
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-Remove duplicate reads at the same position, then convert acceptable format to BED format.
-filterdup tool from macs2
-
-@citation@
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-
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diff -r 059d9131dce7 -r a2b093982c38 macs2_macros.xml
--- a/macs2_macros.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-
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- macs2
- numpy
- scipy
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- 2.1.0.20140616
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- #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
- --gsize "${ effective_genome_size_options.gsize }"
- #else:
- --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }"
- #end if
-
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- macs2 --version
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- #if $tsize == -1.0:
- --tsize "${ tsize }"
- #end if
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-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
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-Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.
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- 10.1186/gb-2008-9-9-r137
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diff -r 059d9131dce7 -r a2b093982c38 macs2_predictd.xml
--- a/macs2_predictd.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-
- Predict 'd' or fragment size from alignment results
-
- R_3_0_1
- gnu_awk
-
-
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- macs2_macros.xml
-
-
- macs2 predictd
- -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
- @tag_size@
- @effective_genome_size@
- --bw "${ band_width }"
- --mfold "${ mfoldlo }" "${ mfoldhi }"
-
- ## remove the timepoint and strip the output
- 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
-
- > "${ outfile }"
-
- &&
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- Rscript predictd
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-**What it does**
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-predictd from macs2
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-Note that pair-end data is not supposed to work with this command.
-
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-@citation@
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diff -r 059d9131dce7 -r a2b093982c38 macs2_randsample.xml
--- a/macs2_randsample.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-
- Randomly sample number or percentage of total reads
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- macs2_macros.xml
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- macs2 randsample
- -t "${ infile }"
- -o "${ outfile }"
-
- --format '${ infile.extension.upper() }'
-
- @tag_size@
- #if $method_options.method_options_selector == 'percentage':
- --percentage "${ method_options.percentage }"
- #else:
- --number "${ method_options.number }"
- #end if
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-**What it does**
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-randsample tool from macs2
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-@citation@
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diff -r 059d9131dce7 -r a2b093982c38 macs2_refinepeak.xml
--- a/macs2_refinepeak.xml Thu Feb 26 22:41:29 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-
- Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)
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- macs2_macros.xml
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- macs2 refinepeak
- -b "${ bed_infile }"
- -i "${ infile }"
- --format '${ infile.extension.upper() }'
- --cutoff "${ cutoff }"
- --window-size "${ winsize }"
- --ofile "${ outfile }"
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-**What it does**
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-(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP.
-
-@citation@
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-