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README annotatePeaks.xml bed2pos.xml findPeaks.xml makeTagDirectory.py makeTagDirectory.xml pos2bed.xml tool_dependencies.xml |
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| diff -r 22b7d878f3d0 -r 7efeace8bd32 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Dec 17 00:22:39 2012 -0500 |
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| @@ -0,0 +1,13 @@ +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 22b7d878f3d0 -r 7efeace8bd32 annotatePeaks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotatePeaks.xml Mon Dec 17 00:22:39 2012 -0500 |
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| @@ -0,0 +1,55 @@ +<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4"> + <requirements> + <requirement type="package">homer</requirement> + </requirements> + <description></description> + <!--<version_command></version_command>--> + <command> + annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated + 2> $out_log || echo "Error running annotatePeaks." >&2 + </command> + <inputs> + <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/> + <param name="genome_selector" type="select" label="Genome version"> + <option value="hg19" selected="true">hg19</option> + </param> + <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="/"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </inputs> + <outputs> + <!--<data format="html" name="html_outfile" label="index" />--> + <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> + <data format="csv" name="out_annotated" label="${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 and options + + http://biowhat.ucsd.edu/homer/ngs/annotation.html + + TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. + + </help> +</tool> + |
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| diff -r 22b7d878f3d0 -r 7efeace8bd32 bed2pos.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed2pos.xml Mon Dec 17 00:22:39 2012 -0500 |
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| @@ -0,0 +1,37 @@ +<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.3"> + <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 + + Converts: BED -(to)-> homer peak positions + + **Homer bed2pos.pl** + + http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html + </help> +</tool> + |
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| diff -r 22b7d878f3d0 -r 7efeace8bd32 findPeaks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findPeaks.xml Mon Dec 17 00:22:39 2012 -0500 |
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| @@ -0,0 +1,58 @@ +<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2"> + <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> $out_log || echo "Error running findPeaks." >&2 + </command> + <inputs> + <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" /> + <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" /> + <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="/"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </inputs> + <outputs> + <!--<data format="html" name="html_outfile" label="index" />--> + <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> + <data format="txt" name="outputPeakFile" label="${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** + + For more options, look under: "Command line options for findPeaks" + + http://biowhat.ucsd.edu/homer/ngs/peaks.html + + TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. + + </help> +</tool> + |
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| diff -r 22b7d878f3d0 -r 7efeace8bd32 makeTagDirectory.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/makeTagDirectory.py Mon Dec 17 00:22:39 2012 -0500 |
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| @@ -0,0 +1,94 @@ +""" + + +""" +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 22b7d878f3d0 -r 7efeace8bd32 makeTagDirectory.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/makeTagDirectory.xml Mon Dec 17 00:22:39 2012 -0500 |
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| @@ -0,0 +1,61 @@ +<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1"> + <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> $out_log || echo "Error running homer_makeTagDirectory." >&2 + + </command> + <inputs> + <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" /> + <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="/"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + <repeat name="alignmentFiles" title="Alignment Files"> + <param name="file" label="Add file" type="data" format="sam,bed" /> + </repeat> + </inputs> + <outputs> + <!--<data format="homerTagDirectory" name="tagDir" label="${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 + + **Homer makeTagDirectory** + + For more options, look under: "Command line options" + + http://biowhat.ucsd.edu/homer/ngs/tagDir.html + + + </help> +</tool> + |
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| diff -r 22b7d878f3d0 -r 7efeace8bd32 pos2bed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pos2bed.xml Mon Dec 17 00:22:39 2012 -0500 |
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| @@ -0,0 +1,37 @@ +<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.3"> + <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($input_peak.name))[0]#.log" /> + </outputs> + <tests> + <test> + <!--<param name="input_file" value="extract_genomic_dna.fa" />--> + <!--<output name="html_file" file="sample_output.html" ftype="html" />--> + </test> + </tests> + + <help> + .. class:: infomark + + Converts: homer peak positions -(to)-> BED format + + **Homer pos2bed.pl** + + http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html + </help> +</tool> + |
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| diff -r 22b7d878f3d0 -r 7efeace8bd32 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 17 00:22:39 2012 -0500 |
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| @@ -0,0 +1,19 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="homer"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://biowhat.ucsd.edu/homer/configureHomer.pl</action> + <action type="shell_command">perl ./configureHomer.pl -install</action> + <action type="shell_command">perl ./configureHomer.pl -install hg19</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Installs homer + </readme> + </package> +</tool_dependency> + |