changeset 28:f0b5827b6051 draft default tip

Uploaded
author kevyin
date Thu, 20 Dec 2012 18:28:03 -0500
parents d27851e0cbbd
children
files README annotatePeaks.xml bed2pos.xml findPeaks.xml makeTagDirectory.py makeTagDirectory.xml pos2bed.xml tool_dependencies.xml
diffstat 8 files changed, 639 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Thu Dec 20 18:28:03 2012 -0500
@@ -0,0 +1,15 @@
+Homer wrapper for Galaxy
+
+The homer tools will need to be accessible from command line
+
+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
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotatePeaks.xml	Thu Dec 20 18:28:03 2012 -0500
@@ -0,0 +1,164 @@
+<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.5">
+    <requirements>
+        <requirement type="package" version="4.1">homer</requirement>
+    </requirements>
+    <description></description>
+    <!--<version_command></version_command>-->
+    <command>
+        annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
+        2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
+    </command>
+    <inputs>
+        <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/>
+        <param name="genome_selector" type="select" label="Genome version">
+            <option value="hg19" selected="true">hg19</option>
+        </param>
+        <param type="text" name="options" label="Extra options" value="" help="See link below for more options">
+          <sanitizer>
+            <valid initial="string.printable">
+             <remove value="&apos;"/>
+             <remove value="/"/>
+            </valid>
+            <mapping initial="none">
+              <add source="&apos;" target="__sq__"/>
+            </mapping>
+          </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+        <data format="csv" name="out_annotated" label="${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.
+
+**Parameter list**
+
+Command line options (not all of them are supported)::
+
+	Usage: annotatePeaks.pl &lt;peak file | tss&gt; &lt;genome version&gt;  [additional options...]
+
+	Available Genomes (required argument): (name,org,directory,default promoter set)
+			-- or --
+		Custom: provide the path to genome FASTA files (directory or single file)
+
+	User defined annotation files (default is UCSC refGene annotation):
+		annotatePeaks.pl accepts GTF (gene transfer formatted) files to annotate positions relative
+		to custom annotations, such as those from de novo transcript discovery or Gencode.
+		-gtf &lt;gtf format file&gt; (-gff and -gff3 can work for those files, but GTF is better)
+
+	Peak vs. tss/tts/rna mode (works with custom GTF file):
+		If the first argument is &quot;tss&quot; (i.e. annotatePeaks.pl tss hg18 ...) then a TSS centric
+		analysis will be carried out.  Tag counts and motifs will be found relative to the TSS.
+		(no position file needed) [&quot;tts&quot; now works too - e.g. 3&apos; end of gene]
+		[&quot;rna&quot; specifies gene bodies, will automaticall set &quot;-size given&quot;]
+		NOTE: The default TSS peak size is 4000 bp, i.e. +/- 2kb (change with -size option)
+		-list &lt;gene id list&gt; (subset of genes to perform analysis [unigene, gene id, accession,
+			 probe, etc.], default = all promoters)
+		-cTSS &lt;promoter position file i.e. peak file&gt; (should be centered on TSS)
+
+	Primary Annotation Options:
+		-mask (Masked repeats, can also add &apos;r&apos; to end of genome name)
+		-m &lt;motif file 1&gt; [motif file 2] ... (list of motifs to find in peaks)
+			-mscore (reports the highest log-odds score within the peak)
+			-nmotifs (reports the number of motifs per peak)
+			-mdist (reports distance to closest motif)
+			-mfasta &lt;filename&gt; (reports sites in a fasta file - for building new motifs)
+			-fm &lt;motif file 1&gt; [motif file 2] (list of motifs to filter from above)
+			-rmrevopp &lt;#&gt; (only count sites found within &lt;#&gt; on both strands once, i.e. palindromic)
+			-matrix &lt;prefix&gt; (outputs a motif co-occurrence files:
+				prefix.count.matrix.txt - number of peaks with motif co-occurrence
+				prefix.ratio.matrix.txt - ratio of observed vs. expected  co-occurrence
+				prefix.logPvalue.matrix.txt - co-occurrence enrichment
+				prefix.stats.txt - table of pair-wise motif co-occurrence statistics
+				additional options:
+				-matrixMinDist &lt;#&gt; (minimum distance between motif pairs - to avoid overlap)
+				-matrixMaxDist &lt;#&gt; (maximum distance between motif pairs)
+			-mbed &lt;filename&gt; (Output motif positions to a BED file to load at UCSC (or -mpeak))
+			-mlogic &lt;filename&gt; (will output stats on common motif orientations)
+		-d &lt;tag directory 1&gt; [tag directory 2] ... (list of experiment directories to show
+			tag counts for) NOTE: -dfile &lt;file&gt; where file is a list of directories in first column
+		-bedGraph &lt;bedGraph file 1&gt; [bedGraph file 2] ... (read coverage counts from bedGraph files)
+		-wig &lt;wiggle file 1&gt; [wiggle file 2] ... (read coverage counts from wiggle files)
+		-p &lt;peak file&gt; [peak file 2] ... (to find nearest peaks)
+			-pdist to report only distance (-pdist2 gives directional distance)
+			-pcount to report number of peaks within region
+		-vcf &lt;VCF file&gt; (annotate peaks with genetic variation infomation, one col per individual)
+			-editDistance (Computes the # bp changes relative to reference)
+			-individuals &lt;name1&gt; [name2] ... (restrict analysis to these individuals)
+		-gene &lt;data file&gt; ... (Adds additional data to result based on the closest gene.
+			This is useful for adding gene expression data.  The file must have a header,
+			and the first column must be a GeneID, Accession number, etc.  If the peak
+			cannot be mapped to data in the file then the entry will be left empty.
+		-go &lt;output directory&gt; (perform GO analysis using genes near peaks)
+		-genomeOntology &lt;output directory&gt; (perform genomeOntology analysis on peaks)
+			-gsize &lt;#&gt; (Genome size for genomeOntology analysis, default: 2e9)
+
+	Annotation vs. Histogram mode:
+		-hist &lt;bin size in bp&gt; (i.e 1, 2, 5, 10, 20, 50, 100 etc.)
+		The -hist option can be used to generate histograms of position dependent features relative
+		to the center of peaks.  This is primarily meant to be used with -d and -m options to map
+		distribution of motifs and ChIP-Seq tags.  For ChIP-Seq peaks for a Transcription factor
+		you might want to use the -center option (below) to center peaks on the known motif
+		** If using &quot;-size given&quot;, histogram will be scaled to each region (i.e. 0-100%), with
+		the -hist parameter being the number of bins to divide each region into.
+			Histogram Mode specific Options:
+			-nuc (calculated mononucleotide frequencies at each position,
+				Will report by default if extracting sequence for other purposes like motifs)
+			-di (calculated dinucleotide frequencies at each position)
+			-histNorm &lt;#&gt; (normalize the total tag count for each region to 1, where &lt;#&gt; is the
+				minimum tag total per region - use to avoid tag spikes from low coverage
+			-ghist (outputs profiles for each gene, for peak shape clustering)
+			-rm &lt;#&gt; (remove occurrences of same motif that occur within # bp)
+
+	Peak Centering: (other options are ignored)
+		-center &lt;motif file&gt; (This will re-center peaks on the specified motif, or remove peak
+			if there is no motif in the peak.  ONLY recentering will be performed, and all other
+			options will be ignored.  This will output a new peak file that can then be reanalyzed
+			to reveal fine-grain structure in peaks (It is advised to use -size &lt; 200) with this
+			to keep peaks from moving too far (-mirror flips the position)
+		-multi (returns genomic positions of all sites instead of just the closest to center)
+
+	Advanced Options:
+		-len &lt;#&gt; / -fragLength &lt;#&gt; (Fragment length, default=auto, might want to set to 0 for RNA)
+		-size &lt;#&gt; (Peak size[from center of peak], default=inferred from peak file)
+			-size #,# (i.e. -size -10,50 count tags from -10 bp to +50 bp from center)
+			-size &quot;given&quot; (count tags etc. using the actual regions - for variable length regions)
+		-log (output tag counts as log2(x+1+rand) values - for scatter plots)
+		-sqrt (output tag counts as sqrt(x+rand) values - for scatter plots)
+		-strand &lt;+|-|both&gt; (Count tags on specific strands relative to peak, default: both)
+		-pc &lt;#&gt; (maximum number of tags to count per bp, default=0 [no maximum])
+		-cons (Retrieve conservation information for peaks/sites)
+		-CpG (Calculate CpG/GC content)
+		-ratio (process tag values as ratios - i.e. chip-seq, or mCpG/CpG)
+		-nfr (report nuclesome free region scores instead of tag counts, also -nfrSize &lt;#&gt;)
+		-norevopp (do not search for motifs on the opposite strand [works with -center too])
+		-noadj (do not adjust the tag counts based on total tags sequenced)
+		-norm &lt;#&gt; (normalize tags to this tag count, default=1e7, 0=average tag count in all directories)
+		-pdist (only report distance to nearest peak using -p, not peak name)
+		-map &lt;mapping file&gt; (mapping between peak IDs and promoter IDs, overrides closest assignment)
+		-noann, -nogene (skip genome annotation step, skip TSS annotation)
+		-homer1/-homer2 (by default, the new version of homer [-homer2] is used for finding motifs)
+
+
+    </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed2pos.xml	Thu Dec 20 18:28:03 2012 -0500
@@ -0,0 +1,37 @@
+<tool id="homer_bed2pos" name="homer_bed2pos" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="4.1">homer</requirement>
+    </requirements>
+    <description></description>
+    <!--<version_command></version_command>-->
+    <command>
+        bed2pos.pl $input_bed 1&gt; $out_pos
+        2&gt; $out_log || echo "Error running bed2pos." >&amp;2
+    </command>
+    <inputs>
+        <param format="tabular,bed" name="input_bed" type="data" label="BED file" />
+    </inputs>
+    <outputs>
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+        <data format="tabular" name="out_pos" label="${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>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findPeaks.xml	Thu Dec 20 18:28:03 2012 -0500
@@ -0,0 +1,122 @@
+<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2">
+    <requirements>
+        <requirement type="package" version="4.1">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&gt; $out_log || echo "Error running findPeaks." >&amp;2
+    </command>
+    <inputs>
+        <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" />
+        <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" />
+        <param type="text" name="options" label="Extra options" value="" help="See link below for more options">
+          <sanitizer>
+            <valid initial="string.printable">
+             <remove value="&apos;"/>
+             <remove value="/"/>
+            </valid>
+            <mapping initial="none">
+              <add source="&apos;" target="__sq__"/>
+            </mapping>
+          </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+        <data format="txt" name="outputPeakFile" label="${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.
+
+**Parameter list**
+
+Command line options (not all of them are supported)::
+
+	Usage: findPeaks &lt;tag directory&gt; [options]
+
+	Finds peaks in the provided tag directory.  By default, peak list printed to stdout
+
+	General analysis options:
+		-o &lt;filename|auto&gt; (file name for to output peaks, default: stdout)
+			&quot;-o auto&quot; will send output to &quot;&lt;tag directory&gt;/peaks.txt&quot;, &quot;.../regions.txt&quot;,
+			or &quot;.../transcripts.txt&quot; depending on the &quot;-style&quot; option
+		-style &lt;option&gt; (Specialized options for specific analysis strategies)
+			factor (transcription factor ChIP-Seq, uses -center, output: peaks.txt,  default)
+			histone (histone modification ChIP-Seq, region based, uses -region -size 500 -L 0, regions.txt)
+			groseq (de novo transcript identification from GroSeq data, transcripts.txt)
+			tss (TSS identification from 5&apos; RNA sequencing, tss.txt)
+			dnase (Hypersensitivity [crawford style (nicking)], peaks.txt)
+
+	chipseq/histone options:
+		-i &lt;input tag directory&gt; (Experiment to use as IgG/Input/Control)
+		-size &lt;#&gt; (Peak size, default: auto)
+		-minDist &lt;#&gt; (minimum distance between peaks, default: peak size x2)
+		-gsize &lt;#&gt; (Set effective mappable genome size, default: 2e9)
+		-fragLength &lt;#|auto&gt; (Approximate fragment length, default: auto)
+		-inputFragLength &lt;#|auto&gt; (Approximate fragment length of input tags, default: auto)
+		-tbp &lt;#&gt; (Maximum tags per bp to count, 0 = no limit, default: auto)
+		-inputtbp &lt;#&gt; (Maximum tags per bp to count in input, 0 = no limit, default: auto)
+		-strand &lt;both|separate&gt; (find peaks using tags on both strands or separate, default:both)
+		-norm # (Tag count to normalize to, default 10000000)
+		-region (extends start/stop coordinates to cover full region considered &quot;enriched&quot;)
+		-center (Centers peaks on maximum tag overlap and calculates focus ratios)
+		-nfr (Centers peaks on most likely nucleosome free region [works best with mnase data])
+			(-center and -nfr can be performed later with &quot;getPeakTags&quot;
+
+	Peak Filtering options: (set -F/-L/-C to 0 to skip)
+		-F &lt;#&gt; (fold enrichment over input tag count, default: 4.0)
+		  -P &lt;#&gt; (poisson p-value threshold relative to input tag count, default: 0.0001)
+		-L &lt;#&gt; (fold enrichment over local tag count, default: 4.0)
+		  -LP &lt;#&gt; (poisson p-value threshold relative to local tag count, default: 0.0001)
+		-C &lt;#&gt; (fold enrichment limit of expected unique tag positions, default: 2.0)
+		-localSize &lt;#&gt; (region to check for local tag enrichment, default: 10000)
+		-inputSize &lt;#&gt; (Size of region to search for control tags, default: 2x peak size)
+		-fdr &lt;#&gt; (False discovery rate, default = 0.001)
+		-poisson &lt;#&gt; (Set poisson p-value cutoff, default: uses fdr)
+		-tagThreshold &lt;#&gt; (Set # of tags to define a peak, default: 25)
+		-ntagThreshold &lt;#&gt; (Set # of normalized tags to define a peak, by default uses 1e7 for norm)
+		-minTagThreshold &lt;#&gt; (Absolute minimum tags per peak, default: expected tags per peak)
+
+	GroSeq Options: (Need to specify &quot;-style groseq&quot;):
+		-tssSize &lt;#&gt; (size of region for initiation detection/artifact size, default: 250)
+		-minBodySize &lt;#&gt; (size of regoin for transcript body detection, default: 1000)
+		-maxBodySize &lt;#&gt; (size of regoin for transcript body detection, default: 10000)
+		-tssFold &lt;#&gt; (fold enrichment for new initiation dectection, default: 4.0)
+		-bodyFold &lt;#&gt; (fold enrichment for new transcript dectection, default: 4.0)
+		-endFold &lt;#&gt; (end transcript when levels are this much less than the start, default: 10.0)
+		-fragLength &lt;#&gt; (Approximate fragment length, default: 150)
+		-uniqmap &lt;directory&gt; (directory of binary files specifying uniquely mappable locations)
+			Download from http://biowhat.ucsd.edu/homer/groseq/
+		-confPvalue &lt;#&gt; (confidence p-value: 1.00e-05)
+		-minReadDepth &lt;#&gt; (Minimum initial read depth for transcripts, default: auto)
+		-pseudoCount &lt;#&gt; (Pseudo tag count, default: 2.0)
+		-gtf &lt;filename&gt; (Output de novo transcripts in GTF format)
+			&quot;-o auto&quot; will produce &lt;dir&gt;/transcripts.txt and &lt;dir&gt;/transcripts.gtf
+    </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/makeTagDirectory.py	Thu Dec 20 18:28:03 2012 -0500
@@ -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
+    
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/makeTagDirectory.xml	Thu Dec 20 18:28:03 2012 -0500
@@ -0,0 +1,146 @@
+<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">
+    <requirements>
+        <requirement type="package" version="4.1">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&gt; $out_log || echo "Error running homer_makeTagDirectory." >&amp;2
+
+    </command>
+    <inputs>
+        <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
+        <param type="text" name="options" label="Extra options" value="" help="See below for more options">
+          <sanitizer>
+            <valid initial="string.printable">
+             <remove value="&apos;"/>
+             <remove value="/"/>
+            </valid>
+            <mapping initial="none">
+              <add source="&apos;" target="__sq__"/>
+            </mapping>
+          </sanitizer>
+        </param>
+        <repeat name="alignmentFiles" title="Alignment Files">
+          <param name="file" label="Add file" type="data" format="sam,bed" help="Alignments in SAM or BED format" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <!--<data format="homerTagDirectory" name="tagDir" label="${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
+
+**Parameter list**
+
+Command line options (not all of them are supported)::
+
+	Usage: makeTagDirectory &lt;directory&gt; &lt;alignment file 1&gt; [file 2] ... [options]
+
+	Creates a platform-independent &apos;tag directory&apos; for later analysis.
+	Currently BED, eland, bowtie, and sam files are accepted. The program will try to
+	automatically detect the alignment format if not specified.  Program will also
+	unzip *.gz, *.bz2, and *.zip files and convert *.bam to sam files on the fly
+	Existing tag directories can be added or combined to make a new one using -d/-t
+	If more than one format is needed and the program cannot auto-detect it properly,
+	make separate tag directories by running the program separately, then combine them.
+	To perform QC/manipulations on an existing tag directory, add &quot;-update&quot;
+
+	Options:
+		-fragLength &lt;# | given&gt; (Set estimated fragment length - given: use read lengths)
+			By default treats the sample as a single read ChIP-Seq experiment
+		-format &lt;X&gt; where X can be: (with column specifications underneath)
+			bed - BED format files:
+				(1:chr,2:start,3:end,4:+/- or read name,5:# tags,6:+/-)
+				-force5th (5th column of BED file contains # of reads mapping to position)
+			sam - SAM formatted files (use samTools to covert BAMs into SAM if you have BAM)
+				-unique (keep if there is a single best alignment based on mapq)
+					-mapq &lt;#&gt; (Minimum mapq for -unique, default: 10, set negative to use AS:i:/XS:i:)
+				-keepOne (keep one of the best alignments even if others exist)
+				-keepAll (include all alignments in SAM file)
+				-mis (Maximum allowed mismatches, default: no limit, uses MD:Z: tag)
+			bowtie - output from bowtie (run with --best -k 2 options)
+				(1:read name,2:+/-,3:chr,4:position,5:seq,6:quality,7:NA,8:misInfo)
+			eland_result - output from basic eland
+				(1:read name,2:seq,3:code,4:#zeroMM,5:#oneMM,6:#twoMM,7:chr,
+							8:position,9:F/R,10-:mismatches
+			eland_export - output from illumina pipeline (22 columns total)
+				(1-5:read name info,9:sequence,10:quality,11:chr,13:position,14:strand)
+			eland_extended - output from illumina pipeline (4 columns total)
+				(1:read name,2:sequence,3:match stats,4:positions[,])
+			mCpGbed - encode style mCpG reporting in extended BED format, no auto-detect
+				(1:chr,2:start,3:end,4:name,5:,6:+/-,7:,8:,9:,10:#C,11:#mC)
+			allC - Lister style output files detailing the read information about all cytosines
+				(1:chr,2:pos,3:strand,4:context,#mC,#totalC,#C
+				-minCounts &lt;#&gt; (minimum number of reads to report mC/C ratios, default: 10)
+				-mCcontext &lt;CG|CHG|CHH|all&gt; (only use C&apos;s in this context, default: CG)
+			HiCsummary - minimal paired-end read mapping information
+				(1:readname,2:chr1,3:5&apos;pos1,4:strand1,5:chr2,6:5&apos;pos2,7:strand2)
+		-force5th (5th column of BED file contains # of reads mapping to position)
+		-d &lt;tag directory&gt; [tag directory 2] ... (add Tag directory to new tag directory)
+		-t &lt;tag file&gt; [tag file 2] ... (add tag file i.e. *.tags.tsv to new tag directory)
+		-single (Create a single tags.tsv file for all &quot;chromosomes&quot; - i.e. if &gt;100 chromosomes)
+		-update (Use current tag directory for QC/processing, do not parse new alignment files)
+		-tbp &lt;#&gt; (Maximum tags per bp, default: no maximum)
+		-precision &lt;1|2|3&gt; (number of decimal places to use for tag totals, default: 1)
+
+		GC-bias options:
+		-genome &lt;genome version&gt; (To see available genomes, use &quot;-genome list&quot;)
+			-or- (for custom genomes):
+		-genome &lt;path-to-FASTA file or directory of FASTA files&gt;
+
+		-checkGC (check Sequence bias, requires &quot;-genome&quot;)
+			-freqStart &lt;#&gt; (offset to start calculating frequency, default: -50)
+			-freqEnd &lt;#&gt; (distance past fragment length to calculate frequency, default: +50)
+			-oligoStart &lt;#&gt; (oligo bias start)
+			-oligoEnd &lt;#&gt; (oligo bias end)
+		-normGC &lt;target GC profile file&gt; (i.e. tagGCcontent.txt file from control experiment)
+			Use &quot;-normGC default&quot; to match the genomic GC distribution
+		-normFixedOligo &lt;oligoFreqFile&gt; (normalize 5&apos; end bias, &quot;-normFixedOligo default&quot; ok)
+		-minNormRatio &lt;#&gt; (Minimum deflation ratio of tag counts, default: 0.25)
+		-maxNormRatio &lt;#&gt; (Maximum inflation ratio of tag counts, default: 2.0)
+		-iterNorm &lt;#&gt; (Sets -max/minNormRatio to 1 and 0, iteratively normalizes such that the
+			resulting distrubtion is no more than #% different than target, i.e. 0.1,default: off)
+
+	Paired-end/HiC options
+		-illuminaPE (when matching PE reads, assumes last character of read name is 0 or 1)
+		-removePEbg (remove paired end tags within 1.5x fragment length on same chr)
+			-PEbgLength &lt;#&gt; (remove PE  reads facing on another within this distance, default: 1.5x fragLen)
+		-restrictionSite &lt;seq&gt; (i.e. AAGCTT for HindIII, assign data &lt; 1.5x fragment length to sites)
+			Must specify genome sequence directory too. (-rsmis &lt;#&gt; to specify mismatches, def: 0)
+			-both, -one, -onlyOne, -none (Keeps reads near restriction sites, default: keep all)
+			-removeSelfLigation (removes reads linking same restriction fragment)
+			-removeRestrictionEnds (removes reads starting on a restriction fragment)
+			-assignMidPoint (will place reads in the middle of HindIII fragments)
+			-restrictionSiteLength &lt;#&gt; (maximum distance from restriction site, default: 1.5x fragLen)
+		-removeSpikes &lt;size bp&gt; &lt;#&gt; (remove tags from regions with &gt; than # times
+			the average tags per size bp, suggest &quot;-removeSpikes 10000 5&quot;)
+
+
+    </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pos2bed.xml	Thu Dec 20 18:28:03 2012 -0500
@@ -0,0 +1,37 @@
+<tool id="homer_pos2bed" name="homer_pos2bed" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="4.1" >homer</requirement>
+    </requirements>
+    <description></description>
+    <!--<version_command></version_command>-->
+    <command>
+        pos2bed.pl $input_peak 1&gt; $out_bed
+        2&gt; $out_log || echo "Error running pos2bed." >&amp;2
+    </command>
+    <inputs>
+        <param format="tabular" name="input_peak" type="data" label="Homer peak positions" />
+    </inputs>
+    <outputs>
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+        <data format="bed" name="out_bed" label="${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($input_peak.name))[0]#.log" />
+    </outputs>
+    <tests>
+        <test>
+            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
+            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
+        </test>
+    </tests>
+
+    <help>
+        .. class:: infomark
+
+        Converts: homer peak positions -(to)-> BED format
+
+        **Homer pos2bed.pl**
+
+        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
+    </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Dec 20 18:28:03 2012 -0500
@@ -0,0 +1,24 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="homer" version="4.1">
+    <install version="4.1">
+      <actions>
+        <action type="download_by_url">http://biowhat.ucsd.edu/homer/configureHomer.pl</action>
+        <action type="shell_command">perl ./configureHomer.pl -install</action>
+        <!--<action type="shell_command">perl ./configureHomer.pl -install hg19</action>-->
+        <action type="move_directory_files">
+          <source_directory>./</source_directory>
+          <destination_directory>$INSTALL_DIR</destination_directory>
+        </action>
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>
+      I'm sorry but this does not work
+      
+    </readme>
+  </package>
+</tool_dependency>
+