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README annotatePeaks.xml bed2pos.xml datatypes_conf.xml findPeaks.xml homerDatatypes.py makeTagDirectory.py makeTagDirectory.xml pos2bed.xml |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 README --- a/README Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,13 +0,0 @@ -Homer wrapper for Galaxy - -Code repo: https://bitbucket.org/gvl/homer - -=========================================: -LICENSE for this wrapper: -=========================================: -Kevin Ying -Garvan Institute: http://www.garvan.org.au -GVL: https://genome.edu.au/wiki/GVL - -http://opensource.org/licenses/mit-license.php - |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 annotatePeaks.xml --- a/annotatePeaks.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,41 +0,0 @@ -<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.2"> - <requirements> - <requirement type="package">homer</requirement> - </requirements> - <description></description> - <!--<version_command></version_command>--> - <command> - annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated - 2> $out_log || echo "Error running annotatePeaks." >&2 - </command> - <inputs> - <param format="tabular,bed" name="input_bed" type="data" label="Homer peak positions or BED format" /> - <param name="genome_selector" type="select" label="Genome version"> - <option value="hg19" selected="true">hg19</option> - </param> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - - .. class:: infomark - - **Homer annoatePeaks** - More information on accepted formats - http://biowhat.ucsd.edu/homer/ngs/annotation.html - - - </help> -</tool> - |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 bed2pos.xml --- a/bed2pos.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,34 +0,0 @@ -<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.2"> - <requirements> - <requirement type="package">homer</requirement> - </requirements> - <description></description> - <!--<version_command></version_command>--> - <command> - bed2pos.pl $input_bed 1> $out_pos - 2> $out_log || echo "Error running bed2pos." >&2 - </command> - <inputs> - <param format="tabular,bed" name="input_bed" type="data" label="BED file" /> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="tabular" name="out_pos" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - .. class:: infomark - - **Homer bed2pos.pl** - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - </help> -</tool> - |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 datatypes_conf.xml --- a/datatypes_conf.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<datatypes> - <datatype_files> - <datatype_file name="homerDatatypes.py"/> - </datatype_files> - <registration> - <datatype extension="homerTagDirectory" type="galaxy.datatypes.homerDatatypes:HomerTagDirectory" display_in_upload="False" mimetype="text/html"/> - </registration> -</datatypes> |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 findPeaks.xml --- a/findPeaks.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,52 +0,0 @@ -<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.0"> - <requirements> - <requirement type="package">homer</requirement> - </requirements> - <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</description> - <!--<version_command></version_command>--> - <command> - findPeaks $tagDir.extra_files_path $options -o $outputPeakFile - - #if $control_tagDir: - -i $control_tagDir.extra_files_path - #end if - - 2> $out_log || echo "Error running findPeaks." >&2 - </command> - <inputs> - <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" /> - <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" /> - <param type="text" name="options" label="Extra options" value="" > - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - - .. class:: infomark - - **Homer findPeaks** - http://biowhat.ucsd.edu/homer/ngs/peaks.html - - </help> -</tool> - |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 homerDatatypes.py --- a/homerDatatypes.py Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,122 +0,0 @@ -""" -homer composite datatypes -NOTE: makeTagDirectory doesn't actually use this!!!! It uses html as the format - I've never got it to properly display the contents of the datatype for after - clicking the "eye" icon, so using html instead - -Use at your peril -Kevin Ying -for the homer wrapper - -Dec 2012 -""" - -import logging, os, sys, time, tempfile, shutil, string, glob -import data -from galaxy import util -from cgi import escape -import urllib, binascii -from galaxy.web import url_for -from galaxy.datatypes import metadata -from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes.data import Text -from galaxy.datatypes.tabular import Tabular -from galaxy.datatypes.images import Html -from galaxy.datatypes.interval import Interval -from galaxy.util.hash_util import * - -gal_Log = logging.getLogger(__name__) -verbose = False - -class HomerTagDirectory(Html): - """ - base class to use for homer tag directory datatypes - composite datatype elements - stored in extra files path - """ - - #MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='HomerTagDirectory', - #readonly=True, set_in_upload=False) - - composite_type = 'auto_primary_file' - #allow_datatype_change = False - file_ext = 'homerTagDirectory' - - def __init__(self, **kwd): - Html.__init__(self, **kwd) - self.add_composite_file('tagInfo.txt', description="tagInfo") - self.add_composite_file('tagAutocorrelation.txt', description="tagAutocorrelation") - self.add_composite_file('tagCountDistribution.txt', description="tagCountDistribution") - self.add_composite_file('tagLengthDistribution.txt', description="tagLengthDistribution") - - def generate_primary_file(self, dataset=None): - rval = ['<html><head><title>Homer Tag Directory Galaxy Composite Dataset </title></head><p/>'] - rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') - for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems(): - fn = composite_name - opt_text = '' - if composite_file.optional: - opt_text = ' (optional)' - if composite_file.get('description'): - rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) ) - else: - rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) ) - rval.append( '</ul></div></html>' ) - return "\n".join( rval ) - - - def regenerate_primary_file(self,dataset): - """ - cannot do this until we are setting metadata - """ - #bn = dataset.metadata.base_name - efp = dataset.extra_files_path - flist = os.listdir(efp) - rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)] - for i,fname in enumerate(flist): - sfname = os.path.split(fname)[-1] - f,e = os.path.splitext(fname) - rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) ) - rval.append( '</ul></body></html>' ) - f = file(dataset.file_name,'w') - f.write("\n".join( rval )) - f.write('\n') - f.close() - - def get_mime(self): - """Returns the mime type of the datatype""" - return 'text/html' - - def set_meta( self, dataset, **kwd ): - - """ - for homer maketagdirectory eg - - """ - Html.set_meta( self, dataset, **kwd ) - if kwd.get('overwrite') == False: - if verbose: - gal_Log.debug('@@@ HomerTagDirectory set_meta called with overwrite = False') - return True - try: - efp = dataset.extra_files_path - except: - if verbose: - gal_Log.debug('@@@ HomerTagDirectory set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name)) - return False - try: - flist = os.listdir(efp) - except: - if verbose: gal_Log.debug('@@@ HomerTagDirectory set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name)) - return False - if len(flist) == 0: - if verbose: - gal_Log.debug('@@@ HomerTagDirectory set_meta failed - %s efp %s is empty?' % (dataset.name,efp)) - return False - self.regenerate_primary_file(dataset) - if not dataset.info: - dataset.info = 'Galaxy HomerTagDirectory datatype object' - if not dataset.blurb: - dataset.blurb = 'Composite file - Homer Galaxy toolkit' - return True - |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 makeTagDirectory.py --- a/makeTagDirectory.py Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,94 +0,0 @@ -""" - - -""" -import re -import os -import sys -import subprocess -import optparse -import shutil -import tempfile - -def getFileString(fpath, outpath): - """ - format a nice file size string - """ - size = '' - fp = os.path.join(outpath, fpath) - s = '? ?' - if os.path.isfile(fp): - n = float(os.path.getsize(fp)) - if n > 2**20: - size = ' (%1.1f MB)' % (n/2**20) - elif n > 2**10: - size = ' (%1.1f KB)' % (n/2**10) - elif n > 0: - size = ' (%d B)' % (int(n)) - s = '%s %s' % (fpath, size) - return s - -class makeTagDirectory(): - """wrapper - """ - - def __init__(self,opts=None, args=None): - self.opts = opts - self.args = args - - def run_makeTagDirectory(self): - """ - makeTagDirectory <Output Directory Name> [options] <alignment file1> [alignment file 2] - - """ - if self.opts.format != "bam": - cl = [self.opts.executable] + args + ["-format" , self.opts.format] - else: - cl = [self.opts.executable] + args - print cl - p = subprocess.Popen(cl) - retval = p.wait() - - - html = self.gen_html(args[0]) - #html = self.gen_html() - return html,retval - - def gen_html(self, dr=os.getcwd()): - flist = os.listdir(dr) - print flist - """ add a list of all files in the tagdirectory - """ - res = ['<div class="module"><h2>Files created by makeTagDirectory</h2><table cellspacing="2" cellpadding="2">\n'] - - flist.sort() - for i,f in enumerate(flist): - if not(os.path.isdir(f)): - fn = os.path.split(f)[-1] - res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, dr))) - - res.append('</table>\n') - - return res - -if __name__ == '__main__': - op = optparse.OptionParser() - op.add_option('-e', '--executable', default='makeTagDirectory') - op.add_option('-o', '--htmloutput', default=None) - op.add_option('-f', '--format', default="sam") - opts, args = op.parse_args() - #assert os.path.isfile(opts.executable),'## makeTagDirectory.py error - cannot find executable %s' % opts.executable - - #if not os.path.exists(opts.outputdir): - #os.makedirs(opts.outputdir) - f = makeTagDirectory(opts, args) - - html,retval = f.run_makeTagDirectory() - f = open(opts.htmloutput, 'w') - f.write(''.join(html)) - f.close() - if retval <> 0: - print >> sys.stderr, serr # indicate failure - - - |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 makeTagDirectory.xml --- a/makeTagDirectory.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,50 +0,0 @@ -<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.0"> - <requirements> - <requirement type="package" >homer</requirement> - </requirements> - <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description> - <!--<version_command></version_command>--> - <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} - #for $alignF in $alignmentFiles - $alignF.file -f $alignF.file.ext - #end for - -o $tagDir - 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 - - </command> - <inputs> - <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" /> - <repeat name="alignmentFiles" title="Alignment Files"> - <param name="file" label="Add file" type="data" format="sam,bed" /> - </repeat> - </inputs> - <outputs> - <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />--> - <data format="html" name="tagDir" label="${title} tag directory" /> - <data format="txt" name="out_log" label="${title}.log" /> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - </outputs> - - - <tests> - <!--<test>--> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - <!--</test>--> - </tests> - - <help> - - .. class:: infomark - - After the job finishes, save the zip file, unzip and open "index.html" - - The actual meme-chip command is displayed under "Command line summary" - - Defaults: - http://meme.nbcr.net/meme/doc/meme-chip.html - - </help> -</tool> - |
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| diff -r 74c1fc7bb164 -r 8cfd322a5907 pos2bed.xml --- a/pos2bed.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,34 +0,0 @@ -<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.2"> - <requirements> - <requirement type="package">homer</requirement> - </requirements> - <description></description> - <!--<version_command></version_command>--> - <command> - pos2bed.pl $input_peak 1> $out_bed - 2> $out_log || echo "Error running pos2bed." >&2 - </command> - <inputs> - <param format="tabular" name="input_peak" type="data" label="Homer peak positions" /> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="bed" name="out_bed" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" /> - <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - .. class:: infomark - - **Homer pos2bed.pl** - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - </help> -</tool> - |