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Commit message:
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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 7efeace8bd32 -r 83dffd6d7733 README --- a/README Mon Dec 17 00:22:39 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 7efeace8bd32 -r 83dffd6d7733 annotatePeaks.xml --- a/annotatePeaks.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,55 +0,0 @@ -<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 7efeace8bd32 -r 83dffd6d7733 bed2pos.xml --- a/bed2pos.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,37 +0,0 @@ -<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 7efeace8bd32 -r 83dffd6d7733 findPeaks.xml --- a/findPeaks.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,58 +0,0 @@ -<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 7efeace8bd32 -r 83dffd6d7733 makeTagDirectory.py --- a/makeTagDirectory.py Mon Dec 17 00:22:39 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 7efeace8bd32 -r 83dffd6d7733 makeTagDirectory.xml --- a/makeTagDirectory.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,61 +0,0 @@ -<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 7efeace8bd32 -r 83dffd6d7733 pos2bed.xml --- a/pos2bed.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,37 +0,0 @@ -<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($input_peak.name))[0]#.log" /> - </outputs> - <tests> - <test> - <!--<param name="input_file" value="extract_genomic_dna.fa" />--> - <!--<output name="html_file" file="sample_output.html" ftype="html" />--> - </test> - </tests> - - <help> - .. class:: infomark - - Converts: homer peak positions -(to)-> BED format - - **Homer pos2bed.pl** - - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - </help> -</tool> - |
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| diff -r 7efeace8bd32 -r 83dffd6d7733 tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 17 00:22:39 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,19 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="homer"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://biowhat.ucsd.edu/homer/configureHomer.pl</action> - <action type="shell_command">perl ./configureHomer.pl -install</action> - <action type="shell_command">perl ./configureHomer.pl -install hg19</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Installs homer - </readme> - </package> -</tool_dependency> - |